Reconciliation of wheat 660K and 90K SNP arrays and their utilization in dough rheological properties of bread wheat

Abstract

• We updated and reconciliated Wheat 660 K and 90 K SNP arrays positions in the genome AK58, that is a currently elite winter wheat cultivar in China. • About 92.3 % and 83 % of SNPs in the Wheat 660 K and 90 K SNP arrays were precisely mapped to the AK58 genome, respectively. • GWAS analysis for 9 quality traits using updated arrays revealed 26 important genetic loci in bread wheat. • An important genetic locus for stability time on 1D showed an 8.4-Mb interval. • QTL mapping for stability time narrowed the 8.4-Mb interval to 1.64 Mb. • Collinearity analysis identified 35 annotation genes in two QTL for stability time, and seven of them were further screened as candidate genes through gene expression and T -test. High-density Wheat 660 K and 90 K SNP arrays are powerful tools for understanding the genetic basis of wheat traits. However, their inconsistantly physical positions that were caused by different versions of Chinese Spring genome during developing arrays are confused and inconvenient for further application. With the repid development of wheat geonome sequencing, we aim to reconciliate Wheat 660 K and 90 K SNP arrays in modern cultivar and reveal the genetic basis of dough rheological properties in bread wheat. We refined physical positions of Wheat 660 K and 90 K SNP arrays in the currently popular wheat cultivar AK58 genome that was released more recently. We next performed genome-wide association studies (GWAS) and linkage analysis to identify important genetic loci related to quality traits using updated and un-updated arrays, respectively. Refining results showed that 92.3 % and 83 % of SNPs in the Wheat 660 K and 90 K SNP arrays were precisely mapped to the AK58 genome, respective. GWAS results by the updated 660 K and 90 K arrays indicated that 26 intervals composed of 1032 significant SNPs were associated with 9 quality traits in multiple environments. The significant interval for stability time on 1D was narrowed into an 8.4-Mb region using the updated arrays, whereas the interval is 405 Mb using the un-updated arrays. Linkage analysis revealed an important QTL QST.henau-1D.2 for stability time with 1.64 Mb. Integration of GWAS and QTL results narrowed the significant interval into 6.46 Mb containing 35 annotation genes by collinearity analysis. After T -test, gene expression analysis, seven of them are potential candidate genes and thus favorable haplotypes are identified to benefit marker-assisted selection. A reconciliation of Wheat 660 K and 90 K arrays promote their efficient applications. Important genetic loci and favorable haplotypes identified in this study provided valuable information for wheat quality breeding.

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