Population structure and marker-trait association studies of iron, zinc and selenium concentrations in seed of field pea (Pisum sativum L.)

Association analyses of iron (Fe), zinc (Zn) and selenium (Se) concentrations in seeds of field pea (Pisum sativum L.) were done using a panel of 94 diverse accessions. The panel genotypes were grown at two locations in the province of Saskatchewan, Canada, in 2011 and 2012 growing seasons. A total of 1,233 EST-based single-nucleotide polymorphism markers (SNPs) equally distributed across the pea genome as Illumina GoldenGate assay were used to genotype the panel accessions and to estimate the population structure. Eight subpopulations were identified which sufficiently explained the genetic structure of the panel genotypes. Bonferroni threshold was used to minimize the false discovery rate by combining the structured association (Q) with kinship (K) in a mixed linear model implemented in Trait Analysis by Association, Evolution and Linkage (TASSEL). A total of nine SNPs (-log(10) p value >= 4.2) were significantly associated with iron, and two SNPs with zinc concentration in seeds; however, none of the markers was associated with seed Se concentration. The SNPs associated with iron and zinc concentrations in seeds were potential for use in marker-assisted selection in pea breeding programs.