1. Genome-Wide Association Mapping for Agronomic and Seed Quality Traits of Field Pea (Pisum sativum L.)
- Author
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Petr Smýkal, Judith Burstin, Alison Sackville, T. H. Noel Ellis, Endale G. Tafesse, Claire Domoney, Thomas D. Warkentin, V. B. Reddy Lachagari, Bunyamin Tar’an, Alexander Mikić, Kevin McPhee, Krishna K. Gali, Rebecca J. McGee, Mick Hybl, Crop Development Centre, University of Saskatchewan, AgriGenome Labs Pvt Ltd, Partenaires INRAE, Dep Plant Sci, North Dakota State University (NDSU), Centre of the Region Haná for Biotechnological and Agricultural Research - Department of Genetic Resources for Vegetables - Medicinal and Special Plants, Crop Research Institute, Forage Crops Department, Institute of Field and Vegetable Crops [Novi Sad], Department of Botany, Faculty of Sciences, Palacky University Olomouc, Grain Legume Genetics Physiology Research, USDA-ARS : Agricultural Research Service, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Department of Metabolic Biology, John Innes Centre [Norwich], School of Biological Sciences [Auckland], University of Auckland [Auckland], and Saskatchewan Ministry of Agriculture and Saskatchewan Pulse Growers
- Subjects
0106 biological sciences ,0301 basic medicine ,[SDV]Life Sciences [q-bio] ,Single-nucleotide polymorphism ,Genome-wide association study ,Plant Science ,lcsh:Plant culture ,Biology ,01 natural sciences ,Pisum ,03 medical and health sciences ,Field pea ,single nucleotide polymorphisms ,Sativum ,genotyping-by-sequencing ,lcsh:SB1-1110 ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Cultivar ,Original Research ,2. Zero hunger ,Genetic diversity ,genome-wide association study ,food and beverages ,genetic diversity ,biology.organism_classification ,Minor allele frequency ,030104 developmental biology ,Agronomy ,field pea ,010606 plant biology & botany - Abstract
Genome-wide association study (GWAS) was conducted to identify loci associated with agronomic (days to flowering, days to maturity, plant height, seed yield and seed weight), seed morphology (shape and dimpling), and seed quality (protein, starch, and fiber concentrations) traits of field pea (Pisum sativum L.). A collection of 135 pea accessions from 23 different breeding programs in Africa (Ethiopia), Asia (India), Australia, Europe (Belarus, Czech Republic, Denmark, France, Lithuania, Netherlands, Russia, Sweden, Ukraine and United Kingdom), and North America (Canada and USA), was used for the GWAS. The accessions were genotyped using genotyping-by-sequencing (GBS). After filtering for a minimum read depth of five, and minor allele frequency of 0.05, 16,877 high quality SNPs were selected to determine marker-trait associations (MTA). The LD decay (LD1/2max,90) across the chromosomes varied from 20 to 80 kb. Population structure analysis grouped the accessions into nine subpopulations. The accessions were evaluated in multi-year, multi-location trials in Olomouc (Czech Republic), Fargo, North Dakota (USA), and Rosthern and Sutherland, Saskatchewan (Canada) from 2013 to 2017. Each trait was phenotyped in at least five location-years. MTAs that were consistent across multiple trials were identified. Chr5LG3_566189651 and Chr5LG3_572899434 for plant height, Chr2LG1_409403647 for lodging resistance, Chr1LG6_57305683 and Chr1LG6_366513463 for grain yield, Chr1LG6_176606388, Chr2LG1_457185, Chr3LG5_234519042 and Chr7LG7_8229439 for seed starch concentration, and Chr3LG5_194530376 for seed protein concentration were identified from different locations and years. This research identified SNP markers associated with important traits in pea that have potential for marker-assisted selection towards rapid cultivar improvement.
- Published
- 2019