Genome-wide association studies uncover candidate genes for Zinc, Iron, and Selenium concentration in barley grains

Abstract

Background Barley (Hordeum vulgare L.) is one of the most important staple food crops worldwide. Mineral concentrations in cereals are important for human health; hence improving Zn, Fe and Se accumulation in grains is an imperative need. This study was designed to understand the genetic architecture of Zn, Fe and Se grain concentrations in barley grains. Results We performed a genome-wide association study (GWAS) for grain Zn, Fe and Se concentrations in 216 spring barley accessions, using field data from 2 years. All the accessions were genotyped with a high-density 9K SNPs array from IlluminaTM. The mean values of estimated BLUEs for Zn, Fe and Se were 38.37, 35.56 and 39.45 µg g− 1 dry weight, respectively. High heritability was equaled 75.65% for Fe across the two environments, while moderate heritability values were detected for Zn and Se. Notably, wide genetic variation was found among genotypes for Zn, Fe and Se concentrations. A total of 222 SNPs associated with Zn, Fe and Se were detected on all chromosomes, where the highest significant associations is linked to Fe accumulation. Three genomic regions include newly identified putative candidate genes, which are related to Zn uptake and transport or represent Homeobox leucine zipper protein. Additionally, several significant associations were physically located inside or near genes which are potentially involved in Zn and Fe homoeostasis of which two candidate genes at 5H (502,454,312–502,455,148 bp) and 7H (205,216,091–205,221,133 bp) were found to be involved in Basic helix loop helix (BHLH) family transcription factor and Squamosa promoter binding-like protein, respectively. Conclusions These findings provide new insights into the genetic basis of Zn, Fe and Se concentration in barley grains that in turn may help plant breeders to select high Zn, Fe and Se-containing genotypes to improve human consumption and grain quality.