GENOME WIDE ASSOCIATION STUDY TO IDENTIFY SINGLE NUCLEOTIDE POLYMORPHISM MARKERS FOR FE, ZN, AND SE CONCENTRATION IN FIELD PEA SEEDS

Abstract

Micronutrient concentration is an important component of crop quality. Iron (Fe), zinc (Zn) and selenium (Se) are essential micronutrients for human health. Previous studies indicated substantial variation in micronutrient concentration in field pea (Pisum sativum L.). The objective of the current research was to evaluate a diverse pea panel for Fe, Zn, and Se concentration, and to identify associated single nucleotide polymorphism (SNP) markers using genome wide association study (GWAS). One hundred and seventy seven diverse pea accessions were assessed for Fe, Zn, and Se concentration from five location-years (2013 Saskatoon, 2014 Fargo, 2015 Saskatoon, 2016 Saskatoon and 2016 Rosthern) using atomic absorption spectroscopy. Accessions differed significantly for Fe and Zn in all location-years, but not for Se (P ≤ 0.05). Year and location effects were significant for all three micronutrients. Mean concentration in the five location-year combined analysis were 50.46, 29.49, and 0.95, and the concentration (μg/g) ranged from 29.22 to 90.53, 12.83 to 51.47 and 0.06 to 8.75 in the ground whole pea seeds for Fe, Zn, and Se, respectively. Concentration of Fe, Zn, and Se were significantly correlated (P ≤ 0.05) between each location with the exception of Se concentration between Fargo and Rosthern. Significant correlations were observed in all the location-years between Zn and Fe concentration (P ≤ 0.05). Se significantly correlated with Fe in all the location years, except 2016 Rosthern (P ≤ 0.05). The correlation between Se and Zn was only significant in 2014 Fargo and 2016 Saskatoon (P ≤ 0.05). Fe and Zn concentration showed significant positive correlations (P ≤ 0.05) with lodging and day to maturity (DTM), but not Se. In general, yield negatively correlated with Fe, Zn, and Se. The pea panel accessions clustered into nine major groups which could be considered consistent with the geographic origin of the accessions. Genotypic data generated from genotyping-by-sequencing were used in genome wide association study (GWAS) to identify significant SNP markers associated with Fe, Zn, and Se concentration. After Bonferroni correction, three significant markers for Fe concentration and seven significant markers for Zn concentration (P ≤ 0.05, -log₁₀ P value ≥ 5.46) were identified. Five markers for Fe, seven markers for Zn and four markers for Se (including few less significant markers) were validated on a pea recombinant inbred line population; PR-07 (Carrera × CDC Striker). The marker Sc1512_36017 co-localized with Sc11336_48840 on LGIIIb which was a flanking marker of quantitative trait loci (QTL) for seed Zn concentration. The markers identified from the present study can be used in marker assisted selection (MAS) in pea breeding to develop new varieties with high Fe, Zn, and Se concentration.