Genome-Wide Association Mapping for Heat Stress Responsive Traits in Field Pea

Abstract

Environmental stress hampers pea productivity. To understand the genetic basis of heat resistance, a genome-wide association study (GWAS) was conducted on six stress responsive traits of physiological and agronomic importance in pea, with an objective to identify the genetic loci associated with these traits. One hundred and thirty-five genetically diverse pea accessions from major pea growing areas of the world were phenotyped in field trials across five environments, under generally ambient (control) and heat stress conditions. Statistical analysis of phenotype indicated significant effects of genotype (G), environment (E), and G × E interaction for all traits. A total of 16,877 known high-quality SNPs were used for association analysis to determine marker-trait associations (MTA). We identified 32 MTAs that were consistent in at least three environments for association with the traits of stress resistance: six for chlorophyll concentration measured by a soil plant analysis development meter; two each for photochemical reflectance index and canopy temperature; seven for reproductive stem length; six for internode length; and nine for pod number. Forty-eight candidate genes were identified within 15 kb distance of these markers. The identified markers and candidate genes have potential for marker-assisted selection towards the development of heat resistant pea cultivars.

Keywords: GWAS; candidate-gene; genetic diversity; genotyping-by-sequencing; heat stress; marker-trait association; pea.

Figure 1

Distribution of average SPAD, PRI, canopy temperature, reproductive stem length, internode length and pod number of 135 GWAS accessions across ambient and stress environments. Note: The ambient (control) environments were 2016 Rosthern, 2016 Saskatoon and 2017 Rosthern; and the heat stress environments were 2015 and 2017 Saskatoon. PRI, photochemical reflectance index.

Figure 2

Manhattan plots and the corresponding Q-Q plots representing the identification of SNP markers associated with chlorophyll concentration measured by a SPAD meter. The Manhattan plots are based on association of 15,608 chromosomal and 1269 non-chromosomal SNPs with SPAD of 135 pea accessions in the multi-year, multi-environment trials. Note: S15, Saskatoon in 2015; R16, Rosthern in 2016; S16, Saskatoon in 2016; R17, Rosthern in 2017; and S17, Saskatoon in 2017.

Figure 3

Manhattan plots and the corresponding Q-Q plots representing the identification of SNP markers associated with reproductive stem length. The Manhattan plots are based on association of 15608 chromosomal and 1269 non-chromosomal SNPs with reproductive stem length of 135 pea accessions in the multi-year, multi-environment trials. Note: R16, Rosthern in 2016; R17, Rosthern in 2017; S15, Saskatoon in 2015; S16, Saskatoon in 2016; and S17, Saskatoon in 2017.

Figure 4

Loading (A) and Score (B) plots of principal component analysis illustrating the overall association of traits and genotype performance across environments. Note: PN, pod number; RSL, reproductive stem length; IL, internode length, CT, canopy temperature; PRI, photochemical reflectance index.