Genome-Wide Association Analysis For Pre-Harvest Sprouting Resistance In U.S. Winter Wheat.

Pre-harvest sprouting (PHS), germination of physiologically matured grains in a wheat spike before harvesting, can cause significant reduction in grain end-use quality and thus in grain sale price. Several quantitative trait loci (QTLs) have been reported and one gene (TaPHS1) on chromosome 3AS has been cloned for PHS resistance. To determine genes controlling PHS resistance in US winter wheat, a genome-wide association analysis was conducted using a panel of 192 elite breeding lines and cultivars including 137 hard winter wheat (HWW) and 55 soft winter wheat (SWW) accessions. Intact spikes were harvested at physiologically maturation, and sprouting rate was repeatedly evaluated in a moist chamber for 7 d at 22℃after the spikes were dried for 14 d. The panel was screened using 457 simple sequence repeats (SSR) and Infinium iSelect Beadchips with 9Kwheat single nucleotide polymorphism (SNP) markers. Structure analysis generated three groups, one SWW and two HWW groups. Association analysis using Q model identified 3 SSRs and 23 SNPs that were significantly associated with PHS resistance(p<10^-3), corresponding to QTLs on chromosome 3A, 4A, 2B, 3B, 5B and 2D, when an averaged germination rate over four experiments was applied. Significant environment and QTL interactions were observed, TaPHS1 and 4AL QTL were detected in three and two different environments, respectively and the 4AL QTL is probably related to low maturation temperature (daytime T<30℃), whereas the TaPHS1 is not that temperature sensitive. Thus expression levels of PHS resistance QTLs may vary with environments, and combination different PHS resistance QTLs may provide good protection for white wheat production.