Genome-wide association study for phosphate responsive root hair length and density in bread wheat

Abstract

The increase in root hair length and density is considered an effective way to deal with external phosphorous (P) limitation. The identification of useful loci for root hair traits is crucial for wheat breeding. Here, We employed a simple, cost-effective, and medium-throughput screening method using cigar rolls to assess P-responsive root hair length (RHL) and density (RHD) in bread wheat at the seedling stage. A set of 113 historical bread wheat cultivars was screened for root hair length and density (RHL/D) under low (0.005 mM KH2PO4) and high P-levels (0.25 mM KH2PO4). Significant variations (p < 0.001) were found among genotypes for length and density under both P treatments. Genotyping was performed using 50 K SNP array data to conduct the genome-wide association study (GWAS) using a multi-locus model (mrMLM) and 67 SNPs linked to RHL/D under phosphorous treatment were identified. Of these, 33 SNPs were associated with RHL and 34 were linked with RHD. The maximum number of SNPs (43) linked to target traits were observed under high-P levels following 24 were identified under low-P conditions. We also identified 6 SNPs associated with target traits causing missense mutations and predicted their candidate genes of which 5 were protein coding. RNA-seq based expression analysis indicated that all genes were expressed in roots of 24 wheat varieties ranging from 0.38 to 101.7 tpm. The least expression (0.41–10.28 tpm) was observed in TraesCS4D02G066200 which consisted of non-translating CDS and was highly expressed in leaf tissues with 14.55–53.67 tpm. Of these genes, TraesCS1A02G313600 solely expressed in roots with no expression (0 tpm) in leaf tissues. This first GWAS study on root hairs in bread wheat illustrates the genetic basis of RHL and RHD and identifies loci that could be an invaluable resource for further functional investigation.