bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Numbers of Single Nucleotide Polymorphisms Required to Measure Genetic Distance in Maize (Zea mays L.)
Authors: Nelson Barry K. , Kahler Alex L. , Kahler Jonathan L. , Mikel Mark A. , Thompson Steven A. , Ferriss Ronald S. , Smith Stephen , Jones Elizabeth S. 
Published: June 2011

ABSTRACTWe examined the number, genomic coverage, and discrimination abilities of single nucleotide polymorphism (SNP) markers required to provide equivalent measures of genetic distance compared to previously assayed simple sequence repeat (SSR) loci among inbred lines of maize (Zea mays L). A diverse set of public inbred lines was profiled with 768 public SNP markers and subsets of 601, 446, 305, 204, 165, 83, and 42 SNP markers were selected based on maintenance of expected heterozygosity (He) and/or even genomic coverage. The effectiveness of each SNP marker set was evaluated by comparison with standard SSR marker sets and pedigree distance values. Each marker set was evaluated using the full set of data for 80 diverse public inbred lines, a subset of inbred lines selected to represent the diversity of the full range of inbreds, and a subset of more closely related Stiff Stalk Synthetic (SSS) inbreds. A set of 305 SNP markers with mean He of greater than 0.4 had comparable or lower genetic distance sampling variance compared with SSR markers and resulted in r values comparable to larger SNP sets when pair‐wise Roger's distances were correlated with distance estimates generated from pedigree or SSR data. We found that, where SNP markers are selected to maintain high He and even genome coverage, then data from only 2 to 3 times the number of SNP markers are needed to reveal associations among lines compared with SSR markers.
Drought Adaptive Traits and Wide Adaptation in Elite Lines Derived from Resynthesized Hexaploid Wheat
Authors: Lopes Marta S. , Reynolds Matthew P. 
Published: June 2011

ABSTRACTIt has been shown previously that under drought, synthetic hexaploid derived wheat (Triticum aestivum L.) lines outperformed recurrent parents in part due to increased root mass at depth and better water extraction capacity. A group of four elite synthetic derived (SYN‐DER) lines and parents was grown under full irrigation and drought conditions to dissect some of the physiological features conferring tolerance to drought. Synthetic derived wheat lines showed on average a 26% yield increase as compared to the parental hexaploid wheats under terminal drought. Different strategies for drought tolerance were observed, including earliness to flowering, greater root mass at depth, greater water extraction capacity, and increased water use efficiency (WUE) at anthesis. Some degree of independence was identified between these traits when comparing SYN‐DER lines suggesting that these traits are regulated by different genes. The elite SYN‐DER line ‘Vorobey’ was an important source of improved root mass at depth under drought. We conclude that the use of wild species of wheat has the potential to improve a range of stress‐adaptive traits and may permit modern bread wheat to become adapted to a wider range of environments including climate change scenarios.
Spike Fertility and Duration of Stem Elongation as Promising Traits to Improve Potential Grain Number (and Yield): Variation in Modern Argentinean Wheats
Authors: González F. G. , Terrile I. I. , Falcón M. O. 
Published: June 2011

ABSTRACTThe identification of physiological traits that determine grain number (and yield) in modern cultivars, and the possible tradeoffs among them, may help to detect promising traits for breeding to increase yield potential. High‐yielding Argentinean wheat (Triticum aestivum L.) cultivars were grown under irrigated and high‐input conditions during two seasons to study (i) yield and grain number m−2 (GN) as a result of stover biomass at harvest (SH) and harvest index (HI); and (ii) spike dry weight at anthesis (SDWa; g m−2) and spike fertility index (SFI; grain number per gram of spike chaff or non‐grain spike biomass). Duration of the stem elongation phase (SEP; first node detectable to anthesis) was analyzed as an alternative to increase SDWa. The HI was highly associated with yield differences between cultivars for both years, independently of stem height. In contrast, SH did not vary among cultivars in either season (P > 0.05). The GN determined yield differences between cultivars and was highly associated with SFI and SDWa for both years and cycles. Some cultivars with the same anthesis date showed stable variation for duration of the SEP between years (despite the year × cultivar interaction observed). As the SFI and duration of the SEP were not related, it seems promising to increase GN in a cultivar with high SFI through an increased duration of the SEP (which may yield higher SWDa) or vice versa.
Increased Ring‐Shaped Chalkiness and Osmotic Adjustment when Growing Rice Grains under Foehn‐Induced Dry Wind Condition
Authors: Wada Hiroshi , Nonami Hiroshi , Yabuoshi Yoshiyuki , Maruyama Atsushi , Tanaka Akio , Wakamatsu Kenichi , Sumi Tomohiko , Wakiyama Yasuyuki , Ohuchida Makoto , Morita Satoshi 
Published: June 2011

ABSTRACTFoehn‐induced dry wind during grain filling increased ring‐shaped chalky kernels in rice (Oryza sativa L.) plants. The objective of this study was to determine physiological mechanisms of the occurrence of ring‐shaped chalky kernels. Rice plants were subjected to water deficit in a paddy field after shade by applying dry high‐speed wind. Additionally, a growth chamber experiment was conducted with plants in pots to measure the water status under the dry wind condition for 24 h by combining in situ turgor (Ψp) assay in developing endosperms with the water potential measurements. The dry (high vapor pressure deficit [VPD]) wind treatment produced the largest number of ring‐shaped chalky kernels due to poor starch accumulation, compared with shade or low‐VPD wind treatment. The inner endosperm cells, where a high frequency of chalkiness was observed, spatially maintained Ψp by osmotic adjustment before the chalky formation with no decline of grain weight. Dry wind reduced photosynthesis due to a partial stomatal closure after water deficit developed. However, these responses, including those related to the plant water status, returned to a level similar to those of the control plants in a day after the dry wind was stopped. We conclude that (i) Ψp maintenance by osmotic adjustment contributes to grain development under water deficit under foehn conditions and (ii) osmotic adjustment has a role in temporally inhibiting starch accumulation in endosperms, resulting in ring‐shaped chalky kernels under foehn‐induced water deficit conditions.
Characterization of Poa supina from the Italian Alps with AFLP Markers and Correlation with Climatic Variables
Authors: Johnson R. C. , Kisha T. J. , Pecetti L. , Romani M. , Richter P. 
Published: June 2011

ABSTRACTSupina bluegrass (Poa supina Schrad.) has the potential for expanded use as a turfgrass, yet its characterization with DNA markers is limited. Our objectives were to characterize amplified fragment length polymorphism (AFLP) variation and determine correlations with climatic variables on in situ leaf collections from 46 locations across the Italian Alps. Using the STRUCTURE program, marker data differentiated the collections into three genetic groups. The groups were verified with analysis of molecular variance and analysis of variance on principal coordinate (PCO) scores (P < 0.01). For PCO analysis, the first three dimensions (Dims) explained 12, 6, and 5% of the total collection‐location variation, respectively, and Dim 1 strongly distinguished the three STRUCTURE groups. Correlations of Dim 1 and 2 scores with collection‐location temperature and precipitation variables were often significant over STRUCTURE groups but generally not within groups (P < 0.05). However, Dim 3 correlations with climatic variables were frequent both within and across STRUCTURE groups, suggesting a more fundamental association. The correlations of PCOs with climate could result from incidental genomic differences and/or from linkage of plant traits with markers that covaried with climate. The results showed considerable marker variation for supina bluegrass across different climatic areas in the Italian Alps, suggesting that phenotypic variation for agronomic and turf traits is also likely.
Genetic Mapping of Fall Armyworm Resistance in Zoysiagrass
Authors: Jessup R. W. , Renganayaki K. , Reinert J. A. , Genovesi A. D. , Engelke M. C. , Paterson A. H. , Kamps T. L. , Schulze S. , Howard A. N. , Giliberto B. , Burson B. L. 
Published: June 2011

ABSTRACTMolecular tools have not identified markers for host‐plant resistance to fall armyworm [Spodoptera frugiperda (J. E. Smith)], one of the most damaging insect pests in turfgrasses in the southeastern United States. Available quantitative trait loci (QTL) in maize (Zea mays L.) have further not been assessed for utility as comparative markers for the trait across related taxa. This study reports a linkage map of the region conferring major control of fall armyworm resistance in zoysiagrass (Zoysia spp.). One genomic simple sequence repeat (ZgAg136) and one amplified fragment length polymorphism (Zgaw216) were linked to and flanked the locus for fall armyworm resistance (Zfawr1) by 6.3 and 8.8 cM, respectively. These markers offer immediate value toward marker‐assisted selection for fall armyworm resistance in zoysiagrass and potentially across additional important crops. Nonsynteny between the fall armyworm resistance loci in zoysiagrass and maize was indicated by the absence of linkage between 38 candidate markers from maize fall armyworm resistance QTL regions and Zfawr1. As a major‐effect locus and putative novel source for fall armyworm resistance gene(s), Zfawr1 is a promising target for further investigation.
Searching for Germplasm Resistant to Sheath Blight from the USDA Rice Core Collection
Authors: Jia Limeng , Yan Wengui , Agrama Hesham A. , Yeater Kathleen , Li Xiaobai , Hu Biaolin , Moldenhauer Karen , McClung Anna , Wu Dianxing 
Published: June 2011

ABSTRACTSheath blight, caused by the fungal pathogen Rhizoctonia solani, is one of the most important and widely distributed diseases capable of infesting numerous crops including rice (Oryza sativa L.). Resistant germplasm with wide variation is essential for controlling this disease via breeding efforts, and genetic background helps design breeding strategies. We used the microchamber method to evaluate the USDA rice core collection, including 1794 accessions from 114 countries, for sheath blight resistance. Seventy‐two molecular markers were used for genotyping. Compared with ‘Jasmine 85’, which has been recognized as one of the most resistant germplasm accessions, 52 accessions were significantly more resistant at the 5% level of probability, and of these 17 were more resistant at the 1% level of probability. The resistant accessions originated from 26 countries in nine geographic regions and are diversified for 13 phenotypic characteristics. The resistant accessions all belonged to the cultivated species O. sativa. Genetic analysis using 72 molecular markers revealed that 45 resistant accessions (87%) were indica type, which were further classified in two groups. Three accessions were identified as aus, two as aromatic, and one each as temperate japonica and tropical japonica. Breeders could use these findings to choose sheath blight resistant accessions for cultivar improvement.
Genetic Diversity of Turkish Olive Varieties Assessed by Simple Sequence Repeat and Sequence‐Related Amplified Polymorphism Markers
Authors: Işk Neslihan , Doğanlar Sami , Frary Anne 
Published: June 2011

ABSTRACTOlive (Olea europaea L.) is one of the most important and characteristic fruit crops of the Mediterranean region. This crop has been grown in Turkey for more than 3000 yr and many varieties are currently grown in five geographic regions. In this study, the genetic diversity of 66 olive varieties from these regions was assessed using simple sequence repeat (SSR) and sequence‐related amplified polymorphism (SRAP) markers. The 13 SSR markers yielded 89 alleles with an average polymorphism information content (PIC) of 0.29 and 6.8 alleles per marker while the 13 SRAP primer combinations generated 103 polymorphic alleles with an average PIC of 0.24 and 7.9 alleles per combination. Although SSR markers revealed higher levels of polymorphism than SRAP markers, both systems revealed considerable molecular genetic diversity in Turkish olive varieties. For both marker types, clustering analysis using the Dice similarity coefficient and the unweighted pair group method with arithmetic means (UPGMA) produced dendrograms with similar clustering and some region‐specific grouping of varieties. Overall, Southeast Anatolian and Marmara varieties were found to be more genetically different than those from the other regions (Aegean, Mediterranean, and Black Sea) and homonymous varieties were identified: three pairs of varieties (‘Egriburun’, ‘Celebi’, and ‘Tasarasi’) had the same names but were genetically distinct.
Mapping QTL Controlling Southern Leaf Blight Resistance by Joint Analysis of Three Related Recombinant Inbred Line Populations
Authors: Negeri Adisu T. , Coles Nathan D. , Holland James B. , Balint‐Kurti Peter J. 
Published: June 2011

ABSTRACTSouthern leaf blight (SLB) is a foliar necrotrophic disease of maize (Zea mays L.) caused by the ascomycete fungus Cochliobolus heterostrophus (Drechs.) Drechs. It is particularly important in warm humid parts of the world where maize is cultivated, such as the southern Atlantic coast area of the United States and parts of India, Africa, and Western Europe. Quantitative trait loci (QTL) for resistance to SLB disease caused by C. heterostrophus race O were identified in three maize recombinant inbred populations assessed in two environments: Clayton, NC, in the summer and Homestead, FL, in the winter. The three populations were derived from the crosses B73 × CML254, CML254 × B97, and B97 × Ki14. Each of these populations was derived from a cross between a temperate maize line (B73 or B97) and a tropical maize line (Ki14 or CML254). Quantitative trait loci were identified by separate analysis of each population and by joint connected and disconnected analyses of all the populations. The most significant QTL identified were on chromosomes 3, 8, 9,and 10. Joint analysis led to more precise position estimates than separate analysis in each case. Results are discussed in the context of previous SLB QTL analysis studies and a recent flowering time QTL study that used the same populations. The chromosome 8 and 9 QTL colocalized with previously identified flowering time QTL which suggested that the perceived effect on SLB resistance at these QTL may have been mediated through an effect on flowering time
Effect of Genetic Divergence of Striga hermonthica (Delile) Benth.–Resistant Maize Inbred Lines on Heterosis and Hybrid Performance under Parasite Pressure
Authors: Menkir Abebe 
Published: June 2011

ABSTRACTStriga hermonthica (Delile) Benth. is a parasitic weed damaging maize and other cereals in Africa. Although S. hermonthica–resistant inbred lines were developed from diverse sources, the effect of their diversity on heterosis under parasite pressure has not been investigated. Sixty‐four hybrids were produced from 16 resistant and four susceptible inbreds using a factorial mating in sets crossing scheme. The hybrids and their parents were evaluated in separate trials with and without S. hermonthica infestation at four environments in Nigeria. Genotypic differences among both inbreds and hybrids were significant for all measured traits under infestation. The hybrids displayed a broad range of midparent heterosis (MPH) for most traits measured under S. hermonthica–infested and noninfested conditions. Mean grain yield and agronomic performance of resistant × resistant cross hybrids were superior to that of susceptible × resistant cross hybrids in the presence of S. hermonthica but not in the absence of the parasite. Correlations between midparent values and hybrid means were large and positive for grain yield but were small for plant height and days to silking. Marker‐based genetic distances of parental lines were not correlated with MPH of all traits recorded under S. hermonthica infestation. Selection for inbreds with greater levels of resistance to S. hermonthica appears to be more effective for developing resistant hybrids than selection of parental pairs based on genetic distance alone.
Assessing the Representativeness and Repeatability of Test Locations for Genotype Evaluation
Authors: Yan Weikai , Pageau Denis , Frégeau‐Reid Judith , Durand Julie 
Published: June 2011

ABSTRACTThe success of a plant breeding program depends on many factors; one crucial factor is the selection of suitable breeding and testing locations. A test location must be discriminating so that genetic differences among genotypes can be easily observed, it must be representative of the target environments so that selected genotypes have the desired adaptation, and its representation of the target environment should also be repeatable so that genotypes selected in 1 yr will have superior performance in future years. Using the yield data of 2006 through 2010 Quebec Oat Registration and Recommendation Trials as an example, we presented a method to visualize the representativeness and repeatability of test locations based on a genotype main effect plus genotype × environment interaction (GGE) biplot. The repeatability of a test location could also be quantified by mean genetic correlations between years within the location. Based on representativeness and repeatability, four categories of test locations were classified and their usefulness in plant breeding discussed.
Eosinophilia as a presenting symptom of the metastatic lung adenocarcinoma with an unknown primary localization
Authors: Machaczka Maciej , Hubert Jerzy , Kasina Filip , Klimkowska Monika 
Published: June 2011

Abstract
Apparent hematological symptoms rarely dominate the clinical picture of an underlying non-hematological malignancy. Malignancy-associated eosinophilia can result from clonal or non-clonal proliferation of eosinophils. Here, we report the case of a 59-year-old man with metastatic adenocarcinoma of the lung with an unknown primary tumor site, which presented as hypereosinophilia, anemia, lymphadenopathy, weight loss, and malaise. Bone marrow biopsy disclosed metastatic adenocarcinoma positive in immunohistochemistry for cytokeratin 7. Further assessment of specimens obtained from the bronchoalveolar lavage and biopsy of the mediastinal lymph nodes confirmed the diagnosis of the metastatic lung cancer, although the primary tumor site remained undiscovered. This case underlines that eosinophilia may represent a rare primary manifestation of an undetected malignancy, and it is thus important to consider this as part of the differential diagnosis in patients presenting with unexplained eosinophilia.
Data intensive scientific analysis with grid computing
Authors: Terzo Olivier , Mossucca Lorenzo , Cucca Manuela , Notarpietro Riccardo 
Published: June 2011

Data intensive scientific analysis with grid computingAt the end of September 2009, a new Italian GPS receiver for radio occultation was launched from the Satish Dhawan Space Center (Sriharikota, India) on the Indian Remote Sensing OCEANSAT-2 satellite. The Italian Space Agency has established a set of Italian universities and research centers to implement the overall processing radio occultation chain. After a brief description of the adopted algorithms, which can be used to characterize the temperature, pressure and humidity, the contribution will focus on a method for automatic processing these data, based on the use of a distributed architecture. This paper aims at being a possible application of grid computing for scientific research.
Bringing introspection into BlobSeer: Towards a self-adaptive distributed data management system
Authors: Carpen-Amarie Alexandra , Costan Alexandru , Cai Jing , Antoniu Gabriel , Bougé Luc 
Published: June 2011

Bringing introspection into BlobSeer: Towards a self-adaptive distributed data management system
Introspection is the prerequisite of autonomic behavior, the first step towards performance improvement and resource usage optimization for large-scale distributed systems. In grid environments, the task of observing the application behavior is assigned to monitoring systems. However, most of them are designed to provide general resource information and do not consider specific information for higher-level services. More precisely, in the context of data-intensive applications, a specific introspection layer is required to collect data about the usage of storage resources, data access patterns, etc. This paper discusses the requirements for an introspection layer in a data management system for large-scale distributed infrastructures. We focus on the case of BlobSeer, a large-scale distributed system for storing massive data. The paper explains why and how to enhance BlobSeer with introspective capabilities and proposes a three-layered architecture relying on the MonALISA monitoring framework. We illustrate the autonomic behavior of BlobSeer with a self-configuration component aiming to provide storage elasticity by dynamically scaling the number of data providers. Then we propose a preliminary approach for enabling self-protection for the BlobSeer system, through a malicious client detection component. The introspective architecture has been evaluated on the Grid'5000 testbed, with experiments that prove the feasibility of generating relevant information related to the state and behavior of the system.
Anomalous capitulum structure and monoecy may confer flexibility in sex allocation and life history evolution in the Ifloga lineage of paper daisies (Compositae: Gnaphalieae)
Authors: Bergh Nicola G. , Verboom G. Anthony 
Published: June 2011

• Premise of the study: Evolutionary significance of the Compositae capitulum and variation in its structure is poorly understood, although it may permit flexibility in sexual expression. Optimal sex ratio differs with life‐history and reproductive strategy. We explore how the genus Ifloga and related members of southern African Gnaphalieae achieved different sex ratios, and the associations of these ratios with annual and perennial life history.• Methods: Sex allocation was measured using the male to female ratio (M/F), a novel approximator of the pollen to ovule ratio (P/O). Life‐history (annuality/perenniality), capitulum structure, capitular sexual system, and M/F were reconstructed on time‐proportional phylogenies. Trait associations were examined using phylogenetically independent contrasts (PICs).• Key results: Annual taxa have strongly female‐biased capitula, as measured by M/F, and either gynomonoecious or monoecious sexual systems, while perennials have equal or male‐biased capitula that are hermaphroditic or monoecious. These results are largely supported by PIC analysis. Different sexual systems afford differing flexibility in sex allocation, with hermaphrodites having the least, and monoecious taxa the greatest, range in M/F. Within Ifloga, the anomalous capitulum evolved in an annual, gynomonoecious ancestor, followed by two independent gains of monoecy. Two subsequent gains of perenniality occurred within a monoecious sublineage.• Conclusions: Different life histories have divergent sex allocation optima and are strongly associated with different sexual systems in gnaphalioid daisies. An anomalous capitulum structure in Ifloga may have facilitated the evolution of monoecy, which in turn may be linked to the evolution of life‐history diversity in the genus.