Abstract:
The present invention is a tool for diagnosis and prediction using biomarker-based risk assessment for chilling-related disorders of Rosaceous fruit crops including apple and pear. Provided are methodology and genes whose relative and absolute expression can accurately indicate disorder risk throughout the production and supply chain of these crops. This technology describes a necessary and novel management tool for stakeholders producing, servicing, or retailing these crops.

Description:
BACKGROUND OF THE INVENTION 
       [0001]    Field of the Invention 
         [0002]    The present invention is a biomarker-based risk assessment tool for predicting, diagnosing and distinguishing postharvest chilling-related physiological disorders of Rosaceous fruit crops, including apple and pear. 
         [0003]    Background of the Invention 
         [0004]    In the fruit industry, multiple browning disorders result in significant annual losses. A major obstacle to developing strategies that reduce such losses is the lack of methods for evaluating the risk of any of the multiple browning disorders materializing at any time during the twelve month storage and distribution period due to chilling stress imposed by the required cold storage. There have been no biomarkers identified that are useful to assess the effect of cold storage stress where the disorder is multifactorial and where the outcome will not become evident for many months. The risk is difficult to determine as existing tests aimed at estimating fruit quality are not linked with conditions associated with browning disorder risk. Thus, there is currently a need to develop more effective techniques for identification of endpoints for monitoring disorder progression during the storage and the distribution period and for evaluating the effectiveness of changes instituted in efforts to treat and control such disorders. To date, no consistently effective risk assessment exists targeting postharvest disorders and control measures are even lacking for many prevalent browning disorders. 
       SUMMARY OF THE INVENTION 
       [0005]    We have identified biomarkers that predict, diagnose, and distinguish multiple postharvest browning disorders during the cold storage period, thereby enabling a strategy for assessing risk for the occurrence of multiple browning disorders throughout the cold storage and distribution periods and for adjusting controls and marketing strategies to reduce product loss. 
         [0006]    In accordance with this discovery, it is an object of the invention to provide a method of using biomarkers to identify stages of the progression of the multiple browning disorders soft scald, soggy breakdown, firm flesh browning, external CO 2  injury and superficial scald during the cold storage period as part of a strategy of risk assessment in order to facilitate storage and supply chain management decisions. 
         [0007]    It is an object of the invention to provide measurable metabolites and identified biomarkers (expressed gene sequences reflecting mRNA changes) that can be monitored to assess risk of storage disorder development as changes in levels of multiple expressed genes precede browning disorder development by weeks or months. 
         [0008]    It is a further object of the invention to provide biomarker profiles whose relative and absolute expression can accurately predict and diagnose disorder risk throughout the production and supply chain of these crops. 
         [0009]    It is another object of the invention to monitor biomarker levels in apple and pear tissues throughout the entire growing and supply chain as a means to predict and diagnose and assess risk for disorder development, to check effectiveness of control strategies, and to adjust disorder control or marketing strategies in order to avoid losses and thereby provide a more consistent, high quality product to consumers. 
         [0010]    It is an additional object of the invention to provide a biomarker-based diagnostic tool as a necessary and novel management tool for stakeholders producing, servicing, or retailing these crops. 
         [0011]    It is an additional object of the invention to provide such monitoring strategies in order to provide effective treatment and control practices that can be monitored by reliance on the same biomarkers as indicators of their effect on maintenance of fruit quality with the result that previously employed crop protectant applications or energy input into the storage environment are no longer necessary. 
         [0012]    Other objects and advantages of this invention will become readily apparent from the ensuing description. 
     
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         [0013]    The patent or application file contains at least one drawing executed in color. 
           [0014]    Copies of this patent or patent application publication with color drawing(s) will be provided by the U.S. Patent and Trademark Office upon request and payment of the necessary fee. 
           [0015]      FIGS. 1A-1E  depict examples of chilling-related postharvest physiological disorders of apple. These disorders are physiologically and etiologically distinct. Superficial scald ( FIG. 1A ) and firm flesh browning ( FIG. 1B ) were chosen to discover risk assessment biomarkers for late-term disorders; soft scald ( FIG. 1C ), soggy breakdown ( FIG. 1D ), and CO 2  injury ( FIG. 1E ) for early term disorders. 
           [0016]      FIG. 2  depicts usage of the combination of harvest maturity and orchard incidence variability to discover risk assessment biomarkers for soft scald and soggy breakdown (shown in  FIGS. 1C and 1D ) and other early-term physiological storage disorders of apple and other Rosaceous fruit crops. Soft scald was categorized for statistical analysis on a scale of 0-3 (0=no incidence, 1=0-10%; 2=10-25% and 3=over 25%). 
           [0017]      FIG. 3A  shows superficial scald development of ‘Granny Smith’ apples.  FIG. 3B  depicts the usage of this combination to discover risk assessment biomarkers for this and other late-term physiological storage disorders of apple and other Rosaceous fruit crops. Control apples (no crop protectants applied) developed the highest incidence of superficial scald ( FIG. 3B ). This “pharmaceutical” contrast was used to discover risk assessment biomarkers for this and other late-term postharvest physiological disorders of Rosaceous fruit crops. Abbreviations (DPA, diphenylamine; 1-MCP, 1-methylcyclo-propene). 
           [0018]      FIG. 4  depicts a summary of overall changes of gene expression in ‘Honeycrisp’ apple from high (green) and low (red) risk orchards. The left graph indicates that the largest impact on the transcriptome occurred between harvest and 2 weeks when cold storage was imposed. 
           [0019]      FIG. 5  shows a metabolic-gene expression correlations network illustrating closely related metabolites (circles, representing a single metabolite) and gene model k-means clusters (triangles, representing many highly correlated genes). Nodes closely positioned and linked with red edges (lines) are highly, positively correlated. Nodes outlined in black are those highly correlated with methanol (R&gt;0.700), a metabolite linked with superficial scald symptom development in ‘Granny Smith’. Risk assessment biomarker genes for superficial scald and other late-term disorders reside in the three highlighted gene model clusters. 
           [0020]      FIG. 6  depicts a testing scheme for a disorder risk management system. If risk assessment biomarker levels are higher (or lower, see Table), decisions on how long a particular lot, alone or compared to other lots, should proceed through the supply chain can be made at key decision points based on the assessed risk for developing various browning disorders. 
       
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
       [0021]    Multiple browning disorders that lead to severe damage of the peel and cortex ( FIG. 1 ) are a major problem in the fruit industry, causing low quality, inconsistent fruit products for the consumer and severe annual losses. Costs for protectants and additional energy costs also add to these losses. We have applied metabolic and gene expression profiling to discover biomarkers that can be used to predict, diagnose, and distinguish economically significant apple postharvest physiological disorders. Changes in levels of multiple expressed genes precede disorder development by weeks or months. The invention reduces product loss caused by multiple browning disorders by indicating which fruit have a high risk for developing the disorders and therefore can serve as a basis for storage and supply chain management decisions. We have identified metabolites and biomarkers (gene sequences reflecting mRNA changes) that can be monitored and used to assess risk of storage disorder development. These identified genes have not been previously associated with fruit chilling stress in Rosaceous crops. Further, these identified genes are very similar among Rosaceous fruit crops. Fruit response to stress events that lead to these collective disorders are detected and monitored using this approach. Unlike previous technologies, this invention targets storage risk assessment and only incorporates differences in fruit quality factors or fruit ripeness or maturity when these conditions impact disorder development. Monitoring biomarker levels in apple and pear tissues throughout the entire growing and supply chain provides a means to check effectiveness of control strategies, diagnose and assess risk for disorder development and, then, adjust disorder control or marketing strategies to avoid losses and provide a more consistent, high quality, disorder-free product to consumers. Integrated production approaches using this new tool potentially reduce unnecessary crop protectant application or energy input into the storage environment by reducing uncertainty of effectiveness of technologies presently in use. 
         [0022]    Expression of risk assessment genes and metabolites levels are evaluated at key decision points from before harvest until the end of the supply chain. mRNA samples are extracted from peel or cortex tissue and the extract prepared depending upon the evaluation method to be employed. Expression levels of the given gene sequences can be monitored using RNAseq Solexa protocols (Solexa, Illumina, Hayward, Calif.). Expression levels are considered absolutely, depending upon the platform employed, and/or relatively, regardless of the platform and may be negatively or positively associated with disorder risk. Expression levels are considered in the context of mitigating conditions and stresses applied during the production chain and alongside levels of metabolites that less accurately indicate elevated risk for certain disorders. 
         [0023]    Softscald and soggy breakdown ( FIGS. 1C and 1D ) are related but distinct disorders associated with low temperature storage. Soft scald symptoms are sharply defined brown lesions on the apple skin which can extend into the flesh (Snowdon, A. L. 1990. A Color Atlas of Post-harvest Diseases and Disorders of Fruits and Vegetables, Vol. 1. CRC Press, Boca Raton, Fla., 213 pp.; Watkins and Rosenberger. 2002. Cornell Fruit Handling and Storage Newsletter, 14pp. [Retrieved from the internet: hort.comell. edu/department/faculty/Watkins/extpubs.] while soggy breakdown is an internal disorder with soft, brown, sponge-like tissue, sometimes including most of the flesh (Watkins and Rosenberger, supra). Softscald and soggy breakdown are early-term severe chilling-provoked browning disorders of apple and pear peel and cortical tissue impacting multiple economically significant cultivars including ‘Honeycrisp’ and Jazz™. Typically symptoms appear following 0-2 months following cold storage imposition. Tests and validation of the biomarkers considered seasonal variation and multiple climatic, orchard, developmental, crop protectant, and storage factors employed using common industry practices. Risk assessment was performed at harvest and within 1-2 weeks following cold storage imposition. Evaluating risk assessment biomarker gene expression levels (Tables 1 and 2) provided an early, accurate assessment of disorder risk in these cultivars up to 4 weeks prior to symptom appearance. Comparing relative levels before and after cold storage imposition and/or among expressed biomarkers provided additional confidence in the assessment. 
         [0024]    CO 2  injury is exhibited externally and/or internally depending on the cultivar and growing conditions (Colgan et al. 1999 . Postharvest Biol. Technol.  16:223-231; Elgar et al. 1998 . Hortsci.  33:719-722; Elgar et al. 1999 . Hortsci.  34:305-309; Fernandez-Trujillo et al. 2001 . J. Amer. Soc. Hort. Sci.  126:235-241; Watkins et al. 1997 . HortScience  32:1242-1246). Susceptible cultivars include ‘Braeburn’, ‘Cortland’, ‘Empire’, ‘Fuji’, ‘Golden Delicious’, ‘Honeycrisp’, and ‘McIntosh’. Diphenylamine (DPA) reduces or prevents development of both external and internal CO 2  injury and, when DPA is not used, significant losses result (Argenta et al. 2002 . Postharvest Biol. Technol.  24:13-24; Burmeister and Dilley.1995 . Postharvest Biol. Technol.  6:1-7; Colgan et al. 1999, supra; Fernandez-Trujillo et al., supra). Unlike superficial scald, 1-methylcyclopropene (1-MCP) treatment exacerbates CO 2  injury (Fawbush et al. 2008 . Postharvest Biol. Technol.  48:92-98). CO 2  injury has been associated with accumulation of succinate in the tissue of fruit exposed to high CO 2  concentrations (Hulme, A. C. 1956 . Nature  178:218-219), but Fernandez-Trujillo et al. (supra) found similar levels of succinate in injured controls and non-injured fruit treated with DPA. Risk assessment biomarker gene expression levels (Table 3) change with disorder risk following cold storage inception caused by chilling and elevated CO 2  and mitigated by crop protectant and other orchard and storage factors. 
         [0025]    Superficial scald is a late-term chilling-related peel browning disorder of multiple apple and pear cultivars; typically symptoms appear after at least 2 months cold storage ( FIG. 3A ) (Bain and Mercer. 1963 . Aust. J. Biol. Sci.  16:442-449). Superficial scald is associated with oxidative stress ostensibly linked to the build-up of oxidation products of the sesquiterpene (E,E)-α-farnesene (Huelin and Coggiola. 1970 . J. Sci. Food Agric.  21:584-589; Whitaker et al. 2000 . Postharvest Biol. Technol.  20:231-241; Rowan et al. 2001 . J. Agri. Food Chem.  49:2780-2787). Pre-storage treatment of apples with DPA inhibits oxidation of α-farnesene and largely prevents scald development (Huelin and Coggiola, supra). Moreover, exposure of apple fruit to the ethylene action inhibitor 1-MCP greatly curtails α-farnesene production and markedly reduces scald incidence and severity (Fan et al. 1999 . J. Agri. Food Chem.  47:3063-3068; Rupasinghe et al. 2000 . J. Hort. Sci. Biotech.  75:271-276; Watkins et al. 2000 . Postharvest Biol. Technol.  19:17-32; Shaham et al. 2003 . J. Am. Soc. Hort. Sci.  128:761-766). Controlled atmosphere storage (low oxygen) can reduce scald incidence and severity (Fidler et al. 1973. In:  Commonwealth Agricultural Bureaux , England. Pp. 113-116; Lau, O. L. 1990 . J. Am. Soc. Hortic. Sci.  115:959-961), but not consistently if risk is high. Symptoms of this disorder typically appear from 4 to 6 months after cold storage imposition and can be controlled during conventional production using multiple approaches and during organic production using controlled atmosphere storage. However, reduced acceptance of antioxidant crop protectants used to control superficial scald and inconsistent efficacy of control using controlled atmosphere storage assures that this disorder remains a significant annual economic world-wide consideration for producers of susceptible apple and pear cultivars, including ‘Granny Smith’ and ‘Delicious’. Risk assessment biomarker gene expression levels were different at harvest (Table 4) depending upon the risk of apples from individual orchards to develop the disorder. Other biomarkers (Table 5) increased dramatically during storage starting at 3 months prior to first symptom appearance in ‘Granny Smith’ apples, providing an early and accurate risk assessment of conditions evoked by production, crop protectant and storage conditions. Monitoring relative biomarker gene expression levels alongside oxidation of superficial scald-associated metabolites, such as α-farnesene and methanol, can improve assessment accuracy using this technology. 
         [0026]    Firm flesh browning is considered a form of chilling injury that results in patterned darkening of the flesh. It is a long term problem of the ‘Empire’ cultivar. ‘Empire’ is considered highly desirable by the fresh cut apple industry and flesh browning is unacceptable. Increasing storage temperatures from 0° C. to 2° C. reduces the symptoms although unacceptable softening occurs at 3° C. 1-MCP treatment is now the industry norm to meet market requirements, but 1-MCP-treated fruit develop flesh browning at both low and high storage temperatures (Jung et al. 2011 . Postharvest Biol. Technol.  59:219-226). DPA and other treatments that control flesh browning are ineffective in 1-MCP-treated fruit. These flesh browning symptoms are visually indistinguishable from those previously considered to be chilling injury. Risk assessment biomarker gene expression levels (Table 6) change with the risk of occurrence of the disorder following cold storage inception caused by chilling and mitigated by crop protectant and other orchard and storage factors. 
         [0027]    Experimental evidence supports that expression levels of these risk assessment biomarkers change similarly with stresses that can lead to multiple early and late storage term disorders. Biomarker expression does not correlate with any traditional quality-associated phenotype such as firmness or flavor loss. Instead, biomarker expression specifically represents changes with stress and storage factors that lead to browning disorder development. 
         [0028]    Apple [ Malus sylvestris  (L.) Mill var.  domestica  (Borkh.) Mansf.] was chosen as the model for discovering biomarkers for Rosaceous fruit postharvest browning disorders as different apple cultivars are susceptible to developing many distinct postharvest browning disorders of the peel and flesh, and our understanding of the controls and etiology of these disorders is best in apples. There is a high degree of gene homology among Rosaceous fruit crops, including pear. This and ripening and postharvest physiological similarities make risk assessment biomarkers behave similarly under high or low risk conditions. 
         [0029]    The present invention provides improved systems and strategies for predicting the progression of multiple browning disorders. According to the present invention, soft scald, soggy breakdown, superficial scald, firm flesh browning and CO 2  injury of Rosaceous fruit may be predicted or diagnosed by obtaining a profile of biomarkers from a sample obtained from Rosaceous fruit tissue. The present invention is particularly useful for predicting and diagnosing soft scald, soggy breakdown, superficial scald, firm flesh browning and CO 2  injury during storage and distribution. 
         [0030]    Biomarker profiles may be a ratio of two or more measurable aspects of a biomarker. A biomarker profile comprises at least one measurement, where the measurements can correspond to the same or different biomarkers. A biomarker profile may also comprise at least three, four, five, 10, 20, 30 or more measurements. The profile of biomarkers obtained from an individual apple tissue specimen, namely the candidate biomarker profile, is compared to a reference biomarker profile. The reference biomarker profile can be generated from one individual or a population of individuals at different time points during storage. 
         [0031]    The reference biomarker profile and the candidate biomarker profiles that are compared in the methods of the present invention may be generated from the same population for the purpose of monitoring disorder progression. In this instance it would be expected that the candidate and reference profiles are generated from biological samples taken at different time points and compared to one another, i.e., the reference profile will be expression of the biomarker at the earlier time point and compared to the candidate&#39;s biomarker expression at the later time point. Such a comparison may be used, for example, to determine the risk status of developing a browning disorder in the individual tissue by repeated measurements over time. The reference biomarker profiles may be chosen from tissue of fruit that has a risk of a browning disorder or the reference biomarker profile may be generated from a healthy individual or population that is not at risk, i.e., those that are in a non-affected environment, in a controlled storage population, or in an environmental crop protected situation. In addition, it would be expected that the candidate and reference profiles are generated from biological samples taken from different orchard locations, reflecting environmental and disorder development differences, and compared to one another. i.e., the reference profile will be expression of the biomarker from a sample with known disorder development and compared to the candidates biomarker expression from another population. 
         [0032]    The methods of the present invention comprise comparing a candidate biomarker profile with a reference biomarker profile. The present invention is based on the identification of new biomarkers of multiple browning disorders. A biomarker is useful if it is specific for a browning disorder and measurable. In particular, of the 63,541 genes screened for assessing risk for soft scald and soggy breakdown and CO 2  injury, the present invention provides the identity of 82 candidates found useful for assessing risk at-harvest (Table 1) and 494 for 2 week risk assessment of peel and/or cortex tissue (Table 2). Accordingly, in one aspect, the present invention provides for the identification, generation, and use of expression profiles of sets of genes selected from the genes disclosed herein. 
         [0000]    
       
         
               
             
               
               
               
               
               
             
           
               
                 TABLE 1 
               
               
                   
               
               
                 Accession numbers (Velasco et al., 2010; Retrieved from the Internet: Rosaceae.org) 
               
               
                 of biomarker genes for soft scald assessment at harvest. Elevated expression levels 
               
               
                 indicate orchards with a higher risk for developing these disorders. 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 MDP0000848515 
                 MDP0000238780 
                 MDP0000260007 
                 MDP0000153149 
                 MDP0000585315 
               
               
                 MDP0000273646 
                 MDP0000216786 
                 MDP0000180580 
                 MDP0000737425 
                 MDP0000298967 
               
               
                 MDP0000808492 
                 MDP0000273866 
                 MDP0000353053 
                 MDP0000910032 
                 MDP0000145050 
               
               
                 MDP0000263844 
                 MDP0000158999 
                 MDP0000547254 
                 MDP0000196325 
                 MDP0000224653 
               
               
                 MDP0000321382 
                 MDP0000270602 
                 MDP0000233661 
                 MDP0000665342 
                 MDP0000246831 
               
               
                 MDP0000823528 
                 MDP0000408705 
                 MDP0000518327 
                 MDP0000291249 
                 MDP0000154589 
               
               
                 MDP0000202817 
                 MDP0000590954 
                 MDP0000312397 
                 MDP0000213383 
                 MDP0000529726 
               
               
                 MDP0000312071 
                 MDP0000639894 
                 MDP0000307665 
                 MDP0000183676 
                 MDP0000754521 
               
               
                 MDP0000797616 
                 MDP0000818877 
                 MDP0000782908 
                 MDP0000266443 
                 MDP0000562305 
               
               
                 MDP0000228366 
                 MDP0000361351 
                 MDP0000737001 
                 MDP0000412192 
                 MDP0000223032 
               
               
                 MDP0000149492 
                 MDP0000264361 
                 MDP0000125882 
                 MDP0000498460 
                 MDP0000163006 
               
               
                 MDP0000225132 
                 MDP0000329063 
                 MDP0000170865 
                 MDP0000665685 
                 MDP0000196079 
               
               
                 MDP0000200783 
                 MDP0000182956 
                 MDP0000862371 
                 MDP0000321792 
                 MDP0000441757 
               
               
                 MDP0000313657 
                 MDP0000599531 
                 MDP0000297583 
                 MDP0000272980 
                 MDP0000317502 
               
               
                 MDP0000268175 
                 MDP0000722139 
                 MDP0000637194 
                 MDP0000125700 
                 MDP0000287262 
               
               
                 MDP0000745534 
                 MDP0000164966 
                 MDP0000389794 
                 MDP0000318068 
                 MDP0000322237 
               
               
                 MDP0000225326 
                 MDP0000125411 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
               
               
               
             
           
               
                 TABLE 2 
               
               
                   
               
               
                 Accession numbers (Velasco et al., 2010; Retrieved from the Internet: 
               
               
                 Rosaceae.org) of biomarker genes for soft scald assessment during cold storage 
               
               
                 following cold storage imposition. Higher or lower expression levels can result from cold 
               
               
                 stress resulting from storage imposition. Where lower expression is associated with 
               
               
                 risk, accession numbers are italicized. 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 
                   MDP0000675982 
                 
                 
                   MDP0000202163 
                 
                 
                   MDP0000219532 
                 
                 
                   MDP0000568913 
                 
                 MDP0000313850 
                 MDP0000391472 
                 MDP0000273608 
               
               
                 
                   MDP0000727481 
                 
                 
                   MDP0000244038 
                 
                 
                   MDP0000131371 
                 
                 
                   MDP0000133673 
                 
                 MDP0000225088 
                 MDP0000143677 
                 MDP0000150382 
               
               
                 
                   MDP0000286751 
                 
                 
                   MDP0000272528 
                 
                 
                   MDP0000312509 
                 
                 
                   MDP0000173235 
                 
                 MDP0000282119 
                 MDP0000172451 
                 MDP0000846736 
               
               
                 
                   MDP0000818940 
                 
                 
                   MDP0000320691 
                 
                 
                   MDP0000434271 
                 
                 
                   MDP0000231298 
                 
                 MDP0000263282 
                 MDP0000910523 
                 MDP0000203897 
               
               
                 
                   MDP0000276370 
                 
                 
                   MDP0000270427 
                 
                 
                   MDP0000281525 
                 
                 
                   MDP0000463638 
                 
                 MDP0000150953 
                 MDP0000446865 
                 MDP0000122897 
               
               
                 
                   MDP0000287631 
                 
                 
                   MDP0000463638 
                 
                 
                   MDP0000215630 
                 
                 
                   MDP0000252369 
                 
                 MDP0000124552 
                 MDP0000283534 
                 MDP0000259550 
               
               
                 
                   MDP0000385730 
                 
                 
                   MDP0000156937 
                 
                 
                   MDP0000250658 
                 
                 
                   MDP0000252854 
                 
                 MDP0000031172 
                 MDP0000226432 
                 MDP0000230300 
               
               
                 
                   MDP0000179388 
                 
                 
                   MDP0000618810 
                 
                 
                   MDP0000167107 
                 
                 
                   MDP0000415894 
                 
                 MDP0000467552 
                 MDP0000249564 
                 MDP0000632679 
               
               
                 
                   MDP0000146003 
                 
                 
                   MDP0000154360 
                 
                 
                   MDP0000252590 
                 
                 
                   MDP0000698038 
                 
                 MDP0000119629 
                 MDP0000250546 
                 MDP0000220511 
               
               
                 
                   MDP0000314632 
                 
                 
                   MDP0000758778 
                 
                 
                   MDP0000376256 
                 
                 
                   MDP0000320586 
                 
                 MDP0000336518 
                 MDP0000181779 
                 MDP0000204836 
               
               
                 
                   MDP0000560122 
                 
                 
                   MDP0000157644 
                 
                 
                   MDP0000376284 
                 
                 
                   MDP0000156837 
                 
                 MDP0000242656 
                 MDP0000175375 
                 MDP0000203543 
               
               
                 
                   MDP0000944409 
                 
                 
                   MDP0000577872 
                 
                 
                   MDP0000325574 
                 
                 
                   MDP0000146856 
                 
                 MDP0000179760 
                 MDP0000376469 
                 MDP0000273646 
               
               
                 
                   MDP0000300382 
                 
                 
                   MDP0000945035 
                 
                 
                   MDP0000171928 
                 
                 
                   MDP0000399796 
                 
                 MDP0000121410 
                 MDP0000481590 
                 MDP0000176602 
               
               
                 
                   MDP0000717305 
                 
                 
                   MDP0000124013 
                 
                 
                   MDP0000603942 
                 
                 MDP0000858559 
                 MDP0000298286 
                 MDP0000208533 
                 MDP0000135436 
               
               
                 
                   MDP0000944724 
                 
                 
                   MDP0000129143 
                 
                 
                   MDP0000165921 
                 
                 MDP0000235661 
                 MDP0000181572 
                 MDP0000121476 
                 MDP0000466420 
               
               
                 
                   MDP0000152960 
                 
                 
                   MDP0000306385 
                 
                 
                   MDP0000804078 
                 
                 MDP0000568045 
                 MDP0000703874 
                 MDP0000153251 
                 MDP0000206763 
               
               
                 
                   MDP0000133675 
                 
                 
                   MDP0000159957 
                 
                 
                   MDP0000240921 
                 
                 MDP0000129787 
                 MDP0000270308 
                 MDP0000707440 
                 MDP0000171170 
               
               
                 
                   MDP0000621193 
                 
                 
                   MDP0000473467 
                 
                 
                   MDP0000221993 
                 
                 MDP0000178319 
                 MDP0000269788 
                 MDP0000273634 
                 MDP0000940411 
               
               
                 
                   MDP0000533216 
                 
                 
                   MDP0000326288 
                 
                 
                   MDP0000293351 
                 
                 MDP0000727431 
                 MDP0000162628 
                 MDP0000278681 
                 MDP0000452125 
               
               
                 
                   MDP0000310493 
                 
                 
                   MDP0000187246 
                 
                 
                   MDP0000843691 
                 
                 MDP0000257928 
                 MDP0000462161 
                 MDP0000121588 
                 MDP0000167303 
               
               
                 
                   MDP0000302680 
                 
                 
                   MDP0000276235 
                 
                 
                   MDP0000828513 
                 
                 MDP0000585111 
                 MDP0000203765 
                 MDP0000610961 
                 MDP0000233110 
               
               
                 
                   MDP0000135249 
                 
                 
                   MDP0000201499 
                 
                 
                   MDP0000231242 
                 
                 MDP0000499186 
                 MDP0000306861 
                 MDP0000912405 
                 MDP0000886138 
               
               
                 
                   MDP0000252890 
                 
                 
                   MDP0000221238 
                 
                 
                   MDP0000504185 
                 
                 MDP0000911051 
                 MDP0000243083 
                 MDP0000932845 
                 MDP0000302461 
               
               
                 
                   MDP0000177861 
                 
                 
                   MDP0000142824 
                 
                 
                   MDP0000148780 
                 
                 MDP0000145104 
                 MDP0000172709 
                 MDP0000058337 
                 MDP0000209944 
               
               
                 
                   MDP0000131979 
                 
                 
                   MDP0000222188 
                 
                 
                   MDP0000321057 
                 
                 MDP0000124296 
                 MDP0000166657 
                 MDP0000132990 
                 MDP0000770103 
               
               
                 
                   MDP0000206752 
                 
                 
                   MDP0000319743 
                 
                 
                   MDP0000725469 
                 
                 MDP0000253047 
                 MDP0000734582 
                 MDP0000867280 
                 MDP0000211758 
               
               
                 
                   MDP0000466766 
                 
                 
                   MDP0000280643 
                 
                 
                   MDP0000469943 
                 
                 MDP0000137428 
                 MDP0000312022 
                 MDP0000233037 
                 MDP0000922120 
               
               
                 
                   MDP0000250234 
                 
                 
                   MDP0000279287 
                 
                 
                   MDP0000218935 
                 
                 MDP0000224592 
                 MDP0000610962 
                 MDP0000389181 
                 MDP0000275383 
               
               
                 
                   MDP0000143460 
                 
                 
                   MDP0000858039 
                 
                 
                   MDP0000129164 
                 
                 MDP0000188710 
                 MDP0000241574 
                 MDP0000933329 
                 MDP0000119002 
               
               
                 
                   MDP0000455477 
                 
                 
                   MDP0000313699 
                 
                 
                   MDP0000217734 
                 
                 MDP0000269907 
                 MDP0000163618 
                 MDP0000202280 
                 MDP0000403071 
               
               
                 
                   MDP0000193127 
                 
                 
                   MDP0000178268 
                 
                 
                   MDP0000322647 
                 
                 MDP0000046192 
                 MDP0000227830 
                 MDP0000192562 
                 MDP0000158194 
               
               
                 
                   MDP0000219538 
                 
                 
                   MDP0000169311 
                 
                 
                   MDP0000204345 
                 
                 MDP0000607654 
                 MDP0000274300 
                 MDP0000730019 
                 MDP0000121241 
               
               
                 
                   MDP0000145382 
                 
                 
                   MDP0000174168 
                 
                 
                   MDP0000228473 
                 
                 MDP0000296179 
                 MDP0000120959 
                 MDP0000182571 
                 MDP0000214069 
               
               
                 
                   MDP0000620250 
                 
                 
                   MDP0000168262 
                 
                 
                   MDP0000163588 
                 
                 MDP0000564193 
                 MDP0000172879 
                 MDP0000285670 
                 MDP0000765891 
               
               
                 
                   MDP0000613170 
                 
                 
                   MDP0000755889 
                 
                 
                   MDP0000182716 
                 
                 MDP0000282431 
                 MDP0000220454 
                 MDP0000423589 
                 MDP0000276057 
               
               
                 
                   MDP0000234570 
                 
                 
                   MDP0000920069 
                 
                 
                   MDP0000284699 
                 
                 MDP0000239301 
                 MDP0000873667 
                 MDP0000159246 
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                   MDP0000204345 
                 
                 
                   MDP0000137477 
                 
                 
                   MDP0000180064 
                 
                 MDP0000766844 
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                   MDP0000757787 
                 
                 
                   MDP0000319787 
                 
                 MDP0000228366 
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                   MDP0000799392 
                 
                 
                   MDP0000545323 
                 
                 
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                 MDP0000188054 
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                 MDP0000719275 
               
               
                 MDP0000757641 
                 MDP0000193241 
                 MDP0000131486 
                 MDP0000903417 
                 MDP0000143473 
               
               
                 MDP0000165187 
                 MDP0000160077 
                 MDP0000272522 
                 MDP0000273225 
                 MDP0000197624 
               
               
                 MDP0000590974 
                 MDP0000297123 
                 MDP0000268258 
                 MDP0000121830 
                 MDP0000564318 
               
               
                 MDP0000014856 
                 MDP0000791166 
                 MDP0000197330 
                 MDP0000151362 
                 MDP0000280632 
               
               
                 MDP0000198015 
                 MDP0000710467 
                 MDP0000250386 
                 MDP0000151457 
                 MDP0000166159 
               
               
                 MDP0000356821 
                 MDP0000222944 
                 MDP0000363287 
                 MDP0000421679 
                 MDP0000418062 
               
               
                 MDP0000762756 
                 MDP0000321469 
                 MDP0000242205 
                 MDP0000279018 
                 MDP0000641544 
               
               
                 MDP0000311618 
                 MDP0000681634 
                 MDP0000272640 
                 MDP0000152774 
                 MDP0000719559 
               
               
                 MDP0000178043 
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         [0033]    Because superficial scald can be adequately controlled using appropriate storage conditions, indicating whether storage conditions are actually working or monitoring risk during storage is also a useful tool for this disorder. 
         [0034]    External CO 2  injury browning disorder can be controlled using application of commercially used postharvest chemicals. We were able to use these methods to discover putative biomarkers, as different treatments following harvest induce contrasting disorder development. Controlled atmosphere combined with treatment of apples with 1-MCP (SmartFresh) following harvest enhances external CO 2  injury. In contrast postharvest treatment with the antioxidant diphenylamine (DPA) almost eliminates external CO 2  injury completely. Candidate biomarker genes from an RNAseq experiment were selected by pairwise comparison using the differential gene expression program edgeR (R, Bioconductor) with a p-value cut off of 0.05. Genes were selected and peel tissue collected from New York state grown ‘Empire’ apples, provoked by storage treatments that affect external CO 2  injury incidence. From a total of 63541 gene models, 2330 that expression changed at least 4-fold and that had an average expression RPKM value of at least 1 per sample were selected as potential predictive or diagnostic biomarkers for external CO 2  injury (Table 3). 
         [0000]    
       
         
               
             
               
               
               
               
               
               
               
             
           
               
                 TABLE 3 
               
               
                   
               
               
                 Accession numbers (Velasco et al., 2010; Retrieved from the Internet: 
               
               
                 Rosaceae.org) of biomarker genes for CO 2  injury assessment during cold storage 
               
               
                 following cold storage imposition. Higher or lower expression levels can result from cold 
               
               
                 stress resulting from storage imposition. 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
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         [0035]    Susceptibility to develop superficial scald is often quite different depending on environmental location of the apples. To discover putative biomarkers, genes were selected from ‘Red Delicious’ apple peel tissue collected from 6 different orchard locations with observed differences in superficial scald injury incidence. Candidate biomarker genes were selected using Pearson correlation analysis (R, Bioconductor) with a p-value cut off of 0.05. Genes that expression changes at harvest correlated with superficial scald injury incidence, with a correlation coefficient of at least 0.6 were selected for further filtering. From a total of 63541 gene models, 1106 that changed at least 4-fold in tissues showing the lowest and highest development of superficial scald and with an average expression value of at least 1 RPKM per sample were selected as potential at harvest predictive biomarkers of superficial scald (Table 4). Because superficial scald can be adequately controlled using appropriate storage conditions, indicating whether storage conditions are actually working or monitoring risk during storage is also a useful tool for this disorder. Increases in superficial scald risk-associated gene expression ( FIG. 5 ) began at 1 month for a few candidates, finally resulting in the selection of 690 candidates for early indication of superficial scald risk (Table 5). Monitoring multiple risk assessment biomarkers can better ensure that changes are based on more biochemical systems associated with risk. 
         [0000]    
       
         
               
             
               
               
               
               
               
               
               
             
           
               
                 TABLE 4 
               
               
                   
               
               
                 Accession numbers (Velasco et al., 2010; Retrieved from the Internet: 
               
               
                 Rosaceae.org) of biomarker genes for superficial scald risk assessment during at- 
               
               
                 harvest. Higher or lower expression levels can result from cold stress resulting from 
               
               
                 storage imposition. 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
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                 MDP0000303332 
                 MDP0000672731 
                 MDP0000195162 
                 MDP0000198166 
                 MDP0000358828 
                 MDP0000232846 
               
               
                 MDP0000136455 
                 MDP0000547461 
                 MDP0000921067 
                 MDP0000283994 
                 MDP0000198165 
                 MDP0000358827 
                 MDP0000212688 
               
               
                 MDP0000836170 
                 MDP0000157404 
                 MDP0000905321 
                 MDP0000269859 
                 MDP0000539433 
                 MDP0000218227 
                 MDP0000294789 
               
               
                 MDP0000253428 
                 MDP0000131100 
                 MDP0000892526 
                 MDP0000245245 
                 MDP0000309329 
                 MDP0000845428 
                 MDP0000178782 
               
               
                 MDP0000357423 
                 MDP0000144441 
                 MDP0000350201 
                 MDP0000123987 
                 MDP0000649828 
                 MDP0000171066 
                 MDP0000175282 
               
               
                 MDP0000476508 
                 MDP0000282829 
                 MDP0000244238 
                 MDP0000130016 
                 MDP0000353843 
                 MDP0000521965 
                 MDP0000473817 
               
               
                 MDP0000155077 
                 MDP0000827385 
                 MDP0000128581 
                 MDP0000263540 
                 MDP0000135731 
                 MDP0000703817 
                 MDP0000293103 
               
               
                 MDP0000347520 
                 MDP0000911025 
                 MDP0000759303 
                 MDP0000308446 
                 MDP0000307013 
                 MDP0000182253 
                 MDP0000347881 
               
               
                 MDP0000284819 
                 MDP0000151150 
                 MDP0000129926 
                 MDP0000536665 
                 MDP0000179767 
                 MDP0000147900 
                 MDP0000145027 
               
               
                 MDP0000153313 
                 MDP0000138241 
                 MDP0000338689 
                 MDP0000320119 
                 MDP0000927456 
                 MDP0000299015 
                 MDP0000192235 
               
               
                 MDP0000168725 
                 MDP0000217322 
                 MDP0000214291 
                 MDP0000270602 
                 MDP0000366710 
                 MDP0000248312 
                 MDP0000180024 
               
               
                 MDP0000225215 
                 MDP0000273029 
                 MDP0000156417 
                 MDP0000309477 
                 MDP0000169670 
                 MDP0000125171 
                 MDP0000204452 
               
               
                 MDP0000601282 
                 MDP0000122897 
                 MDP0000284030 
                 MDP0000905253 
                 MDP0000466284 
                 MDP0000319160 
                 MDP0000715969 
               
               
                 MDP0000712194 
                 MDP0000430717 
                 MDP0000901915 
                 MDP0000319434 
                 MDP0000284060 
                 MDP0000253891 
                 MDP0000345094 
               
               
                 MDP0000263628 
                 MDP0000288155 
                 MDP0000848695 
                 MDP0000184238 
                 MDP0000321380 
                 MDP0000607421 
                 MDP0000311110 
               
               
                 MDP0000463867 
                 MDP0000280105 
                 MDP0000237754 
                 MDP0000320056 
                 MDP0000262020 
                 MDP0000338804 
                 MDP0000666817 
               
               
                 MDP0000323375 
                 MDP0000940296 
                 MDP0000179659 
                 MDP0000412665 
                 MDP0000181372 
                 MDP0000312397 
                 MDP0000290889 
               
               
                 MDP0000158864 
                 MDP0000532093 
                 MDP0000242263 
                 MDP0000220347 
                 MDP0000750839 
                 MDP0000157962 
                 MDP0000811844 
               
               
                 MDP0000304763 
                 MDP0000163728 
                 MDP0000349199 
                 MDP0000314259 
                 MDP0000759782 
                 MDP0000127498 
                 MDP0000265213 
               
               
                 MDP0000202739 
                 MDP0000464599 
                 MDP0000317931 
                 MDP0000531930 
                 MDP0000281707 
                 MDP0000252478 
                 MDP0000201389 
               
               
                 MDP0000202282 
                 MDP0000186558 
                 MDP0000317621 
                 MDP0000280705 
                 MDP0000163771 
                 MDP0000274156 
                 MDP0000368785 
               
               
                 MDP0000174216 
                 MDP0000335354 
                 MDP0000427753 
                 MDP0000119925 
                 MDP0000265387 
                 MDP0000294667 
                 MDP0000191197 
               
               
                 MDP0000619638 
                 MDP0000237586 
                 MDP0000288670 
                 MDP0000319790 
                 MDP0000887754 
                 MDP0000318193 
                 MDP0000307516 
               
               
                 MDP0000503774 
                 MDP0000469664 
                 MDP0000138538 
                 MDP0000884147 
                 MDP0000815791 
                 MDP0000226601 
                 MDP0000202801 
               
               
                 MDP0000650358 
                 MDP0000126222 
                 MDP0000308563 
                 MDP0000390645 
                 MDP0000695737 
                 MDP0000394412 
                 MDP0000210087 
               
               
                 MDP0000540543 
                 MDP0000249284 
                 MDP0000132849 
                 MDP0000815097 
                 MDP0000128876 
                 MDP0000512808 
                 MDP0000229726 
               
               
                 MDP0000770369 
                 MDP0000192796 
                 MDP0000203347 
                 MDP0000672208 
                 MDP0000501447 
                 MDP0000206198 
                 MDP0000582861 
               
               
                 MDP0000282275 
                 MDP0000455726 
                 MDP0000228424 
                 MDP0000618272 
                 MDP0000250153 
                 MDP0000309575 
                 MDP0000392250 
               
               
                 MDP0000249539 
                 MDP0000275365 
                 MDP0000258078 
                 MDP0000349401 
                 MDP0000214532 
                 MDP0000813922 
                 MDP0000859897 
               
               
                 MDP0000257001 
                 MDP0000351483 
                 MDP0000543082 
                 MDP0000597996 
                 MDP0000161414 
                 MDP0000204437 
                 MDP0000123015 
               
               
                 MDP0000210684 
                 MDP0000176300 
                 MDP0000352413 
                 MDP0000741407 
                 MDP0000210970 
                 MDP0000171067 
                 MDP0000681724 
               
               
                 MDP0000473932 
                 MDP0000814937 
                 MDP0000300945 
                 MDP0000166861 
                 MDP0000443502 
                 MDP0000430870 
                 MDP0000844941 
               
               
                 MDP0000265810 
                 MDP0000153500 
                 MDP0000321445 
                 MDP0000167564 
                 MDP0000437672 
                 MDP0000225547 
               
               
                 MDP0000137990 
                 MDP0000215281 
                 MDP0000836081 
                 MDP0000658885 
                 MDP0000287293 
                 MDP0000317819 
               
               
                 MDP0000307857 
                 MDP0000203726 
                 MDP0000590966 
                 MDP0000706809 
                 MDP0000243937 
                 MDP0000205256 
               
               
                 MDP0000679688 
                 MDP0000346532 
                 MDP0000740877 
                 MDP0000877316 
                 MDP0000408508 
                 MDP0000361511 
               
               
                 MDP0000790026 
                 MDP0000415189 
                 MDP0000244886 
                 MDP0000410116 
                 MDP0000288633 
                 MDP0000206985 
               
               
                 MDP0000283898 
                 MDP0000225170 
                 MDP0000285682 
                 MDP0000287729 
                 MDP0000118810 
                 MDP0000581272 
               
               
                 MDP0000292276 
                 MDP0000308201 
                 MDP0000818140 
                 MDP0000497915 
                 MDP0000830519 
                 MDP0000178513 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
               
               
               
             
           
               
                 TABLE 5 
               
               
                   
               
               
                 Accession numbers (Velasco et al., 2010; Retrieved from the Internet: 
               
               
                 Rosaceae.org) of biomarker genes for superficial scald risk assessment during cold 
               
               
                 storage. Biomarker expression levels increase as risk of developing superficial scald 
               
               
                 increases. 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 MDP0000595271 
                 MDP0000231076 
                 MDP0000199110 
                 MDP0000153000 
                 MDP0000568825 
                 MDP0000593593 
                 MDP0000289804 
               
               
                 MDP0000868045 
                 MDP0000416548 
                 MDP0000532986 
                 MDP0000258908 
                 MDP0000197984 
                 MDP0000194046 
                 MDP0000148178 
               
               
                 MDP0000188613 
                 MDP0000899821 
                 MDP0000719836 
                 MDP0000299801 
                 MDP0000178304 
                 MDP0000404409 
                 MDP0000210595 
               
               
                 MDP0000266097 
                 MDP0000755113 
                 MDP0000261679 
                 MDP0000307124 
                 MDP0000380032 
                 MDP0000170792 
                 MDP0000267350 
               
               
                 MDP0000243843 
                 MDP0000242622 
                 MDP0000507003 
                 MDP0000908881 
                 MDP0000298232 
                 MDP0000726332 
                 MDP0000254208 
               
               
                 MDP0000209662 
                 MDP0000250936 
                 MDP0000737001 
                 MDP0000487738 
                 MDP0000144205 
                 MDP0000131645 
                 MDP0000326412 
               
               
                 MDP0000288533 
                 MDP0000508761 
                 MDP0000166704 
                 MDP0000487946 
                 MDP0000864442 
                 MDP0000195510 
                 MDP0000150480 
               
               
                 MDP0000511650 
                 MDP0000825508 
                 MDP0000142251 
                 MDP0000151829 
                 MDP0000867150 
                 MDP0000281064 
                 MDP0000137225 
               
               
                 MDP0000279839 
                 MDP0000231666 
                 MDP0000192074 
                 MDP0000119634 
                 MDP0000599845 
                 MDP0000257010 
                 MDP0000296432 
               
               
                 MDP0000162146 
                 MDP0000267909 
                 MDP0000251656 
                 MDP0000419926 
                 MDP0000803862 
                 MDP0000886270 
                 MDP0000150841 
               
               
                 MDP0000745371 
                 MDP0000342540 
                 MDP0000825373 
                 MDP0000194902 
                 MDP0000216945 
                 MDP0000711379 
                 MDP0000313224 
               
               
                 MDP0000217451 
                 MDP0000327191 
                 MDP0000509613 
                 MDP0000218404 
                 MDP0000235548 
                 MDP0000278477 
                 MDP0000829416 
               
               
                 MDP0000228499 
                 MDP0000471879 
                 MDP0000771404 
                 MDP0000656802 
                 MDP0000213526 
                 MDP0000913661 
                 MDP0000123888 
               
               
                 MDP0000759646 
                 MDP0000127244 
                 MDP0000307340 
                 MDP0000242083 
                 MDP0000199076 
                 MDP0000666771 
                 MDP0000633461 
               
               
                 MDP0000323702 
                 MDP0000792088 
                 MDP0000564334 
                 MDP0000187493 
                 MDP0000452083 
                 MDP0000261468 
                 MDP0000183814 
               
               
                 MDP0000182342 
                 MDP0000582214 
                 MDP0000198406 
                 MDP0000425918 
                 MDP0000172542 
                 MDP0000211356 
                 MDP0000570881 
               
               
                 MDP0000219062 
                 MDP0000668140 
                 MDP0000390049 
                 MDP0000431280 
                 MDP0000285612 
                 MDP0000921402 
                 MDP0000226995 
               
               
                 MDP0000216638 
                 MDP0000271312 
                 MDP0000313778 
                 MDP0000265094 
                 MDP0000420611 
                 MDP0000437033 
                 MDP0000251966 
               
               
                 MDP0000913598 
                 MDP0000161016 
                 MDP0000251516 
                 MDP0000572564 
                 MDP0000300811 
                 MDP0000200811 
                 MDP0000716496 
               
               
                 MDP0000906115 
                 MDP0000739955 
                 MDP0000186193 
                 MDP0000881966 
                 MDP0000233842 
                 MDP0000253215 
                 MDP0000256573 
               
               
                 MDP0000523579 
                 MDP0000715270 
                 MDP0000200799 
                 MDP0000291687 
                 MDP0000459010 
                 MDP0000127739 
                 MDP0000219838 
               
               
                 MDP0000782085 
                 MDP0000319910 
                 MDP0000252171 
                 MDP0000210560 
                 MDP0000663105 
                 MDP0000628093 
                 MDP0000173635 
               
               
                 MDP0000140483 
                 MDP0000137919 
                 MDP0000205035 
                 MDP0000148289 
                 MDP0000120413 
                 MDP0000812018 
                 MDP0000163017 
               
               
                 MDP0000450991 
                 MDP0000188101 
                 MDP0000135974 
                 MDP0000285672 
                 MDP0000205216 
                 MDP0000168714 
                 MDP0000323136 
               
               
                 MDP0000287302 
                 MDP0000786311 
                 MDP0000284571 
                 MDP0000175733 
                 MDP0000223003 
                 MDP0000149907 
                 MDP0000576205 
               
               
                 MDP0000298230 
                 MDP0000420223 
                 MDP0000434420 
                 MDP0000192671 
                 MDP0000158470 
                 MDP0000638442 
                 MDP0000258979 
               
               
                 MDP0000292031 
                 MDP0000697764 
                 MDP0000566567 
                 MDP0000319522 
                 MDP0000760179 
                 MDP0000515106 
                 MDP0000311720 
               
               
                 MDP0000295562 
                 MDP0000151884 
                 MDP0000545379 
                 MDP0000278157 
                 MDP0000756254 
                 MDP0000325497 
                 MDP0000222790 
               
               
                 MDP0000899351 
                 MDP0000298062 
                 MDP0000211549 
                 MDP0000191837 
                 MDP0000679369 
                 MDP0000707567 
                 MDP0000297105 
               
               
                 MDP0000191661 
                 MDP0000858175 
                 MDP0000202051 
                 MDP0000193898 
                 MDP0000369596 
                 MDP0000767257 
                 MDP0000506825 
               
               
                 MDP0000759591 
                 MDP0000839921 
                 MDP0000699004 
                 MDP0000120546 
                 MDP0000532630 
                 MDP0000568474 
                 MDP0000159103 
               
               
                 MDP0000586674 
                 MDP0000152670 
                 MDP0000246484 
                 MDP0000294847 
                 MDP0000608985 
                 MDP0000255415 
                 MDP0000160390 
               
               
                 MDP0000175691 
                 MDP0000569069 
                 MDP0000223057 
                 MDP0000156554 
                 MDP0000696814 
                 MDP0000212925 
                 MDP0000313485 
               
               
                 MDP0000230387 
                 MDP0000804928 
                 MDP0000162215 
                 MDP0000570395 
                 MDP0000374719 
                 MDP0000490696 
                 MDP0000279462 
               
               
                 MDP0000264639 
                 MDP0000125618 
                 MDP0000186011 
                 MDP0000201196 
                 MDP0000263161 
                 MDP0000578396 
                 MDP0000839209 
               
               
                 MDP0000649783 
                 MDP0000713068 
                 MDP0000139458 
                 MDP0000554480 
                 MDP0000263768 
                 MDP0000698220 
                 MDP0000148399 
               
               
                 MDP0000548790 
                 MDP0000142250 
                 MDP0000629887 
                 MDP0000209821 
                 MDP0000836661 
                 MDP0000286238 
                 MDP0000305699 
               
               
                 MDP0000645274 
                 MDP0000264441 
                 MDP0000875406 
                 MDP0000735747 
                 MDP0000237989 
                 MDP0000147814 
                 MDP0000864660 
               
               
                 MDP0000157209 
                 MDP0000129648 
                 MDP0000265644 
                 MDP0000862169 
                 MDP0000207066 
                 MDP0000294725 
                 MDP0000884047 
               
               
                 MDP0000278858 
                 MDP0000249405 
                 MDP0000305630 
                 MDP0000674589 
                 MDP0000316162 
                 MDP0000137211 
                 MDP0000275507 
               
               
                 MDP0000307943 
                 MDP0000148746 
                 MDP0000253802 
                 MDP0000279440 
                 MDP0000173593 
                 MDP0000163095 
                 MDP0000798346 
               
               
                 MDP0000126517 
                 MDP0000129626 
                 MDP0000232042 
                 MDP0000322404 
                 MDP0000407300 
                 MDP0000336146 
                 MDP0000142278 
               
               
                 MDP0000418277 
                 MDP0000288378 
                 MDP0000576110 
                 MDP0000680345 
                 MDP0000010587 
                 MDP0000181915 
                 MDP0000126274 
               
               
                 MDP0000298577 
                 MDP0000431556 
                 MDP0000122993 
                 MDP0000829170 
                 MDP0000899508 
                 MDP0000718806 
                 MDP0000222189 
               
               
                 MDP0000297821 
                 MDP0000127134 
                 MDP0000217423 
                 MDP0000314043 
                 MDP0000227115 
                 MDP0000885737 
                 MDP0000478232 
               
               
                 MDP0000197160 
                 MDP0000805606 
                 MDP0000276506 
                 MDP0000951901 
                 MDP0000417791 
                 MDP0000310641 
                 MDP0000582841 
               
               
                 MDP0000274090 
                 MDP0000300045 
                 MDP0000160434 
                 MDP0000431120 
                 MDP0000184528 
                 MDP0000589981 
                 MDP0000673917 
               
               
                 MDP0000140386 
                 MDP0000126570 
                 MDP0000310866 
                 MDP0000770211 
                 MDP0000133801 
                 MDP0000153532 
                 MDP0000718381 
               
               
                 MDP0000659260 
                 MDP0000192078 
                 MDP0000137826 
                 MDP0000206991 
                 MDP0000543167 
                 MDP0000176441 
                 MDP0000302538 
               
               
                 MDP0000150279 
                 MDP0000575170 
                 MDP0000350845 
                 MDP0000287264 
                 MDP0000205588 
                 MDP0000167199 
                 MDP0000119590 
               
               
                 MDP0000123893 
                 MDP0000585849 
                 MDP0000305384 
                 MDP0000248928 
                 MDP0000281804 
                 MDP0000119754 
                 MDP0000257423 
               
               
                 MDP0000123894 
                 MDP0000153831 
                 MDP0000202780 
                 MDP0000242255 
                 MDP0000136653 
                 MDP0000307516 
                 MDP0000118790 
               
               
                 MDP0000309383 
                 MDP0000161424 
                 MDP0000316694 
                 MDP0000163217 
                 MDP0000390252 
                 MDP0000884108 
                 MDP0000174365 
               
               
                 MDP0000154589 
                 MDP0000248504 
                 MDP0000863049 
                 MDP0000180877 
                 MDP0000164511 
                 MDP0000181206 
                 MDP0000547418 
               
               
                 MDP0000233761 
                 MDP0000394116 
                 MDP0000140755 
                 MDP0000304795 
                 MDP0000119010 
                 MDP0000563553 
                 MDP0000194040 
               
               
                 MDP0000171771 
                 MDP0000454229 
                 MDP0000415910 
                 MDP0000337931 
                 MDP0000866259 
                 MDP0000210996 
                 MDP0000251295 
               
               
                 MDP0000245234 
                 MDP0000124626 
                 MDP0000947607 
                 MDP0000323033 
                 MDP0000484484 
                 MDP0000880784 
                 MDP0000922391 
               
               
                 MDP0000740656 
                 MDP0000247130 
                 MDP0000260159 
                 MDP0000215049 
                 MDP0000641583 
                 MDP0000461727 
                 MDP0000180642 
               
               
                 MDP0000455515 
                 MDP0000320477 
                 MDP0000231668 
                 MDP0000221346 
                 MDP0000453190 
                 MDP0000160547 
                 MDP0000270644 
               
               
                 MDP0000271781 
                 MDP0000633953 
                 MDP0000293001 
                 MDP0000128089 
                 MDP0000119512 
                 MDP0000310001 
                 MDP0000272396 
               
               
                 MDP0000479863 
                 MDP0000251955 
                 MDP0000273029 
                 MDP0000229280 
                 MDP0000755938 
                 MDP0000841490 
                 MDP0000297304 
               
               
                 MDP0000488789 
                 MDP0000163690 
                 MDP0000230627 
                 MDP0000241967 
                 MDP0000222539 
                 MDP0000309587 
                 MDP0000805778 
               
               
                 MDP0000196402 
                 MDP0000175240 
                 MDP0000253952 
                 MDP0000240253 
                 MDP0000229843 
                 MDP0000129379 
                 MDP0000240930 
               
               
                 MDP0000398765 
                 MDP0000131182 
                 MDP0000264920 
                 MDP0000214697 
                 MDP0000333250 
                 MDP0000246999 
                 MDP0000263706 
               
               
                 MDP0000193050 
                 MDP0000173687 
                 MDP0000255777 
                 MDP0000162375 
                 MDP0000850015 
                 MDP0000610787 
                 MDP0000192492 
               
               
                 MDP0000279713 
                 MDP0000512061 
                 MDP0000269554 
                 MDP0000188229 
                 MDP0000255915 
                 MDP0000265042 
                 MDP0000719386 
               
               
                 MDP0000236634 
                 MDP0000617396 
                 MDP0000695252 
                 MDP0000221319 
                 MDP0000143011 
                 MDP0000129167 
                 MDP0000308284 
               
               
                 MDP0000223496 
                 MDP0000794656 
                 MDP0000301420 
                 MDP0000212713 
                 MDP0000127028 
                 MDP0000176769 
                 MDP0000162481 
               
               
                 MDP0000663049 
                 MDP0000843477 
                 MDP0000169686 
                 MDP0000179238 
                 MDP0000909653 
                 MDP0000124428 
                 MDP0000841118 
               
               
                 MDP0000663236 
                 MDP0000313248 
                 MDP0000180684 
                 MDP0000928674 
                 MDP0000692392 
                 MDP0000317974 
                 MDP0000185324 
               
               
                 MDP0000178522 
                 MDP0000286385 
                 MDP0000185304 
                 MDP0000584567 
                 MDP0000256726 
                 MDP0000202352 
                 MDP0000302858 
               
               
                 MDP0000275424 
                 MDP0000171719 
                 MDP0000299702 
                 MDP0000210562 
                 MDP0000210067 
                 MDP0000767331 
                 MDP0000268763 
               
               
                 MDP0000167207 
                 MDP0000709303 
                 MDP0000282415 
                 MDP0000127563 
                 MDP0000156421 
                 MDP0000205389 
                 MDP0000004754 
               
               
                 MDP0000241046 
                 MDP0000134135 
                 MDP0000468038 
                 MDP0000291544 
                 MDP0000304817 
                 MDP0000166723 
                 MDP0000160413 
               
               
                 MDP0000295604 
                 MDP0000680183 
                 MDP0000174149 
                 MDP0000863151 
                 MDP0000285243 
                 MDP0000121656 
                 MDP0000162600 
               
               
                 MDP0000131308 
                 MDP0000747526 
                 MDP0000261432 
                 MDP0000208546 
                 MDP0000121669 
                 MDP0000146135 
                 MDP0000164159 
               
               
                 MDP0000431281 
                 MDP0000243676 
                 MDP0000216602 
                 MDP0000543088 
                 MDP0000279550 
                 MDP0000165503 
                 MDP0000342721 
               
               
                 MDP0000532631 
                 MDP0000731356 
                 MDP0000639167 
                 MDP0000660892 
                 MDP0000732635 
                 MDP0000146390 
                 MDP0000321664 
               
               
                 MDP0000328533 
                 MDP0000012541 
                 MDP0000687873 
                 MDP0000882895 
                 MDP0000160662 
                 MDP0000133428 
                 MDP0000192847 
               
               
                 MDP0000865079 
                 MDP0000138296 
                 MDP0000289339 
                 MDP0000219521 
                 MDP0000226405 
                 MDP0000375867 
                 MDP0000159140 
               
               
                 MDP0000242052 
                 MDP0000269900 
                 MDP0000802413 
                 MDP0000276576 
                 MDP0000252597 
                 MDP0000720497 
                 MDP0000144324 
               
               
                 MDP0000314081 
                 MDP0000199234 
                 MDP0000723934 
                 MDP0000672731 
                 MDP0000253189 
                 MDP0000155746 
                 MDP0000196869 
               
               
                 MDP0000133671 
                 MDP0000162721 
                 MDP0000298547 
                 MDP0000231093 
                 MDP0000157089 
                 MDP0000933945 
                 MDP0000668914 
               
               
                 MDP0000585014 
                 MDP0000126098 
                 MDP0000900186 
                 MDP0000297797 
                 MDP0000201903 
                 MDP0000270083 
                 MDP0000225047 
               
               
                 MDP0000917197 
                 MDP0000123910 
                 MDP0000736035 
                 MDP0000257119 
                 MDP0000228838 
                 MDP0000176923 
                 MDP0000618087 
               
               
                 MDP0000126873 
                 MDP0000157408 
                 MDP0000363760 
                 MDP0000157879 
                 MDP0000318500 
                 MDP0000304378 
                 MDP0000184157 
               
               
                 MDP0000292176 
                 MDP0000119600 
                 MDP0000129506 
                 MDP0000421759 
                 MDP0000167088 
                 MDP0000831840 
                 MDP0000189570 
               
               
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                 MDP0000218952 
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                 MDP0000192816 
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                 MDP0000241928 
               
               
                 MDP0000300351 
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                 MDP0000164161 
                 MDP0000440918 
               
               
                 MDP0000812560 
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                 MDP0000190430 
                 MDP0000274901 
               
               
                 MDP0000012534 
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                 MDP0000891965 
                 MDP0000175839 
                 MDP0000298769 
               
               
                 MDP0000268320 
                 MDP0000757070 
                 MDP0000135041 
                 MDP0000205725 
                 MDP0000131763 
                 MDP0000138284 
                 MDP0000215026 
               
               
                 MDP0000276264 
                 MDP0000832469 
                 MDP0000262811 
                 MDP0000202900 
                 MDP0000242266 
                 MDP0000318293 
                 MDP0000328419 
               
               
                 MDP0000711374 
                 MDP0000788707 
                 MDP0000163669 
                   
                   
                   
                 MDP0000134278 
               
               
                 MDP0000131004 
                 MDP0000130822 
                 MDP0000897807 
               
               
                 MDP0000227886 
                 MDP0000122413 
                 MDP0000269136 
               
               
                 MDP0000882268 
                 MDP0000130200 
                 MDP0000734649 
               
               
                 MDP0000199661 
                 MDP0000318900 
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                 MDP0000155809 
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                 MDP0000241462 
               
               
                 MDP0000689033 
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                 MDP0000213383 
                 MDP0000306888 
                 MDP0000125850 
               
               
                   
               
             
          
         
       
     
         [0036]    Firm flesh browning disorder can be controlled using appropriate storage conditions. We were able to use these methods to discover putative biomarkers, since different treatments following harvest, induce contrasting disorder development. Controlled atmosphere combined with lower temperature (0.5° C.) storage causes increased injury over that observed at warmer storage temperature (3.0° C.). In addition, treatment of apples with 1-MCP (SmartFresh) following harvest also enhances firm flesh browning injury. Candidate biomarker genes were selected by pairwise comparison using the differential gene expression program edgeR (R, Bioconductor) with a p-value cut off of 0.05. Genes were selected from cortex/flesh tissue collected from New York state grown ‘Empire’ apples, provoked by storage treatments that affect firm flesh browning injury incidence. From a total of 63541 gene models, 2581 had an expression change of at least 4-fold, and had an average expression RPKM value of at least 1 per sample, and were selected as potential predictive or diagnostic biomarkers for firm flesh browning (Table 6). 
         [0000]    
       
         
               
             
               
               
               
               
               
               
               
             
           
               
                 TABLE 6 
               
               
                   
               
               
                 Accession numbers (Velasco et al., 2010; Retrieved from the Internet: 
               
               
                 Rosaceae.org) of biomarker genes for firm flesh browning risk assessment during cold 
               
               
                 storage. Higher or lower expression levels can result from cold stress resulting from 
               
               
                 storage imposition. 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
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                 MDP0000942873 
               
               
                 MDP0000310940 
                 MDP0000132381 
                 MDP0000217451 
                 MDP0000309530 
                 MDP0000708692 
                 MDP0000229338 
                 MDP0000944409 
               
               
                 MDP0000311556 
                 MDP0000132436 
                 MDP0000217745 
                 MDP0000309676 
                 MDP0000709073 
                 MDP0000231369 
                 MDP0000947607 
               
               
                 MDP0000312449 
                 MDP0000132623 
                 MDP0000218252 
                 MDP0000309805 
                 MDP0000709523 
                 MDP0000231477 
                 MDP0000949486 
               
               
                 MDP0000312701 
                 MDP0000132726 
                 MDP0000218451 
                 MDP0000310374 
                 MDP0000711379 
                 MDP0000232264 
                 MDP0000950422 
               
               
                 MDP0000312765 
                 MDP0000132855 
                 MDP0000218748 
                 MDP0000310430 
                 MDP0000711832 
                 MDP0000232789 
               
               
                 MDP0000312878 
                 MDP0000132952 
                 MDP0000218810 
                 MDP0000310641 
                 MDP0000711891 
                 MDP0000233356 
               
               
                   
               
             
          
         
       
     
         [0037]    The methods of the present invention may be practiced using any set of genes selected from the candidate genes disclosed herein, as long as the expression profiles of the genes within a given set discriminate between browning disorder progression outcomes. 
         [0038]    The identification of such sets of genes may be performed by any suitable selection method, including, but not limited to, cluster analysis, supported vector machines, neural networks or other algorithms. A set of genes identified by such selection methods is generally capable of predicting the classification of an unknown sample based on the expression levels of genes used for the discrimination. “Leave one out” cross-validation may be used to test the performance of various models and to help identify weights (genes) that are uninformative (e.g., redundant) or detrimental to the predictive ability of the gene model. 
         [0039]    As will be appreciated by those of ordinary skill in the art, sets of genes whose expression profiles correlate with browning disorder progression, and which can discriminate between browning disorder progression outcomes, may be used to identify/study unknown Rosaceous tissue samples. Accordingly, the present invention provides methods for characterizing Rosaceous tissue in Rosaceous fruit crops suspected of having the risk of developing multiple browning disorders. 
         [0040]    The diagnostic/prognostic methods of the present invention generally involve the determination of expression levels of a set of genes in a Rosaceous tissue sample. Determination of gene expression levels in the practice of the inventive methods may be performed by any suitable method. For example, determination of gene expression levels may be performed by detecting the expression of mRNA expressed from the genes of interest and/or by detecting the expression of a polypeptide encoded by the genes. Here, we have exemplified the determination of gene expression by the RNAseq method. 
         [0041]    Our method can be readily adapted to currently available, existing platforms for measuring biomarkers. The expected end users of our products include apple producers, storage operators, shippers, retailers, agricultural laboratories, and agrichemical service providers. The same or similar equipment is already regularly employed world-wide by agricultural/agrichemical service providers to measure biomarkers and for other chemical analysis (plant nutrient levels, plant growth regulators, chemical residue analysis). Other existing easy to use, field-based platforms, many of which are already employed in apple production and apple packing plants can be adapted for biomarker measurement in diverse settings including hand-held electronic devices, dip-stick tests, and bench-top, hand-held, and packing-line mounted non-destructive sorting sensors. Examples of agricultural applications using gene expression biomarkers include an easy-to-use, mail-in platform that measures biomarkers that determine optimum apple and pear fruit harvest date. 
         [0042]    As used herein, the term “gene” refers to a polynucleotide that encodes a discrete macromolecular product, be it RNA or a protein, and may include regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-encoding sequences) the coding sequence. As more than one polynucleotide may encode a discrete product, the term also includes alleles and polymorphisms of a gene that encode the same product, or a functionally associated (including gain, loss, or modulation of function) analog thereof. 
         [0043]    The term “gene expression” refers to the process by which RNA and proteins are made from the instructions encoded in genes. Gene expression include transcription and/or translation of nucleic acid material. 
         [0044]    The terms “gene expression pattern” and “gene expression profile” are used herein interchangeably. They refer to the expression of an individual gene or of a set of genes. A gene expression pattern may include information regarding the presence of target transcripts in a sample, and the relative or absolute abundance levels of target transcripts. 
         [0045]    The term “differentially expressed gene” refers to a gene whose level of expression is different in a subject (or a population of subjects) afflicted with a disorder relative to its level of expression in a healthy or control subject (or a population of healthy or control subjects). The term also includes a gene whose level of expression is different at different stages of, as described here, browning disorder. As will be appreciated by those skilled in the art, a gene may be differentially expressed at the nucleic acid level and/or protein level, may undergo alternative splicing resulting in a different polypeptide product, or the protein could be a target of posttranslational modification and degradation. Differential expression includes quantitative, as well as qualitative, differences in the temporal or cellular expression pattern in a gene or its expression products. As described in greater details below, a differentially expressed gene, alone or in combination with other differentially expressed genes, is useful in a variety of different applications in diagnostic, therapeutic, prognosis and related areas. The expression patterns of the differentially expressed genes disclosed herein can be described as a fingerprint or a signature of browning disorder progression. They can be used as a point of reference to compare and characterize unknown samples and samples for which further information is sought. 
         [0046]    The term “RNA transcript” refers to the product resulting from transcription of a DNA sequence. When the RNA transcript is the original, unmodified product of a RNA polymerase catalyzed transcription, it is referred to as the primary transcript. An RNA transcript that has been processed (e.g., spliced, etc.) will differ in sequence from the primary transcript. A processed RNA transcript that is translated into protein is often called a messenger RNA (mRNA). The term “messenger RNA or mRNA” refers to a form of RNA that serves as a template to direct protein biosynthesis. Typically, but not always, the amount of any particular type of mRNA (i.e., having the same sequence, and originating from the same gene) reflects the extent to which a gene has been expressed. 
         [0047]    The term “complementary DNA or cDNA” refers to a DNA molecule that is complementary to mRNA. cDNA can be made by DNA polymerase (e.g., reverse transcriptase) or by directed chemical synthesis. 
         [0048]    The term “complementary” refers to nucleic acid sequences that base-pair according to the standard Watson-Crick complementary rules, or that are capable of hybridizing to a particular nucleic acid segment under relatively stringent conditions. Nucleic acid polymers are optionally complementary across only portions of their entire sequences. 
         [0049]    The term “hybridizing” refers to the binding of two single stranded nucleic acids via complementary base pairing. The terms “specific hybridization” and “specific binding” are used herein interchangeably. They refer to a process in which a nucleic acid molecule preferentially binds, duplexes, or hybridizes to a particular nucleic acid sequence under stringent conditions (e.g., in the presence of competitor nucleic acids with a lower degree of complementarity to the hybridizing strand). In certain embodiments of the present invention, these terms more specifically refer to a process in which a nucleic acid fragment (or segment) from a test sample preferentially binds to a particular genetic probe and to a lesser extent or not at all, to other genetic probes, for example, when these genetic probes are immobilized on an array. 
         [0050]    The term “gene expression array” refers to an array comprising a plurality of genetic probes immobilized on a substrate surface that can be used for quantitation of mRNA expression levels. The term “genetic probe”, as used herein, refers to a nucleic acid molecule of known sequence, which has its origin in a defined region of the genome and can be a short DNA sequence (i.e., an oligonucleotide), a PCR product, or mRNA isolate. Genetic probes are gene-specific DNA sequences to which nucleic acid fragments from a test sample are hybridized. Genetic probes specifically bind to nucleic acid of complementary or substantially complementary sequence through one or more types of chemical bonds, usually through hydrogen bond formation. Here, we have used RNAseq profiling. 
         [0051]    As used herein, the term “a reagent that specifically detects expression levels” refers to one or more reagents used to detect the expression of one or more genes (e.g., genes selected from the groups of 82 (Table 1), 494 (Table 2) and 2330 (Table 3) genes provided herein. Examples of suitable reagents include, but are not limited to, nucleic acid probes capable of specifically hybridizing to the gene of interest, PCR primers capable of specifically amplifying the gene of interest, and antibodies capable of specifically binding to proteins expressed by the gene of interest. The term “amplify” is used in the broad sense to mean creating an amplification product. “Amplification”, as used herein, generally refers to the process of producing multiple copies of a desired sequence, particularly those of a sample. A “copy” does not necessarily mean perfect sequence complementarity or identity to the template sequence. 
         [0052]    The term “browning disorder profile” refers to a presentation of expression levels of a set of genes in Rosaceous fruit tissue (e.g., tissue at time of harvest, tissue after cold storage imposition). In preferred embodiments, profiles are generated from pooled samples comprising tissue samples from a plurality of fruits at the same stage. 
         [0053]    As used herein, the term “modulation of browning disorder progression” refers to the ability of a treatment or management strategy to increase or decrease the likelihood that browning disorder will occur. Generally, useful strategies are those that decrease the likelihood of multiple browning disorder progression. 
       EXAMPLES 
       [0054]    Having now generally described this invention, the same will be better understood by reference to certain specific examples, which are included herein only to further illustrate the invention and are not intended to limit the scope of the invention as defined by the claims. 
       Example 1 
     Biomarker Discovery: Early Term Physiological Disorder Risk Assessment 
       [0055]    For initial candidate selection, ‘Honeycrisp’ apples were obtained from 15 orchards distributed among the Lake Chelan/Brewster, Columbia Basin, and Yakima Valley growing regions in Washington State and the Hood River growing region of Oregon between September 2 and Oct. 21, 2011. No pre-harvest treatments were applied, with the exception of Retain™, an ethylene biosynthesis inhibitor, (Valent BioScience Corporation, Libertyville, Ill., USA) to Orchard M. To determine the effects of harvest-timing on postharvest soft scald and soggy breakdown, fruit from one site was harvested at three different times, to represent an early, mid-, and late harvest (Orchard A). On the day of harvest, quality was assessed. Fruit were stored at 1° C. with no atmospheric modification and after 12 weeks, the final incidence of soft scald and soggy breakdown was assessed. For the selection process, the intent was to account for orchard to orchard variation of soft scald/soggy breakdown incidence given the impacts of pre-harvest environment and cultural controls as well as harvest maturity. 
       Example 2 
     Biomarker Discovery: Late Term Physiological Disorder Risk Assessment 
       [0056]    ‘Granny Smith’ apples were harvested 140 days after full bloom (approximately 1 month prior to commercial harvest) at a research orchard near Orondo, Wash. After transport to the laboratory, analysis of fruit maturity and application of DPA and 1-MCP were performed. Apples were stored in air at 1° C. for up to 6 months. Six replications of 3 fruit per treatment were removed from storage at 1, 2, and 4 weeks and 2, 3, 4, and 6 months. Upon removal from storage, scald development was rated on a 0-4 scale and peel sampled and stored from each treatment for subsequent analysis. In a parallel experiment, additional apples were treated with 2000 mg L −1  DPA after 1-4 weeks, and 2 months after storage inception to determine the length of the transitional period during which scald can be suppressed. Scald development on these fruit was evaluated after 2, 3, 4, and 6 months storage. 
       Example 3 
     Gene Expression Evaluation: RNA Extraction and RNAseq Profiling 
       [0057]    Harvested apple tissue was immediately snap frozen in liquid nitrogen and stored at −80° C. until required. Tissue was ground into a fine powder in liquid N 2  and total RNA was extracted from 500 mg of tissue in 0.8 mL of extraction buffer (4M guanidine isothiocyanate, 25 mM EDTA, 2.5% polyvinylpyrollidone (MW 40,000), 2% sarkosyl, 1% β-mercaptoethanol, 0.2M sodium acetate, pH 5.0) at 70° C. for 10 min. Following incubation, chloroform (0.8 mL) was added, tubes vortexed and then spun in a benchtop centrifuge at top speed for 15 minutes. The resulting upper aqueous phase was collected, and a half volume of ethanol added and mixed by inversion. Total RNA was then purified through columns as per the manufacturer&#39;s instructions (Qiagen, RNAeasy), and eluted in nuclease free water. The resulting total RNA was checked for integrity via gel electrophoresis then quantified and diluted appropriately. 
         [0058]    Libraries for RNAseq were made using 2 μg of total RNA following the method of Zhong et al. (2011 . Cold Spring Harbor Protocols  8:940-949) and Gapper et al. (2013 . AoB Plants  5:plt021) with slight modification. In short, mRNA was isolated from total RNA, mRNA was fragmented and used as a template to produce cDNA by reverse transcription using Superscript III (Invitrogen). Following first strand cDNA synthesis, the second strand was synthesized with a dNTP mix incorporating dUTP instead of dTTP by DNA polymerase (Enzymatics). The ends of the double stranded cDNAs were then repaired (Enzymatics), dA tailed by the Klenow enzyme (Enzymatics) and universal adapters ligated to the double stranded cDNA fragments. Following ligation of adapters, the second strand was digested by Uracil DNA Glycosylase (UDG), to enable strand specific enrichment of the library. The UDG digested cDNA was then used as a template to enrich the libraries by PCR with Illumina Tru-seq primers using the high fidelity enzyme Phusion (New England Biolabs) with the following conditions: 95° C. 2 min; 15 cycles of 98° C. 11 s, 65° C. 30 s, 72° C. 25 s; 72° C. 2 min; 4° C. soak. 
         [0059]    Libraries were quantified, and 20 ng of each pooled for sequencing. Up to 48 libraries were multiplexed per sequencing reaction using an Illumina HiSeq 2500 next generation sequencer at the Weill Medicine School Sequencing Facility (Cornell University, New York City, N.Y.). Three biological replicates were sequenced for each sample. Short (40 bp) single-end, strand-specific RNASeq reads were filtered by aligning to adapter, ribosomal RNA and tRNA sequences using Bowtie (allowing two mismatches). The resulting high quality reads were aligned to the apple genome (Velasco et al. 2010 . Nat. Genet.  42(10):833-839) using Tophat (allowing 1 segment mismatch) (Benjamini and Hochberg. 1995 . J. Royal Stat. Soc. Series B  ( Method .) 57(1):289-300). Following alignments, raw counts were normalized to reads per kilobase of exon model per million mapped reads (RPKM). 
       Example 4 
     In Vitro Transcription and Chilling Stress 
       [0060]    Soft Scald and Soggy Breakdown. 
         [0061]    Only genes with expression levels over 2 RPKM for any replication were considered for candidate selection. Only genes whose expression was variable across the whole data set were considered for subsequent correlation analysis. Peel and cortex expression levels (RPKM) at harvest and following 2 weeks cold storage were compared with soft scald and soggy breakdown incidence (coded as 0=no incidence, 1=0-10%; 2=10-25%; 3=over 25%) taken at 12 weeks using Pearson&#39;s correlation analysis. Gene expression with a correlation coefficient above R 2 =10.5001 or R 2 =10.7001 for at-harvest and 2 week comparisons (respectively) were considered candidate biomarkers for risk assessment monitoring. 
         [0062]    Soft scald and soggy breakdown began to develop beginning at 4 weeks in some high risk orchards eventually developing to maximum incidence and severity by 12 weeks, as expected from earlier work using this cultivar ( FIG. 2 ). The RNAseq protocol provided one of many sensitive, accurate, and precise platform for candidate expression evaluation in both apple peel and flesh. Of the 63,541 genes screened in this experiment, 82 candidates were found useful for assessing risk at-harvest (Table 1) and 494 for 2 week risk assessment of peel and/or cortex tissue (Table 2). Biomarker gene expression primarily increased although some decreased with increasing risk. Accordingly, a summary of overall gene expression levels indicated that more models were linked with eventual injury at 2 weeks, or following cold storage imposition, rather than at-harvest ( FIG. 4 ) indicating that the cold stress that provokes the injury followed by candidate expression evaluation will provide the most accurate risk assessment. Given the dramatic change in gene expression provoked by cold storage imposition, measuring candidate expression levels both before and at one or more points following cold storage may yield even more accurate information by documenting upward or downward trends. Similarly, monitoring multiple risk assessment biomarkers can better ensure that changes are based on more biochemical systems associated with risk. 
         [0063]    Superficial Scald. 
         [0064]    Only genes with peel expression levels over 2 RPKM for any time point were considered for modeling and candidate selection yielding 35,644 gene models for subsequent screening. Gene models alongside superficial scald incidence were clustered across all 3 treatments over the 6 month storage period using k-means correlation clustering algorithm (Matlab) yielding 86 clusters. Gene models with increasing expression in control fruit, but not antioxidant or 1-MCP-treated fruit 2 months or more prior to superficial scald incidence, were considered candidates. K-means correlations clustering was used to group genes similarly expressed over the entire experiment in all treatments. Clusters comprised of superficial scald risk storage monitoring biomarker candidates were those that correlated R 2 =0.700 with conjugated trienol (CTOL) levels or injury incidence. 
         [0065]    The first symptoms of superficial scald began to develop on control fruit between 2 and 3 months and continued to increase in severity until 6 months as is typical for this cultivar when stored in air without any control steps taken ( FIG. 3B ). Both crop protectants either eliminated or markedly reduced symptom development while providing two physiologically different means of control to select the most accurate risk assessment candidates from. Because superficial scald can be adequately controlled using appropriate storage conditions, indicating whether storage conditions are actually working or monitoring risk during storage is the most useful tool for this disorder. Increases in superficial scald risk-associated gene expression began at 1 month for a few candidates ( FIG. 5 ) 690 candidates for early indication of scald risk (Table 3). Monitoring multiple risk assessment biomarkers can better ensure that changes are based on more biochemical systems associated with risk. 
       Example 5 
     Risk Assessment 
       [0066]    Multiple candidates are part of previously unidentified metabolic responses to stress and, monitoring these candidates appear to be effective for assessing risk across disorders and cultivars following, or during, cold stress events. Changes in expression levels before and following cold storage imposition as well as fold difference between high risk and low risk orchards for developing soft scald/soggy breakdown (early-term disorders) are included as examples of broadly effective risk assessment biomarkers (Table 7). For soft scald/soggy breakdown risk assessment, the fold difference from the highest incidence orchard to lowest incidence orchard is indicated as well as the % change in expression following cold storage imposition. For superficial scald, a late-term disorder, the time from first detection of risk using a specific biomarker until symptom appearance and the % change in expression during that period are indicated. Expression of many of these genes change dramatically indicating repeated measurement around the point of cold storage imposition may be used to improve confidence. Monitoring the same genes during storage of cultivars at risk for developing superficial scald or other late-term apple and pear physiological disorders leads to expression changes that ultimately culminate in symptom development 1 month or more later. Increased expression of up to 98% transpired up to 6 weeks prior to disorder development. Biomarker genes are from multiple stress-related biochemical processes not related to stress in fruit prior to this discovery. Monitoring biomarkers from multiple processes can be used for a more confident evaluation. For instance, candidates putatively involved in phenolic metabolism and indole acetic acid (IAA) metabolism could be monitored in tandem. 
         [0000]    
       
         
               
             
               
               
             
               
               
               
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 7 
               
             
             
               
                   
               
               
                 Apple protein Accession Numbers (Velasco et al., 2010; Retrieved 
               
               
                 from the Internet: Rosaceae.org) of biomarker genes for early 
               
               
                 and late term apple peel and flesh disorders. 
               
             
          
           
               
                   
                 Late-term disorders 
               
             
          
           
               
                   
                 Early-term disorders 
                 Time before 
                   
               
             
          
           
               
                 Gene accession 
                 Fold 
                 % 
                 symptoms 
                 % 
               
               
                 number 
                 difference 1   
                 change 2   
                 (weeks) 3   
                 change 4   
               
               
                   
               
             
          
           
               
                 MDP0000591260 
                 7.8*, nd     
                 75.0 
                 8 
                 52.8 
               
               
                 MDP0000272351 
                 6.4, 11  
                 89.0 
                 8 
                 41.9 
               
               
                 MDP0000145813 
                 11.5, 13.8 
                 43.9 
                 8 
                 82.0 
               
               
                 MDP0000551974 
                 16.9, 56.6 
                 86.4 
                 8 
                 46.2 
               
               
                 MDP0000424447 
                 21.9, 54.4 
                 85.6 
                 8 
                 36.6 
               
               
                 MDP0000215525 
                 20.2, 29.0 
                 46.3 
                 8 
                 83.9 
               
               
                 MDP0000715898 
                 12.7, 15.5 
                 81.9 
                 6 
                 60.1 
               
               
                 MDP0000306121 
                 18.2, 30.0 
                 46.6 
                 8 
                 84.3 
               
               
                 MDP0000290801 
                 19.1, 41.0 
                 56.2 
                 8 
                 83.4 
               
               
                 MDP0000307237 
                 17.9, 27.4 
                 40.4 
                 6 
                 81.1 
               
               
                 MDP0000769764 
                 20.1, 224  
                 59.6 
                 8 
                 77.7 
               
               
                 MDP0000545122 
                 13.6, 27.0 
                 88.2 
                 6 
                 44.7 
               
               
                 MDP0000733506 
                 22.0, 31.3 
                 82.4 
                 8 
                 48.0 
               
               
                 MDP0000617956 
                 47.6, nd     
                 82.3 
                 8 
                 46.9 
               
               
                 MDP0000755567 
                 11.6, 25.2 
                 96.6 
                 6 
                 17.9 
               
               
                 MDP0000334047 
                 11.0, 8.09 
                 64.4 
                 6 
                 36.7 
               
               
                 MDP0000688645 
                 34.2, 16.4 
                 98.1 
                 8 
                 43.9 
               
               
                 MDP0000576682 
                 4.8, nd  
                 −10.6 
                 6 
                 66.2 
               
               
                 MDP0000191939 
                 4.0, 3.1 
                 −6.3 
                 8 
                 46.7 
               
               
                 MDP0000195213 
                 15.3, 19.4 
                 63.3 
                 8 
                 41.8 
               
               
                 MDP0000211643 
                 19.5, 8.2  
                 82.2 
                 8 
                 20.3 
               
               
                 MDP0000292164 
                  9.0, 16.4 
                 64.7 
                 6 
                 50.2 
               
               
                 MDP0000130244 
                 51.0, 20.5 
                 96.8 
                 6 
                 75.2 
               
               
                 MDP0000190809 
                  4.9, 10.0 
                 62.8 
                 6 
                 −22.1 
               
               
                 MDP0000748916 
                 10.0, 4.2  
                 48.8 
                 6 
                 21.6 
               
               
                 MDP0000199009 
                 8.4, 5.3 
                 62.8 
                 6 
                 21.5 
               
               
                 MDP0000143611 
                 1.8, 2.8 
                 17.9 
                 8 
                 46.7 
               
               
                 MDP0000166302 
                 1.6, 2.1 
                 18.9 
                 8 
                 24.5 
               
               
                 MDP0000278475 
                 3.3, 4.3 
                 34.8 
                 8 
                 21.8 
               
               
                 MDP0000640906 
                 4.1, 8.1 
                 85.9 
                 6 
                 28.0 
               
               
                   
               
               
                   1 Fold difference of biomarker levels at 2 weeks between GH (highest risk) and GLE1 (lowest risk). 
               
               
                   2 Percent gene expression change in GH harvest to 2 weeks. 
               
               
                   3 The time (in weeks) between elevated biomarker levels in high risk fruit and symptom development at 3 months. 
               
               
                   4 Percent change in gene expression in high risk fruit from 2 to 8 weeks. 
               
             
          
         
       
     
         [0067]    As apple and pear fruit transition through the supply chain, they undergo many stress events. Our invention allows for an easy means for interrogating fruit undergoing these transitions to assess risk for developing these disorders.  FIG. 6  provides a scheme for some of the ways which our biomarker-based risk assessment scheme can be used to direct storage and marketing decisions that can mitigate or avoid disorder development. 
         [0068]    All publications and patents mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent was specifically and individually indicated to be incorporated by reference. 
         [0069]    The foregoing description and certain representative embodiments and details of the invention have been presented for purposes of illustration and description of the invention. It is not intended to be exhaustive or to limit the invention to the precise forms disclosed. It will be apparent to practitioners skilled in this art that modifications and variations may be made therein without departing from the scope of the invention.