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Plant Genome

Rahul Chandnani, Changsoo Kim, Hui Guo, Tariq Shehzad, Jason G Wallace, Daohua He, Zhengsheng Zhang, Jinesh D Patel, Jeevan Adhikari, Sameer Khanal, Andrew H Paterson
In mapping populations segregating for many loci, the large amount of variation among genotypes often masks small-effect quantitative trait loci (QTL). This problem can be reduced by development of populations with fewer chromosome segments segregating. Here, we report early QTL detection in reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum L. 'Acala Maxxa' (GH) and G. barbadense L. 'Pima S6' (GB). A total of 297 BCF and BCF progeny rows-127 segregating for GB chromosome segments in GH background and 170 segregating for GH chromosome segments in GB background-were evaluated in three environments...
March 2018: Plant Genome
Joseph Evans, Millicent D Sanciangco, Kin H Lau, Emily Crisovan, Kerrie Barry, Chris Daum, Hope Hundley, Jerry Jenkins, Megan Kennedy, Govindarajan Kunde-Ramamoorthy, Brieanne Vaillancourt, Ananta Acharya, Jeremy Schmutz, Malay Saha, Shawn M Kaeppler, E Charles Brummer, Michael D Casler, C Robin Buell
Switchgrass ( is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals. In total, over 37 million single nucleotide polymorphisms (SNPs) were identified and a set of 1...
March 2018: Plant Genome
Hamid Khazaei, Michael Fedoruk, Carolyn T Caron, Albert Vandenberg, Kirstin E Bett
The dimensions of lentil ( Medik.) seeds are important quality parameters that are major determinants of market preference, cooking time, and post-harvest milling quality. Knowledge of the genetic control of traits related to seed dimensions would be useful for crop improvement. The principal aim of this study was to identify single nucleotide polymorphism (SNP) markers linked to genes that control seed diameter, seed thickness, and seed plumpness. Association mapping analysis with SNP markers was used to study the seed dimensions of 138 diverse cultivated lentil accessions grown at two locations in Saskatchewan, Canada, in 2011 and 2012...
March 2018: Plant Genome
Jared Crain, Suchismita Mondal, Jessica Rutkoski, Ravi P Singh, Jesse Poland
Genomics and phenomics have promised to revolutionize the field of plant breeding. The integration of these two fields has just begun and is being driven through big data by advances in next-generation sequencing and developments of field-based high-throughput phenotyping (HTP) platforms. Each year the International Maize and Wheat Improvement Center (CIMMYT) evaluates tens-of-thousands of advanced lines for grain yield across multiple environments. To evaluate how CIMMYT may utilize dynamic HTP data for genomic selection (GS), we evaluated 1170 of these advanced lines in two environments, drought (2014, 2015) and heat (2015)...
March 2018: Plant Genome
Samira Mafi Moghaddam, Mark A Brick, Dimas Echeverria, Henry J Thompson, Leslie A Brick, Rian Lee, Sujan Mamidi, Phillip E McClean
Common bean ( L.) is the most consumed edible grain legume worldwide and contains a wide range of nutrients for human health including dietary fiber. Diets high in beans are associated with lower rates of chronic diseases such as obesity and type 2 diabetes, and the content of dietary fibers varies among different market classes of dry bean. In this study, we evaluated the dietary fiber content in a Middle American diversity panel (MDP) of common bean and evaluated the genetic architecture of the various dietary fiber components...
March 2018: Plant Genome
Juan E Rosas, Sebastián Martínez, Pedro Blanco, Fernando Pérez de Vida, Victoria Bonnecarrère, Gloria Mosquera, Maribel Cruz, Silvia Garaycochea, Eliana Monteverde, Susan McCouch, Silvia Germán, Jean-Luc Jannink, Lucía Gutiérrez
Stem rot and aggregated sheath spot are the two major stem and sheath diseases affecting rice (Oryza sativa L.) in temperate areas. A third fungal disease, sheath blight, is a major disease in tropical areas. Resistance to these diseases is a key objective in rice breeding programs but phenotyping is challenged by the confounding effects of phenological and morphological traits such as flowering time (FT) and plant height (PH). This study sought to identify quantitative trait loci (QTL) for resistance to these three diseases after removing the confounding effects of FT and PH...
March 2018: Plant Genome
Jareerat Chunthawodtiporn, Theresa Hill, Kevin Stoffel, Allen Van Deynze
Bell pepper ( L.) is a group of fruit vegetables that has large variation in fruit shape, fruit size, and horticultural traits. Using unadapted sources of germplasm to bring in novel alleles while maintaining favorable quality and horticultural traits is challenging for breeding in pepper. A genetic map with 318 loci from genotype-by-sequencing (GBS) and single nucleotide polymorphism assays was generated from a recombinant inbred line population derived from a cultivated bell-type 'Maor' and a landrace highly resistant to , 'Criollo de Morelos-334'...
March 2018: Plant Genome
Weizhen Liu, Yukiko Naruoka, Kaitlin Miller, Kimberly A Garland-Campbell, Arron H Carter
Stripe rust resistance is a critical need for wheat cultivars in the US Pacific Northwest (PNW). Our previous genome-wide association study (GWAS) for stripe rust resistance in a set of PNW winter wheat accessions (Panel-2) identified multiple marker-trait associations (MTAs) for both all-stage and field resistance. In this study, we conducted additional GWAS using a different set of PNW winter wheat accessions (Panel-1) that contained recently bred soft white winter wheat breeding lines and cultivars. A total of 12 all-stage resistance MTAs and eight field resistance MTAs were identified...
March 2018: Plant Genome
Uche Godfrey Okeke, Deniz Akdemir, Ismail Rabbi, Peter Kulakow, Jean-Luc Jannink
The HarvestPlus program for cassava ( Crantz) fortifies cassava with β-carotene by breeding for carotene-rich tubers (yellow cassava). However, a negative correlation between yellowness and dry matter (DM) content has been identified. We investigated the genetic control of DM in white and yellow cassava. We used regional heritability mapping (RHM) to associate DM with genomic segments in both subpopulations. Significant segments were subjected to candidate gene analysis and candidates were validated with prediction accuracies...
March 2018: Plant Genome
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March 2018: Plant Genome
Kendra A McClure, Kyle M Gardner, Gavin M Douglas, Jun Song, Charles F Forney, John DeLong, Lihua Fan, Lina Du, Peter M A Toivonen, Daryl J Somers, Istvan Rajcan, Sean Myles
The apple ( × Borkh.) is an economically and culturally important crop grown worldwide. Growers of this long-lived perennial must produce fruit of adequate quality while also combatting abiotic and biotic stress. Traditional apple breeding can take up to 20 yr from initial cross to commercial release, but genomics-assisted breeding can help accelerate this process. To advance genomics-assisted breeding in apple, we performed genome-wide association studies (GWAS) and genomic prediction in a collection of 172 apple accessions by linking over 55,000 single nucleotide polymorphisms (SNPs) with 10 phenotypes collected over 2 yr...
March 2018: Plant Genome
Helen H Tai, David De Koeyer, Mads Sønderkær, Sanne Hedegaard, Martin Lagüe, Claudia Goyer, Lana Nolan, Charlotte Davidson, Kyle Gardner, Jonathan Neilson, Jamuna Risal Paudel, Agnes Murphy, Benoit Bizimungu, Hui Ying Wang, Xingyao Xiong, Dennis Halterman, Kåre Lehmann Nielsen
Kleb. is a pathogenic fungus causing wilting, chlorosis, and early dying in potato ( L.). Genetic mapping of resistance to was done using a diploid population of potato. The major quantitative trait locus (QTL) for resistance was found on chromosome 5. The gene, controlling earliness of maturity and tuberization, was mapped within the interval. Another QTL on chromosome 9 co-localized with the wilt resistance gene marker. Epistasis analysis indicated that the loci on chromosomes 5 and 9 had a highly significant interaction, and that functioned downstream of The alleles were sequenced and found to encode StCDF1...
March 2018: Plant Genome
Xin Xu, Rajiv Sharma, Alessandro Tondelli, Joanne Russell, Jordi Comadran, Florian Schnaithmann, Klaus Pillen, Benjamin Kilian, Luigi Cattivelli, William T B Thomas, Andrew J Flavell
A collection of 379 Hordeum vulgare cultivars, comprising all combinations of spring and winter growth habits with two and six row ear type, was screened by genome wide association analysis to discover alleles controlling traits related to grain yield. Genotypes were obtained at 6,810 segregating gene-based single nucleotide polymorphism (SNP) loci and corresponding field trial data were obtained for eight traits related to grain yield at four European sites in three countries over two growth years. The combined data were analyzed and statistically significant associations between the traits and regions of the barley genomes were obtained...
March 2018: Plant Genome
Marilyn L Warburton, Erika D Womack, Juliet D Tang, Adam Thrash, J Spencer Smith, Wenwei Xu, Seth C Murray, W Paul Williams
Maize ( L.) is a staple crop of economic, industrial, and food security importance. Damage to the growing ears by corn earworm [ (Boddie)] is a major economic burden and increases secondary fungal infections and mycotoxin levels. To identify biochemical pathways associated with native resistance mechanisms, a genome-wide association analysis was performed, followed by pathway analysis using a gene-set enrichment-based approach. The gene-set enrichment exposed the cumulative effects of genes in pathways to identify those that contributed the most to resistance...
March 2018: Plant Genome
Dongzhi Lin, Kailun Zheng, Zhaohui Liu, Zhikang Li, Sheng Teng, Jianlong Xu, Yanjun Dong
Transcriptionally active chromosome (TAC) is a component of protein-DNA complexes with RNA polymerase activity, expressed in the plastid. However, the function of rice TAC proteins is still poorly understood. In this paper, we first report the identification of a new rice ( L.) mutant () in the gene encoding TAC. The mutant displayed an albino phenotype and malformed chloroplasts before the three-leaf stage when grown at low temperatures (20°C) and a normal phenotype at higher temperatures (>28°C). Map-based cloning revealed that encodes a novel chloroplast-targeted TAC protein in rice...
March 2018: Plant Genome
Syed Gul Abbas Shah Sani, Peter L Chang, Asif Zubair, Noelia Carrasquilla-Garcia, Matilde Cordeiro, Ramachandra Varma Penmetsa, M Farooq H Munis, Sergey V Nuzhdin, Douglas R Cook, Eric J von Wettberg
Chickpea ( L.) production in arid regions, such as those predominant in Pakistan, faces immense challenges of drought and heat stress. Addressing these challenges is made more difficult by the lack of genetic and phenotypic characterization of available cultivated varieties and breeding materials. Genotyping-by-sequencing offers a rapid and cost-effective means to identify genome-wide nucleotide variation in crop germplasm. When combined with extended crop phenotypes deduced from climatic variation at sites of collection, the data can predict which portions of genetic variation might have roles in climate resilience...
March 2018: Plant Genome
Neele Wendler, Martin Mascher, Axel Himmelbach, Federica Bini, Jochen Kumlehn, Nils Stein
L., a wild grass and close relative of cultivated barley ( L.), gained importance in plant breeding as inducer of haploid plants in crosses with barley and also as a genetic resource for introgression of disease resistance/tolerance genes into cultivated barley. Genetic mapping of genes introgressed from is a prerequisite for their efficient utilization in barley breeding, but often hindered due to repressed recombination. The mechanism underlying the reduced frequency or lack of meiotic recombination between ...
November 2017: Plant Genome
Dong Zhang, Katherine A Easterling, Nicholi J Pitra, Mark C Coles, Edward S Buckler, Hank W Bass, Paul D Matthews
Hop ( L.) breeding programs seek to exploit genetic resources for bitter flavor, aroma, and disease resistance. However, these efforts have been thwarted by segregation distortion including female-biased sex ratios. To better understand the transmission genetics of hop, we genotyped 4512 worldwide accessions of hop, including cultivars, landraces, and over 100 wild accessions using a genotyping-by-sequencing (GBS) approach. From the resulting ∼1.2 million single-nucleotide polymorphisms (SNPs), prequalified GBS markers were validated by inferences in population structures and phylogeny...
November 2017: Plant Genome
Birgit Samans, Boulos Chalhoub, Rod J Snowdon
Polyploidization has played a major role in crop plant evolution, leading to advantageous traits that have been selected by humans. Here, we describe restructuring patterns in the genome of L., a recent allopolyploid species. Widespread segmental deletions, duplications, and homeologous chromosome exchanges were identified in diverse genome sequences from 32 natural and 20 synthetic accessions, indicating that homeologous exchanges are a major driver of postpolyploidization genome diversification. Breakpoints of genomic rearrangements are rich in microsatellite sequences that are known to interact with the meiotic recombination machinery...
November 2017: Plant Genome
Münevver Doğramaci, James V Anderson, Wun S Chao, David P Horvath, Alvaro G Hernandez, Mark A Mikel, Michael E Foley
Leafy spurge ( L.) is an invasive weed of North America and its perennial nature attributed to underground adventitious buds (UABs) that undergo seasonal cycles of para-, endo-, and ecodormancy. Recommended rates of glyphosate (∼1 kg ha) destroy aboveground shoots but plants still regenerate vegetatively; therefore, it is considered glyphosate-tolerant. However, foliar application of glyphosate at higher rates (2.2-6.7 kg ha) causes sublethal effects that induce UABs to produce stunted, bushy phenotypes. We investigated the effects of glyphosate treatment (±2...
November 2017: Plant Genome
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