The peach volatilome modularity is reflected at the genetic and environmental response levels in a QTL mapping population

BackgroundThe improvement of fruit aroma is currently one of the most sought-after objectives in peach breeding programs. To better characterize and assess the genetic potential for increasing aroma quality by breeding, a quantity trait locus (QTL) analysis approach was carried out in an F1 population segregating largely for fruit traits.ResultsLinkage maps were constructed using the IPSC peach 9 K Infinium ® II array, rendering dense genetic maps, except in the case of certain chromosomes, probably due to identity-by-descent of those chromosomes in the parental genotypes. The variability in compounds associated with aroma was analyzed by a metabolomic approach based on GC-MS to profile 81 volatiles across the population from two locations. Quality-related traits were also studied to assess possible pleiotropic effects. Correlation-based analysis of the volatile dataset revealed that the peach volatilome is organized into modules formed by compounds from the same biosynthetic origin or which share similar chemical structures. QTL mapping showed clustering of volatile QTL included in the same volatile modules, indicating that some are subjected to joint genetic control. The monoterpene module is controlled by a unique locus at the top of LG4, a locus previously shown to affect the levels of two terpenoid compounds. At the bottom of LG4, a locus controlling several volatiles but also melting/non-melting and maturity-related traits was found, suggesting putative pleiotropic effects. In addition, two novel loci controlling lactones and esters in linkage groups 5 and 6 were discovered.ConclusionsThe results presented here give light on the mode of inheritance of the peach volatilome confirming previously loci controlling the aroma of peach but also identifying novel ones.

Related papers:

title: Effects of individual selection on agronomical and morphological traits and essential oil of a “Greek basil” population
abstract: Abstract“Greek basil” (Ocimum basilicum L.) is a common local cultivar in Greece, also known as “fine-leaved” basil, because of its small-narrow leaves. It is used mainly as ornamental plant in pots and gardens. Its variation in terms of the time of florescence and the shape of the vegetative development (compact or loose ball, reverse cone, other shapes) led to the improvement of a “Greek basil” population, by selecting plants with late blooming, compact ball shape and big size, potentially suited for ornamental uses. After three cycles of individual selection in nil competition conditions, by applying the above selection criteria, the florescence of the selected population started at the beginning of August, instead of mid June of the initial population, and the percentage of plants with compact ball shape increased from 55 to 90%. Moreover, significant variation was observed in the essential oil yield and composition due to the applied selection. The percentage oil yield increased from 0.15 to 0.53%. The main oil constituents eugenol and linalool raised from 8.60 to 12.90% (49%) and from 36.80 to 49.75% (34.90%) respectively, while the methyl (E) cinnamate, though it was present (19.20%) in the initial population, it was not even detected in the improved population.

title: Inheritance of aroma compounds in a model population of Fragaria x ananassa Duch
abstract: The inheritance of important aroma compounds is demonstrated by the use of a model population of Fragaria x ananassa. Two cultivars were chosen for the crossing, 'Mieze Schindler' and 'Elsanta', which differ strongly in pedigree, phenotype, and fruit traits, including flavour. Two hundred seedlings of this cross-combination were randomly selected from a population of 438 seedlings and propagated, with three plants per seedling. Aroma analysis was performed by automated headspace solid phase micro-extraction in combination with non-targeted data analysis (pattern recognition). This method can assist breeding programmes by the preparation and analysis of hundreds of samples by a simple procedure. The method was backed up by the substance identification using gas chromatography/mass spectrometry. Data processing of 78 detectable volatile compounds by Chromstat™ in the F 1 population showed very high variability of the volatile patterns. The ester methyl anthranilate (MA) is a discriminative key compound, being present only in the mother cultivar 'Mieze Schindler', and not detectable in 'Elsanta'. Methyl anthranilate was detectable in one fourth of the F 1 population. This low degree of inheritance shows that this important compound is easily lost in the breeding process, which could explain why all investigated modern cultivars do not contain MA. The results are valuable for the choice of breeding partners and for selection in seedling populations.

title: CONSUMER PERCEPTIONS OF QUALITY: APRICOTS, CANTALOUPES, PEACHES, PEARS, STRAWBERRIES, AND TOMATOES
abstract: Consumers are increasing their produce consumption; however, complaints of inconsistent produce quality and improper consumer handling practices could reduce consumer satisfaction with and demand for specific produce items. Seventy to eighty percent of consumers buy cantaloupes, peaches, pears, strawberries and tomatoes at the supermarket; only about half buy apricots at the supermarket. Apricots are not purchased at any location by almost 30% of consumers. Satisfaction with quality is highest for cantaloupes, lowest for tomatoes and apricots. Consumer complaints center around flavor and textural changes which develop in ripening. Both consumer handling practices and fresh product quality contribute to dissatisfaction.

title: CONSUMER AND RETAILER SATISFACTION WITH THE QUALITY AND SIZE OF CALIFORNIA PEACHES AND NECTARINES
abstract: Over 200 consumers and produce buyers representing 15 major supermarkets were interviewed in 1992 to determine factors considered in peach and nectarine selection and interest in fruit below marketing order minimum sizes. Fruit firmness, color and aroma are the most important characteristics consumers use to judge quality. More consumers are satisfied with the size of peaches and nectarines available in the market than are satisfied with the quality. Very few prefer smaller sized fruit and those who have purchased small prebagged fruit, believe it is inferior and a poor value. Retailers, including those marketing in lower income areas, do not find current size standards restrictive nor are they interested in purchasing smaller fruit. Retailers believe growers should focus on quality and better tasting varieties. Both consumers and retailers consider mealy peaches a problem. Results indicate that marketing orders should emphasize quality and maturity indicators.

title: How quality relates to price in California fresh peaches
abstract: During a single season, researchers compared California fresh peaches for quality and price at the producer and retail levels. While prices at both levels declined during the season, they responded differently to changes in quality characteristics. The results suggest a potential for increased revenues from marketing sweeter, more mature fruit.

title: A Non-Targeted Approach Unravels the Volatile Network in Peach Fruit
abstract: Volatile compounds represent an important part of the plant metabolome and are of particular agronomic and biological interest due to their contribution to fruit aroma and flavor and therefore to fruit quality. By using a non-targeted approach based on HS-SPME-GC-MS, the volatile-compound complement of peach fruit was described. A total of 110 volatile compounds (including alcohols, ketones, aldehydes, esters, lactones, carboxylic acids, phenolics and terpenoids) were identified and quantified in peach fruit samples from different genetic backgrounds, locations, maturity stages and physiological responses. By using a combination of hierarchical cluster analysis and metabolomic correlation network analysis we found that previously known peach fruit volatiles are clustered according to their chemical nature or known biosynthetic pathways. Moreover, novel volatiles that had not yet been described in peach were identified and assigned to co-regulated groups. In addition, our analyses showed that most of the co-regulated groups showed good intergroup correlations that are therefore consistent with the existence of a higher level of regulation orchestrating volatile production under different conditions and/or developmental stages. In addition, this volatile network of interactions provides the ground information for future biochemical studies as well as a useful route map for breeding or biotechnological purposes.

title: Identification of key odor volatile compounds in the essential oil of nine peach accessions.
abstract: Volatile compounds, together with sugars and acids, are the main chemical species determining the characteristic aroma and flavor of food. In peach, more than 100 volatiles have been identified.



The essential oil of six peach and three nectarine accessions used in Italian breeding programs was obtained by steam distillation, and the volatiles were investigated. A total of 47 known volatiles, two unidentified compounds and nine hydrocarbons were identified, including 12 aldehydes, six alcohols, three acids, three esters, six terpenes, two phenylalanine derivates, two C(13) norisoprenoids, one ketone (C(9)) and 10 lactones. A wide variation in the number of volatiles and in their concentration was observed among the nine accessions. Twenty-one compounds presented odor activity values (OAVs) higher than 1 in at least one of the accessions and were therefore putatively considered as key odorants in the peach volatile composition.



This study reports the identification, quantification and potency, based on the OAVs, of the most important volatile compounds, along with fruit quality characteristics, of nine different peach/nectarine accessions and will help future peach volatile breeding programs for the selection of odor-rich accessions to be used in the development of new improved cultivars.

title: Differences in key odorants of handmade juice of yellow-flesh peaches (Prunus persica L.) induced by the workup procedure.
abstract: Application of aroma extract dilution analysis (AEDA) on a flavor extract isolated from a freshly prepared, enzyme-inactivated peach juice using solvent extraction and high-vacuum distillation (extract I) revealed 24 odor-active regions in the gas chromatogram. Flavor dilution (FD) factors ranged from 4 to 512. The highest FD factors were determined for beta-damascenone (cooked-apple-like) and gamma-decalactone (peach-like). Cooking of peaches for 2 h in an apparatus equipped for simultaneous steam distillation/extraction (extract II) yielded an overall more intense aroma extract (extract II). By AEDA, 30 odorants were detected in the FD-factor region of 4-16384 and were subsequently identified. The results revealed that in extract II, besides the two above-mentioned aroma compounds, both had FD factors of 16 384; delta-decalactone, gamma-dodecalactone additionally, and 6-dodeceno-gamma-lactone contributed with very high FD factors (FD 8192) to the overall aroma. In general, the thermal treatment led to the formation of 15 new odorants which were not detected in I. Furthermore, the lactones and beta-damascenone were significantly increased in II, thereby indicating their generation from precursors in the fresh juice.

title: Aroma characterization of various apricot varieties using headspace–solid phase microextraction combined with gas chromatography–mass spectrometry and gas chromatography–olfactometry
abstract: The characterization of the aromatic profile of several apricot cultivars with molecular tracers in order to obtain objective data concerning the aromatic quality of this fruit was undertaken using headspace–solid phase microextraction (HS–SPME). Six apricot cultivars were selected according to their organoleptic characteristics: Iranien, Orangered, Goldrich, Hargrand, Rouge du Roussillon and A4025. The aromatic intensity of these varieties measured by HS–SPME–Olfactometry were defined and classified according to the presence and the intensity of grassy, fruity and apricot like notes. In the six varieties, 23 common volatile compounds were identified by HS–SPME–GC–MS. Finally, 10 compounds, ethyl acetate, hexyl acetate, limonene, β-cyclocitral, γ-decalactone, 6-methyl-5-hepten-2-one, linalool, β-ionone, menthone and (E)-hexen-2-al were recognized by HS–SPME–GC–O as responsible of the aromatic notes involved in apricot aroma and considered as molecular tracers of apricot aromatic quality which could be utilized to discriminate apricot varieties.

title: Characterization of the key aroma compounds in apricots (Prunus armeniaca) by application of the molecular sensory science concept.
abstract: An aroma extract dilution analysis applied on an aroma distillate prepared from fresh apricots revealed (R)-gamma-decalactone, (E)-beta-damascenone, delta-decalactone, and (R/S)-linalool with the highest flavor dilution (FD) factors among the 26 odor-active compounds identified. On the basis of quantitative measurements performed by application of stable isotope dilution assays, followed by a calculation of odor activity values (OAVs), beta-ionone, (Z)-1,5-octadien-3-one, gamma-decalactone, (E,Z)-2,6-nonadienal, linalool, and acetaldehyde appeared with OAVs >100, whereas in particular certain lactones, often associated with an apricot aroma note, such as gamma-undecalactone, gamma-nonalactone, and delta-decalactone, showed very low OAVs (<5). An aroma recombinate prepared by mixing the 18 most important odorants in concentrations as they occurred in the fresh fruits showed an overall aroma very similar to that of apricots. Omission experiments indicated that previously unknown constituents of apricots, such as (E,Z)-2,6-nonadienal or (Z)-1,5-octadien-3-one, are key contributors to the apricot aroma.

title: Physical and chemical changes during the maturation of peaches (cv. Majestic).
abstract: The study was undertaken to determine the relationship between the changes in sugars and nonvolatile acids relative to the aroma volatile compounds during maturation and to determine if such changes could be useful indices of maturity for Majestic peaches.

title: Volatile compound production during growth and ripening of peaches and nectarines
abstract: Peaches (Prunus persica L., Batsch; cv. Glohaven) and nectarines (P. persica L., Batsch, var. nucipersica; cv. Maria Laura) were picked weekly from 57 days after full bloom (DAFB) to complete ripening on the tree in order to study the changes in volatile composition during fruit growth and ripening. Volatile substances were sampled from sliced pulp by dynamic headspace and analyzed by capillary Gas Chromatography (cGC) and gas chromatography/mass spectrometry. Volatile composition varied greatly, both quantitatively and qualitatively over time and between cultivars. Aldehydes, alcohols and esters showed a decreasing trend during fruit growth, with the exception of acetoin and (Z)-3-hexenol which reached the highest amounts in mature fruits. Glohaven peaches produced great amounts of lactones, mainly γ- and δ-decalactone, and γ- and δ-dodecalactone. Maria Laura nectarines produced less volatiles but more of esters and terpenoids (linalool and terpinolene) than peaches. As a consequence, nectarine aroma was more floral and fruity.

title: Expression of genes associated with aroma formation derived from the fatty acid pathway during peach fruit ripening.
abstract: Changes in characteristic aroma volatiles, levels of fatty acids as aroma precursors, and expression patterns of related genes, including lipoxygenase (LOX), hydroperoxide lyase (HPL), alcohol dehydrogenase (ADH), alcohol acyltransferase (AAT), and fatty acid desaturase (FAD), were studied in peach ( Prunus persica L. Batsch., cv. Yulu) fruit during postharvest ripening at 20 degrees C. Concentrations of n-hexanal, (E)-2-hexenal, (E)-2-hexenol, and (Z)-3-hexenol decreased, whereas the production of (Z)-3-hexenyl acetate, gamma-hexalactone, gamma-octalactone, gamma-decalactone, and delta-decalactone increased with fruit ripening. Lactones showed a clear pattern concomitant with the climacteric rise in ethylene production, with gamma-decalactone being the principal volatile compound at the late ripening stage. Of the LOX family genes, PpLOX2 and PpLOX3 had relatively high transcript levels initially followed by a decline with fruit ripening, while levels of PpLOX1 and PpLOX4 transcripts were upregulated by accumulated ethylene production. Expression of PpHPL1, PpADH1, PpADH2, and PpADH3 showed similar decreasing patterns during ripening. Expression levels of PpAAT1 showed a rapid increase during the first 2 days of postharvest ripening followed by a gradual decrease. Contents of polyunsaturated linoleic and linolenic acids increased, and saturated palmitic acid levels tended to decline as the fruit ripened. The increased levels of unsaturated fatty acids closely paralleled increasing expression of PpFAD1 and PpFAD2. The significance of gene expression changes in relation to aroma volatile production is discussed.

title: Changes in physicochemical characteristics and volatile constituents of yellow- and white-fleshed nectarines during maturation and artificial ripening.
abstract: Changes in the volatile composition during maturation and artificial ripening of yellow-fleshed nectarines were investigated by means of GC-FID and GC-MS over three years (1999-2001). Unripe and commercially ripe fruits were placed in ripening chambers until complete ripening and compared to tree-ripe nectarines. Firmness, weight, soluble solids (SS), titratable acidity (TA), SS/TA ratio, organic acids, and sugars were also determined. Furthermore, the tree-ripe and artificially ripened yellow-fleshed nectarines were subjected to sensory analysis by a taste panel. In 2001, a similar experiment on white-fleshed nectarines (cv. Vermeil) was performed to compare with the results obtained on yellow-fleshed nectarines. Levels of volatiles compounds, in particular, lactones and C(13) norisoprenoids, were found to be the same or higher in the artificially ripened nectarines compared with the tree-ripe nectarines. In addition, no significant difference was observed for sweetness, sourness, and the intensities of "peach odors" or "peach aroma" in the sensory analysis between the tree-ripe samples and the artificially ripened nectarines. However, in the latter the levels of SS and the SS/TA ratio were very close to those observed in the initial unripe samples and significantly lower than those observed in tree-ripe nectarines.

title: Effect of cold storage and maturity on the physical and chemical characteristics and volatile constituents of peaches (cv. Cresthaven)
abstract: In general, size, weight, soluble solids (SS), sucrose content, SS/TA ratio, volatiles, and Minolta a value increased with increased maturity of unripened fruit. Minolta L and b values, glucose, fructose, and sorbitol contents, and total phenolics did not vary significantly by maturity. Titratable acidity and hue angle decreased with increased maturity. After 4-week storage, significant deterioration probably will occur

title: Changes In Composition of Volatile Compounds in High Pressure Treated Peach
abstract: The headspace volatile components of high pressure treated (400 MPa, 20 o C, 10 min) white peach (Prunus percica L. cv. Shimizu) were analyzed by capillary gas chromatography-mass spectrometry (GC-MS) and compared with headspace volatiles of ripe intact peach, crushed peach, and heat-treated peach. To examine the flavor quality, the high pressure treated peaches packed in pouches were stored at 25 and 40 o C for various periods and analyzed by GC-MS. The enzymical formation of benzaldehyde, C 6 aldehydes, and alcohols by disruption of the fruit tissues was observed in the high pressure treated fruit and crushed fruit. The influence of high-pressure treatment for β-glucosidase activity related to formation of glycosidically bound volatiles was examined

title: Influence of fruit bagging on aroma volatiles and skin coloration of ‘Hakuho’ peach (Prunus persica Batsch)
abstract: The influence of bagging on aroma volatiles and skin coloration of ‘Hakuho’ peach ( Prunus persica ) was examined over a 2-year-period. In 2002, fruit were covered with orange paper bags before pit hardening, and with single and triple parchment paper bags and orange paper bags (percentage transmission of sunlight: 80%, 50%, and 15%, respectively) 15 days before harvest. Non-bagged fruit were used as controls. The fruit harvested at the firm-mature stage and stored for 3 days thereafter were evaluated. In both study years, bagging generally caused earlier ripening, particularly in 2002. However, fruit maturity did not show any significant differences among the treatments in 2003. Fruit weight, soluble solids content (SSC), and titratable acidity (TA) were not affected by bagging treatments. The area and intensity of the skin's red color were increased with increasing bag exposure to sunlight. The non-bagged fruit accumulated the largest amount of anthocyanin, whereas the fruit covered with orange bags had the smallest amount of anthocyanin. The high chlorophyll content and the brown blemishes on the skin of non-bagged fruit, as well as the low L values, were responsible for the low visual quality. By contrast, fruit covered with orange bags appeared bright red and had high L values, both of which accounted for the good visual quality. Whereas bagging did not affect total aroma volatile production by whole fruit, significant differences were observed in the aroma volatile content between skin and flesh. A significant difference was observed in the γ- and δ-decalactone levels among fruit with different bag treatments. The aroma volatile content was the lowest in non-bagged fruit that were exposed to full sunlight. The results indicate that bagging of ‘Hakuho’ peach can improve fruit skin color through the reduction of chlorophyll content and increase fruit flavor through the increase in aroma volatile content.

title: Genetic dissection of aroma volatile compounds from the essential oil of peach fruit: QTL analysis and identification of candidate genes using dense SNP maps
abstract: Volatile organic compounds (VOCs) in plants are involved in aroma and pest resistance. These compounds form a complex mixture whose composition is specific to species and often to varieties. Despite their importance as essential factors that determine peach fruit quality, understanding of molecular, genetic, and physiological mechanisms underlying aroma formation is limited. The aim of this study was the identification in peach of quantitative trait loci (QTLs) for fruit VOCs to understand their genetic basis using an F1 population of 126 seedlings deriving from the cross between “Bolero” (B) and “OroA” (O), two peach cultivars differing in their aroma profile. Dense single nucleotide polymorphism (SNP) and SSR maps covering the eight linkage groups of the peach genome were constructed by genotyping with the International Peach SNP Consortium peach SNP array v1, and data for 23 VOCs with high or unknown “odor activity value” were obtained by gas chromatography–mass spectrometry analysis of fruit essential oil in the years 2007 and 2008. A total of 72 QTLs were identified, most consistent in both years. QTLs were identified for the 23 VOCs studied, including three major QTLs for nonanal, linalool, and for p-menth-1-en-9-al stable in both years. Collocations between candidate genes and major QTLs were identified taking advantage of the peach genome sequence: genes encoding two putative terpene synthases and one lipoxygenase (Lox) might be involved in the biosynthesis of linalool and p-menth-1-en-9-al, and nonanal, respectively. Implications for marker-assisted selection and future research on the subject are discussed.

title: Expression profiling of genes involved in the formation of aroma in two peach genotypes.
abstract: The expression profile of flavour-related genes during ripening was investigated in two peach genotypes, Bolero and OroA, which have been selected for their contrasting aroma/ripening behaviour. A new peach microarray containing 4776 oligonucleotide probes corresponding to a set of ESTs specifically enriched in secondary metabolism (μPEACH2.0) was designed to investigate transcriptome changes during three fruit ripening stages, revealing 1807 transcripts differentially expressed within and between the two genotypes. Differences in the expression of genes involved in the biosynthesis of aroma compounds were detected during the ripening process within and between the two genotypes. In particular, a subset of 12 transcripts involved in metabolism of esters, norisoprenoids, phenylpropanoids and lactones, varied in expression during ripening and between Bolero and OroA.

title: Comparative analysis of expressed sequence tags from tissues in ripening stages of peach (Prunus persica L. Batsch)
abstract: Expressed sequence tag (EST) represents a resource for gene discovery, genome annotation and comparative genomics in plants. ESTs were derived by sequencing clones from five libraries created from two different fruit tissues (skin and mesocarp), at four ripening stages (from post-allegation to post-climacteric) in three different genotypes of peach (OroA, Bolero and Suncrest). A total of 10,847 EST sequences were produced (dataset A); in addition, 21,857 peach ESTs (dataset B) were obtained from public databases. Clustering and assembly of both datasets gave 17,858 unigenes. Analysis of the sequences allowed the assignment of a putative function to 70.8% of the ESTs. In order to define the relationship among fruit tissues transcriptome, a gene ontology analysis was performed. Differences among organs and among different maturation stages of the same organs were identified in organelle, signal transducer and antioxidant activity. A distance matrix of pairwise correlation coefficients analysis was applied between the libraries. Shoot appeared to outgroup and our analysis proved to be an efficient tool to parallel and complement gene expression studies (for example, based on microarray analysis). We conducted an analysis of the frequency of genes putatively involved in the metabolism of some volatiles, which pointed to a predominant presence of those transcripts in the skin. The metabolic pathways of esters and lactones were selected for further isolation and cloning of key genes. The EST database is available at the web site www.itb.cnr.it/estree.

title: Changes in aroma-related volatiles and gene expression during low temperature storage and subsequent shelf-life of peach fruit
abstract: Melting flesh peach ( Prunus persica L. Batsch., cv. Hujingmilu) fruit were harvested and stored at 0, 5, 8 °C for up to 21 d. Data on emission of characteristic aroma-related volatiles, and expression patterns of related genes, including lipoxygenase (LOX), hydroperoxide lyase (HPL), alcohol dehydrogenase (ADH), and alcohol acyltransferase (AAT), were obtained from fruit at the different low temperatures for 7, 14 and 21 d and a subsequent shelf-life for 3 d after each of those storage times. Production of volatiles was markedly influenced by storage temperature and time. In general, fruit at 5 °C were sensitive to chilling injury (CI) and had the lowest levels of volatile compounds, especially fruity note volatiles such as esters and lactones. An electronic nose (e-nose) was used to evaluate peach aroma, and the CI fruit could be separated from those at low temperature but which had not developed the disorder. Relative expression levels of genes involved in the LOX pathway were repressed in fruit with CI. Of the LOX family genes, PpLOX1 and PpLOX3 were upregulated in association with accumulated ethylene during shelf-life, while levels of PpLOX2 and PpLOX4 declined after removal. Expression of PpHPL1 , PpADH1 , PpADH2 , and PpADH3 exhibited similar decreasing patterns during shelf-life, whereas transcript levels of PpAAT1 were induced. The results suggest that reduced levels of fruity note volatiles in fruit with CI were the consequence of modifications in expression of PpLOX1 , PpLOX3 and PpAAT1 ; the significance of ethylene in relation to aroma-related volatiles production after cold storage is discussed.

title: Postharvest temperature influences volatile lactone production via regulation of acyl-CoA oxidases in peach fruit.
abstract: The biosynthesis of volatile compounds in plants is affected by environmental conditions. Lactones are considered to be peach-like aroma volatiles; however, no enzymes or genes associated with their biosynthesis have been characterized. White-fleshed (cv. Hujingmilu) and yellow-fleshed (cv. Jinxiu) melting peach (Prunus persica L. Batsch) fruit were used as materials in two successive seasons and responses measured to four different temperature treatments. Five major lactones accumulated during postharvest peach fruit ripening at 20 °C. Peach fruit at 5 °C, which induces chilling injury (CI), had the lowest lactone content during subsequent shelf life after removal, while 0 °C and a low-temperature conditioning (LTC) treatment alleviated development of CI and maintained significantly higher lactone contents. Expression of PpACX1 and activity of acyl-CoA oxidase (ACX) with C16-CoA tended to increase during postharvest ripening both at 20 °C and during shelf life after removal from cold storage when no CI was developed. There was a positive correlation between ACX and lactones in peach fruit postharvest. Changes in lactone production in response to temperatures are suggested to be a consequence of altered expression of PpACX1 and long-chain ACX activity.

title: Study of 'Redhaven' peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism
abstract: BackgroundCarotenoids are plant metabolites which are not only essential in photosynthesis but also important quality factors in determining the pigmentation and aroma of flowers and fruits. To investigate the regulation of carotenoid metabolism, as related to norisoprenoids and other volatile compounds in peach (Prunus persica L. Batsch.), and the role of carotenoid dioxygenases in determining differences in flesh color phenotype and volatile composition, the expression patterns of relevant carotenoid genes and metabolites were studied during fruit development along with volatile compound content. Two contrasted cultivars, the yellow-fleshed 'Redhaven' (RH) and its white-fleshed mutant 'Redhaven Bianca' (RHB) were examined.ResultsThe two genotypes displayed marked differences in the accumulation of carotenoid pigments in mesocarp tissues. Lower carotenoid levels and higher levels of norisoprenoid volatiles were observed in RHB, which might be explained by differential activity of carotenoid cleavage dioxygenase (CCD) enzymes. In fact, the ccd4 transcript levels were dramatically higher at late ripening stages in RHB with respect to RH. The two genotypes also showed differences in the expression patterns of several carotenoid and isoprenoid transcripts, compatible with a feed-back regulation of these transcripts. Abamine SG - an inhibitor of CCD enzymes - decreased the levels of both isoprenoid and non-isoprenoid volatiles in RHB fruits, indicating a complex regulation of volatile production.ConclusionsDifferential expression of ccd4 is likely to be the major determinant in the accumulation of carotenoids and carotenoid-derived volatiles in peach fruit flesh. More in general, dioxygenases appear to be key factors controlling volatile composition in peach fruit, since abamine SG-treated 'Redhaven Bianca' fruits had strongly reduced levels of norisoprenoids and other volatile classes. Comparative functional studies of peach carotenoid cleavage enzymes are required to fully elucidate their role in peach fruit pigmentation and aroma.

title: An integrative “omics” approach identifies new candidate genes to impact aroma volatiles in peach fruit
abstract: BackgroundEver since the recent completion of the peach genome, the focus of genetic research in this area has turned to the identification of genes related to important traits, such as fruit aroma volatiles. Of the over 100 volatile compounds described in peach, lactones most likely have the strongest effect on fruit aroma, while esters, terpenoids, and aldehydes have minor, yet significant effects. The identification of key genes underlying the production of aroma compounds is of interest for any fruit-quality improvement strategy.ResultsVolatile (52 compounds) and gene expression (4348 genes) levels were profiled in peach fruit from a maturity time-course series belonging to two peach genotypes that showed considerable differences in maturation characteristics and postharvest ripening. This data set was analyzed by complementary correlation-based approaches to discover the genes related to the main aroma-contributing compounds: lactones, esters, and phenolic volatiles, among others. As a case study, one of the candidate genes was cloned and expressed in yeast to show specificity as an ω-6 Oleate desaturase, which may be involved in the production of a precursor of lactones/esters.ConclusionsOur approach revealed a set of genes (an alcohol acyl transferase, fatty acid desaturases, transcription factors, protein kinases, cytochromes, etc.) that are highly associated with peach fruit volatiles, and which could prove useful in breeding or for biotechnological purposes.

title: The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
abstract: Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.

title: Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm
abstract: Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs. The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species.

title: The plant volatilome: methods of analysis.
abstract: Analysis of plant volatile organic compounds (VOCs) and essential oils (EOs, collectively called the plant volatilome) is an invaluable technique in plant biology, as it provides the qualitative and quantitative composition of bioactive compounds. From a physiological standpoint, the plant volatilome is involved in some critical processes, namely plant-plant interactions, the signaling between symbiotic organisms, the attraction of pollinating insects, a range of biological activities in mammals, and as an endless source of novel drugs and drug leads. This chapter analyses and discusses the most advanced methods of analysis of the plant volatilome.

title: Genetic Analysis of Strawberry Fruit Aroma and Identification of O-Methyltransferase FaOMT as the Locus Controlling Natural Variation in Mesifurane Content1[C][W][OA]
abstract: Improvement of strawberry (Fragaria × ananassa) fruit flavor is an important goal in breeding programs. To investigate genetic factors controlling this complex trait, a strawberry mapping population derived from genotype ‘1392’, selected for its superior flavor, and ‘232’ was profiled for volatile compounds over 4 years by headspace solid phase microextraction coupled to gas chromatography and mass spectrometry. More than 300 volatile compounds were detected, of which 87 were identified by comparison of mass spectrum and retention time to those of pure standards. Parental line ‘1392’ displayed higher volatile levels than ‘232’, and these and many other compounds with similar levels in both parents segregated in the progeny. Cluster analysis grouped the volatiles into distinct chemically related families and revealed a complex metabolic network underlying volatile production in strawberry fruit. Quantitative trait loci (QTL) detection was carried out over 3 years based on a double pseudo-testcross strategy. Seventy QTLs covering 48 different volatiles were detected, with several of them being stable over time and mapped as major QTLs. Loci controlling γ-decalactone and mesifurane content were mapped as qualitative traits. Using a candidate gene approach we have assigned genes that are likely responsible for several of the QTLs. As a proof of concept we show that one homoeolog of the O-methyltransferase gene (FaOMT) is the locus responsible for the natural variation of mesifurane content. Sequence analysis identified 30 bp in the promoter of this FaOMT homoeolog containing putative binding sites for basic/helix-loop-helix, MYB, and BZIP transcription factors. This polymorphism fully cosegregates with both the presence of mesifurane and the high expression of FaOMT during ripening.

title: Metabolic characterization of loci affecting sensory attributes in tomato allows an assessment of the influence of the levels of primary metabolites and volatile organic contents
abstract: Numerous studies have revealed the extent of genetic and phenotypic variation between both species and cultivars of tomato. Using a series of tomato lines resulting from crosses between a cherry tomato and three independent large fruit cultivar (Levovil, VilB, and VilD), extensive profiling of both central primary metabolism and volatile organic components of the fruit was performed. In this study, it was possible to define a number of quantitative trait loci (QTLs) which determined the levels of primary metabolites and/or volatile organic components and to evaluate their co-location with previously defined organoleptic QTLs. Correlation analyses between either the primary metabolites or the volatile organic compounds and organoleptic properties revealed a number of interesting associations, including pharmaceutical aroma–guaiacol and sourness–alanine, across the data set. Considerable correlation within the levels of primary metabolites or volatile organic compounds, respectively, were also observed. However, there was relatively little association between the levels of primary metabolites and volatile organic compounds, implying that they are not tightly linked to one another. A notable exception to this was the strong association between the levels of sucrose and those of a number of volatile organic compounds. The combined data presented here are thus discussed both with respect to those obtained recently from wide interspecific crosses of tomato and within the framework of current understanding of the chemical basis of fruit taste.

title: Quantitative trait loci affecting reproductive phenology in peach
abstract: BackgroundThe reproductive phenology of perennial plants in temperate climates is largely conditioned by the duration of bud dormancy, and fruit developmental processes. Bud dormancy release and bud break depends on the perception of cumulative chilling and heat during the bud development. The objective of this work was to identify new quantitative trait loci (QTLs) associated to temperature requirements for bud dormancy release and flowering and to fruit harvest date, in a segregating population of peach.ResultsWe have identified QTLs for nine traits related to bud dormancy, flowering and fruit harvest in an intraspecific hybrid population of peach in two locations differing in chilling time accumulation. QTLs were located in a genetic linkage map of peach based on single nucleotide polymorphism (SNP) markers for eight linkage groups (LGs) of the peach genome sequence. QTLs for chilling requirements for dormancy release and blooming clustered in seven different genomic regions that partially coincided with loci identified in previous works. The most significant QTL for chilling requirements mapped to LG1, close to the evergrowing locus. QTLs for heat requirement related traits were distributed in nine genomic regions, four of them co-localizing with QTLs for chilling requirement trait. Two major loci in LG4 and LG6 determined fruit harvest time.ConclusionsWe identified QTLs associated to nine traits related to the reproductive phenology in peach. A search of candidate genes for these QTLs rendered different genes related to flowering regulation, chromatin modification and hormone signalling. A better understanding of the genetic factors affecting crop phenology might help scientists and breeders to predict changes in genotype performance in a context of global climate change.

title: A rapid DNA isolation procedure for small quantities of fresh leaf tissue
abstract: A stopped flow kinetic analysis has been performed with a homogeneous protein fraction of plant glutamate dehydrogenase. The enzyme exerts strong negative cooperativity with ammonium as variable substrate. The limiting initial rate constants for low substrate concentrations, as calculated from the kinetic data, indicate that the catalytic efficiency of the enzyme increases at low ammonium concentrations. From this it becomes evident that the reductive amination reaction is highly adaptive to the ammonium environment.

title: Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers.
abstract: We have used a "two-way pseudo-testcross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct two moderate density genetic linkage maps for species of Eucalyptus. In the cross between two heterozygous individuals many single-dose RAPD markers will be heterozygous in one parent, null in the other and therefore segregate 1:1 in their F1 progeny following a testcross configuration. Meiosis and gametic segregation in each individual can be directly and efficiently analyzed using RAPD markers. We screened 305 primers of arbitrary sequence, and selected 151 to amplify a total of 558 markers. These markers were grouped at LOD 5.0, theta = 0.25, resulting in the maternal Eucalyptus grandis map having a total of 240 markers into 14 linkage groups (1552 cM) and the paternal Eucalyptus urophylla map with 251 markers in 11 linkage groups (1101 cM) (n = 11 in Eucalyptus). Framework maps ordered with a likelihood support > or = 1000:1 were assembled covering 95% of the estimated genome size in both individuals. Characterization of genome complexity of a sample of 48 mapped random amplified polymorphic DNA (RAPD) markers indicate that 53% amplify from low copy regions. These are the first reported high coverage linkage maps for any species of Eucalyptus and among the first for any hardwood tree species. We propose the combined use of RAPD markers and the pseudo-testcross configuration as a general strategy for the construction of single individual genetic linkage maps in outbred forest trees as well as in any highly heterozygous sexually reproducing living organisms. A survey of the occurrence of RAPD markers in different individuals suggests that the pseudo-testcross/RAPD mapping strategy should also be efficient at the intraspecific level and increasingly so with crosses of genetically divergent individuals. The ability to quickly construct single-tree genetic linkage maps in any forest species opens the way for a shift from the paradigm of a species index map to the heterodox proposal of constructing several maps for individual trees of a population, therefore mitigating the problem of linkage equilibrium between marker and trait loci for the application of marker assisted strategies in tree breeding.

title: Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP.
abstract: A computerized procedure to construct integrated genetic maps is presented. The computer program (Join Map) can handle raw data from F2s, backcrosses and recombinant inbred lines, as well as listed pair-wise recombination frequencies. The procedure is useful for combining linkage data that have been collected in different experiments; the result is a mathematical alignment of the distinct genetic maps. Data from single experiments can be dealt with as well. In view of the fast growing amount of linkage information for molecular markers, which is often being generated by different research groups, integrated maps provide useful information on the map position of genes and DNA markers. 
 
The procedure performs a sequential build-up of the map and, at each step, a numerical search for the best fitting order of markers. Weighted least squares is used for the estimation of map distances.

title: MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations.
abstract: With the advent of RFLPs, genetic linkage maps are now being assembled for a number of organisms including both inbred experimental populations such as maize and outbred natural populations such as humans. Accurate construction of such genetic maps requires multipoint linkage analysis of particular types of pedigrees. We describe here a computer package, called MAPMAKER, designed specifically for this purpose. The program uses an efficient algorithm that allows simultaneous multipoint analysis of any number of loci. MAPMAKER also includes an interactive command language that makes it easy for a geneticist to explore linkage data. MAPMAKER has been applied to the construction of linkage maps in a number of organisms, including the human and several plants, and we outline the mapping strategies that have been used.

title: MapChart: software for the graphical presentation of linkage maps and QTLs.
abstract: Over the last 15 years a wealth of linkage maps and quantitative trait loci (QTL) mapping results have become available. The pace of generating this genetic information is accelerating owing to advances in molecular marker technology and the development of software for linkage analysis and QTL mapping. A graphical presentation of this information is often needed, both for publication purposes and for easy and intuitive interpretation. However, the development of tools for the graphical presentation of linkage maps and QTLs has lagged behind. DrawMap (Van Ooijen 1994) was an early program capable of drawing genetic linkage maps. However, the output of this program was not very well suited for use in modern word processors and presentation software. Authors in this field have therefore, of necessity, resorted to the use of general graphics software to compose charts of their linkage and QTL maps. This is always a laborious process, with sometimes disappointing results. Also, each time a map is recalculated when new data become available, this process has to be repeated. For this reason I developed MapChart, a software package that takes as input the linkage and QTL data and generates charts of linkage maps and QTLs. These charts can easily be exported to word processing or presentation software. The charts are exported as vector graphics (Windows enhanced metafiles) rather than bitmaps, which makes them easy to rescale and to edit further if desired.

title: A Novel Approach for Nontargeted Data Analysis for Metabolomics. Large-Scale Profiling of Tomato Fruit Volatiles1[w]
abstract: To take full advantage of the power of functional genomics technologies and in particular those for metabolomics, both the analytical approach and the strategy chosen for data analysis need to be as unbiased and comprehensive as possible. Existing approaches to analyze metabolomic data still do not allow a fast and unbiased comparative analysis of the metabolic composition of the hundreds of genotypes that are often the target of modern investigations. We have now developed a novel strategy to analyze such metabolomic data. This approach consists of (1) full mass spectral alignment of gas chromatography (GC)-mass spectrometry (MS) metabolic profiles using the MetAlign software package, (2) followed by multivariate comparative analysis of metabolic phenotypes at the level of individual molecular fragments, and (3) multivariate mass spectral reconstruction, a method allowing metabolite discrimination, recognition, and identification. This approach has allowed a fast and unbiased comparative multivariate analysis of the volatile metabolite composition of ripe fruits of 94 tomato (Lycopersicon esculentum Mill.) genotypes, based on intensity patterns of >20,000 individual molecular fragments throughout 198 GC-MS datasets. Variation in metabolite composition, both between- and within-fruit types, was found and the discriminative metabolites were revealed. In the entire genotype set, a total of 322 different compounds could be distinguished using multivariate mass spectral reconstruction. A hierarchical cluster analysis of these metabolites resulted in clustering of structurally related metabolites derived from the same biochemical precursors. The approach chosen will further enhance the comprehensiveness of GC-MS-based metabolomics approaches and will therefore prove a useful addition to nontargeted functional genomics research.

title: Cytoscape: a software environment for integrated models of biomolecular interaction networks.
abstract: networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

title: QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations
abstract: QTLNetwork is a software package for mapping and visualizing the genetic architecture underlying complex traits for experimental populations derived from a cross between two inbred lines. It can simultaneously map quantitative trait loci (QTL) with individual effects, epistasis and QTL-environment interaction. Currently, it is able to handle data from F(2), backcross, recombinant inbred lines and double-haploid populations, as well as populations from specific mating designs (immortalized F(2) and BC(n)F(n) populations). The Windows version of QTLNetwork was developed with a graphical user interface. Alternatively, the command-line versions have the facility to be run in other prevalent operating systems, such as Linux, Unix and MacOS.


AVAILABILITY
http://ibi.zju.edu.cn/software/qtlnetwork.

title: High density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.)
abstract: Single nucleotide polymorphisms (SNPs) were used to construct an integrated SNP linkage map of peach (Prunus persica (L.) Batsch). A set of 1,536 SNPs were evaluated with the GoldenGate® Genotyping assay in two mapping populations, Pop-DF, and Pop-DG. After genotyping and filtering, a final set of 1,400 high quality SNPs in Pop-DF and 962 in Pop-DG with full map coverage were selected and used to construct two linkage maps with JoinMap®4.0. The Pop-DF map covered 422 cM of the peach genome and included 1,037 SNP markers, and Pop-DG map covered 369 cM and included 738 SNPs. A consensus map was constructed with 588 SNP markers placed in eight linkage groups (n = 8 for peach), with map coverage of 454 cM and an average distance of 0.81 cM/marker site. Placements of SNPs on the “peach v1.0” physical map were compared to placement on the linkage maps and several differences were observed. Using the SNP linkage map of Pop-DG and phenotypic data collected for three harvest seasons, a QTL analysis for fruit quality traits and chilling injury symptoms was carried out with the mapped SNPs. Significant QTL effects were detected for mealiness (M) and flesh bleeding (FBL) QTLs on linkage group 4 and flesh browning (FBr) on linkage group 5. This study represents one of the first examples of QTL detection for quality traits and chilling injury symptoms using a high-density SNP map in a single peach F1 family.

title: A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
abstract: Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs). This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM) and barley (Oregon Wolfe Barley) recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

title: QTL analysis of fruit quality traits in two peach intraspecific populations and importance of maturity date pleiotropic effect
abstract: Two intraspecific peach breeding populations have been used to conduct a quantitative trait locus (QTL) analysis of fruit quality traits: an F1 from the cross Bolero (B) x OroA (O) and an F2 from the cross Contender (C) x Ambra (A). A total of 344 Prunus simple sequence repeats (SSRs) were analyzed in B, O, C, A parents and CxA F1 hybrid. Eight SSR were mapped for the first time in peach. A multiplex-ready polymerase chain reaction (PCR) protocol has allowed considerable time and cost saving during genotyping steps. Two maps (B map and O map) were produced for BxO population following the pseudo-test cross strategy and one for CxA. No marker could be mapped on G6 for the B map, on G4 and G8 for the O map and on G5 for the CxA map. Both populations were phenotyped over 2 years for maturity date (MD), fruit weight, external fruit skin overcolor, juice total soluble solids (SSC, Brix degree), juice titrable acidity and juice pH. Data for blooming time and flower type were scored only for BxO in 2007. All traits had a normal distribution, except for MD which was bimodal in BxO and trimodal in CxA, where it was scored as a co-dominant trait. Up to two QTLs per trait were detected in each population, and most of them were located in the same region forming clusters of QTLs, especially on G4. This is likely due to a major pleiotropic effect of MD masking the identification of other QTLs for different traits.

title: QTL analysis of agronomic traits in a BC1 peach population
abstract: The purpose of the present study was to identify tight linkage between important agronomic traits and molecular markers with the aim of using them in Marker Assisted Selection (MAS) in the peach breeding programs at ISF. Quantitative trait loci (QTLs) influencing several agronomic traits were identified in a BC1 population issued from a cross between a selection of Prunus persica (IF 7310828) used as female recurrent parent and an accession of the related wild species P. ferganensis carrying a source of resistance to powdery mildew. One hundred and nine molecular markers (RFLPs, SSRs and RAPDs), spaced through the genome, were used to analyze 70 random progeny of this population. Fourteen characters, including blooming time, ripening time, disease resistance and traits related to tree architecture and fruit quality, were analyzed for 3-5 years on each tree of the BC1 progeny. QTLs were identified for internode length, blooming time, ripening time, skin color, soluble solids content and Sphaerotheca pannosa resistance. Most of the QTLs were consistent through the years showing that the expression of the genes is largely independent of the environmental conditions. All of them displayed the same effect as the parental phenotype. For each trait the detected QTLs explained up to 42% of the total variance.

title: QTL analysis of quality traits in an advanced backcross between Prunus persica cultivars and the wild relative species P. davidiana
abstract: Genetic control of the different attributes involved in peach quality has been investigated in an advanced backcross population derived from a cross between Prunus davidiana clone P1908, a wild parent with poor agronomic performance, and a commercial variety, Summergrand. A total of 24 physical and biochemical traits were investigated. Quantitative trait loci (QTLs) were detected for all the traits studied. We identified alleles from P. davidiana with agronomically favorable effects regarding fruit and stone sizes, sugar and acid concentrations and red flesh coloration, in clear contrast to its phenotype. We identified three main regions of the genome where alleles from P. davidiana had negative effects on multiple traits. In other regions, co-locations of QTLs with opposite effects on quality traits were also detected. We discuss the nature of these co-locations in the light of the probable physiological mechanisms involved. Strategies to cope with negative correlations between favorable traits and co-locations of P. davidiana alleles with negative effects on quality traits and positive effects regarding resistance to powdery mildew are discussed from a breeding point of view.

title: Comparison of the genetic determinism of two key phenological traits, flowering and maturity dates, in three Prunus species: peach, apricot and sweet cherry
abstract: The present study investigates the genetic determinism of flowering and maturity dates, two traits highly affected by global climate change. Flowering and maturity dates were evaluated on five progenies from three Prunus species, peach, apricot and sweet cherry, during 3–8 years. Quantitative trait locus (QTL) detection was performed separately for each year and also by integrating data from all years together. High heritability estimates were obtained for flowering and maturity dates. Several QTLs for flowering and maturity dates were highly stable, detected each year of evaluation, suggesting that they were not affected by climatic variations. For flowering date, major QTLs were detected on linkage groups (LG) 4 for apricot and sweet cherry and on LG6 for peach. QTLs were identified on LG2, LG3, LG4 and LG7 for the three species. For maturity date, a major QTL was detected on LG4 in the three species. Using the peach genome sequence data, candidate genes underlying the major QTLs on LG4 and LG6 were investigated and key genes were identified. Our results provide a basis for the identification of genes involved in flowering and maturity dates that could be used to develop cultivar ideotypes adapted to future climatic conditions.

title: Comparative mapping and marker-assisted selection in Rosaceae fruit crops.
abstract: The development of saturated linkage maps using transferable markers, restriction fragment length polymorphisms, and micro-satellites has provided a foundation for fruit tree genetics and breeding. A Prunus reference map with 562 such markers is available, and a further set of 13 maps constructed with a subset of these markers has allowed genome comparison among seven Prunus diploid (x = 8) species (almond, peach, apricot, cherry, Prunus ferganensis, Prunus davidiana, and Prunus cerasifera); marker colinearity was the rule with all of them. Preliminary results of the comparison between apple and Prunus maps suggest a high level of synteny between these two genera. Conserved genomic regions have also been detected between Prunus and Arabidopsis. By using the data from different linkage maps anchored with the reference Prunus map, it has been possible to establish, in a general map, the position of 28 major genes affecting agronomic characters found in different species. Markers tightly linked to the major genes responsible for the expression of important traits (disease/pest resistances, fruit/nut quality, self-incompatibility, etc.) have been developed in apple and Prunus and are currently in use for marker-assisted selection in breeding programs. Quantitative character dissection using linkage maps and candidate gene approaches has already started. Genomic tools such as the Prunus physical map, large EST collections in both Prunus and Malus, and the establishment of the map position of high numbers of ESTs are required for a better understanding of the Rosaceae genome and to foster additional research and applications on fruit tree genetics.

title: Endopolygalacturonase: a Candidate Gene for Freestone and Melting Fleshin Peach
abstract: Peach fruit are handled, processed, and marketed according to their stone adhesion and fruit softening type. Uncertainty exists over whether these simply inherited traits are controlled by two linked loci, Freestone (F) and Melting flesh (M) or one multi-allelic locus, and whether M is controlled by the cell wall degrading enzyme, endopolygalacturonase. From morphological and molecular analysis of two related segregating populations of peach, we conclude that a single locus containing at least one gene for endopolygalacturonase, controls both F and M with at least three effective alleles. A simple diagnostic PCR test is now available for the three major phenotypes of freestone melting flesh (FMF), clingstone melting flesh (CMF), and clingstone non-melting flesh (CNMF).

title: Monoterpene and sesquiterpene synthases and the origin of terpene skeletal diversity in plants.
abstract: The multitude of terpene carbon skeletons in plants is formed by enzymes known as terpene synthases. This review covers the monoterpene and sesquiterpene synthases presenting an up-to-date list of enzymes reported and evidence for their ability to form multiple products. The reaction mechanisms of these enzyme classes are described, and information on how terpene synthase proteins mediate catalysis is summarized. Correlations between specific amino acid motifs and terpene synthase function are described, including an analysis of the relationships between active site sequence and cyclization type and a discussion of whether specific protein features might facilitate multiple product formation.