Genetic and genomic studies on wheat pre-harvest sprouting resistance

Abstract

Wheat pre-harvest sprouting (PHS), germination of physiologically matured grains in a wheat spike before harvesting, can cause significant reduction in grain yield and end-use quality. Many quantitative trait loci (QTL) for PHS resistance have been reported in different sources. To determine the genetic architecture of PHS resistance and its relationship with grain color (GC) in US hard winter wheat, a genome-wide association study (GWAS) on both PHS resistance and GC was conducted using in a panel of 185 U.S. elite breeding lines and cultivars and 90K wheat SNP arrrays. PHS resistance was assessed by evaluating sprouting rates in wheat spikes harvested from both greenhouse and field experiments. Thirteen QTLs for PHS resistance were identified on 11 chromosomes in at least two experiments, and the effects of these QTLs varied among different environments. The common QTLs for PHS resistance and GC were identified on the long arms of the chromosome 3A and 3D, indicating pleiotropic effect of the two QTLs. Significant QTLs were also detected on chromosome arms 3AS and 4AL, which were not related to GC, suggesting that it is possible to improve PHS resistance in white wheat. To identify markers closely linked to the 4AL QTL, genotyping-by-sequencing (GBS) technology was used to analyze a population of recombinant inbred lines (RILs) developed from a cross between two parents, “Tutoumai A” and “Siyang 936”, contrasting in 4AL QTL. Several closely linked GBS SNP markers to the 4AL QTL were identified and some of them were coverted to KASP for marker-assisted breeding. To investigate effects of the two non-GC related QTLs on 3AS and 4AL, both QTLs were transferered from “Tutoumai A” and “AUS1408” into a susceptible US hard winter wheat breeding line, NW97S186, through marker-assisted backcrossing using the gene marker TaPHS1 for 3AS QTL and a tightly linked KASP marker we developed for 4AL QTL. The 3AS QTL (TaPHS1) significantly interacted with environments and genetic backgrounds, whereas 4AL QTL (TaMKK3-A) interacted with environments only. The two QTLs showed additive effects on PHS resistance, indicating pyramiding these two QTLs can increase PHS resistance. To improve breeding selection efficiency, genomic prediction using genome-wide markers and marker-based prediction (MBP) using selected trait-linked markers were conducted in the association panel. Among the four genomic prediction methods evaluated, the ridge regression best linear unbiased prediction (rrBLUP) provides the best prediction among the tested methods (rrBLUP, BayesB, BayesC and BayesC0). However, MBP using 11 significant SNPs identified in the association study provides a better prediction than genomic prediction. Therefore, for traits that are controlled by a few major QTLs, MBP may be more effective than genomic selection.