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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Plant Sci. | doi: 10.3389/fpls.2019.01538

Genome-wide association mapping for agronomic and seed quality traits of field pea (Pisum sativum L.)

  • 1University of Saskatchewan, Canada
  • 2AgriGenome labs, India
  • 3Montana State University, United States
  • 4Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Centre of the Region Haná for Biotechnological and Agricultural Research, Czechia
  • 5Institute of Field and Vegetable Crops, Serbia
  • 6Department of Botany, Faculty of Science, Palacký University in Olomouc, Czechia
  • 7Grain Legume Genetics Physiology Research, Agricultural Research Service, United States Department of Agriculture, United States
  • 8INRA Centre Dijon Bourgogne Franche-Comté, France
  • 9John Innes Centre (JIC), United Kingdom
  • 10School of Biological Sciences, Faculty of Science, University of Auckland, New Zealand

Genome-wide association study (GWAS) was completed 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 fibre 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 Saskatoon, 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 are potential for marker-assisted selection towards rapid cultivar improvement.

Keywords: Field pea (Pisum sativum L.), genetic diversity, Genome-Wide Association Study, Genotyping by sequencing (GBS), single nucelotide polymorphisms

Received: 17 Apr 2019; Accepted: 04 Nov 2019.

Copyright: © 2019 Gali, Sackville, Tafesse, Lachagari, McPhee, Hybl, Mikic, Smýkal, Mcgee, Burstin, Domoney, Ellis, Tar'an and Warkentin. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Tom Warkentin, University of Saskatchewan, Saskatoon, S7N 5A2, Saskatchewan, Canada, tom.warkentin@usask.ca