Genome-Wide Association Mapping for Agronomic and Seed Quality Traits of Field Pea (Pisum sativum L.).

Krishna Kishore Gali,T.H Noel Ellis,Thomas D Warkentin,Rebecca Mcgee,Claire Domoney,Alexander Mikić,Judith Burstin,Bunyamin Tar'An,Alison Sackville,Kevin Mcphee,V.B Reddy Lachagari,Mick Hybl,Endale G Tafesse,Petr Smýkal

doi:10.3389/fpls.2019.01538

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.

Highlights

Pea (Pisum sativum L., 2n = 14) is an important cool season pulse crop grown in more than 100 countries on over 12 million hectares worldwide (FAOSTAT 2016; http://www. fao.org/faostat/en/#data/QC)
With the availability of cost-effective, high throughput Single nucleotide polymorphism (SNP) genotyping methods and genomic resources, Genome-wide association study (GWAS) has been used as an effective method to identify alleles associated with traits of many crop species including legumes (Desgroux et al, 2016; Sun et al, 2017; Mourad et al, 2018)
The current GWAS was undertaken to identify SNP markers associated with several important field pea breeding traits

Summary

Introduction

Pea (Pisum sativum L., 2n = 14) is an important cool season pulse crop grown in more than 100 countries on over 12 million hectares worldwide To enhance the productivity of pea production and meet the global demand for pea consumption, over the last three decades pea breeding programs worldwide have made significant improvement in yield, disease resistance, plant architecture, and lodging resistance (Warkentin et al, 2015). In order to meet future demands, pea breeding must focus both on crop productivity and improving seed quality (Duc et al, 2015). The use of diverse genetic resources is important for breeding crop varieties (Glaszmann et al, 2010). Significant morphological diversity exists within pea accessions (Warkentin et al, 2015). Knowledge of the genetic diversity of pea accessions is of importance to select genetically diverse parents and to broaden the genetic basis of the cultivated peas

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