Association Analysis of Baking and Milling Quality Traits in an Elite Soft Red Winter Wheat Population

Abstract

Although grain yield is the most important trait for growers, milling and baking industries demand high‐quality and scab‐free grains for various end products. To accelerate breeding of wheat (Triticum aestivum L.) cultivars with high grain quality, genetic dissection of quality traits is necessary. Genome‐wide association studies (GWAS) were conducted to identify genomic regions responsible for milling and baking quality traits in soft red winter wheat (SRWW). Seven quality traits were evaluated in two locations and 2 yr for 270 elite SRWW lines. These traits include flour yield, softness equivalent, flour protein, and four solvent (lactose, sodium carbonate, sucrose, and water) retention capacity measurements. In this study, 27,449 single nucleotide polymorphism (SNP) markers were developed by using both genotyping‐by‐sequencing and 90K SNP array technologies. A linear mixed model in GWAS, accounting for population structure and kinship, was fitted to identify 18 [−log(P) ≥ 4.0] genomic regions on 12 different chromosomes associated with the quality traits. Only one of these associations seems to be a previously identified quantitative trait locus, whereas others are novel associations. The most significant associations for quality traits were identified on chromosomes 1B, 2A, 2B, 4B, 5A, 7A, and 7D. Candidate gene searches, facilitated by the wheat genome assembly, led us to the identification of putative genes related to SRWW quality traits including fasciclin‐like arabinogalactan. The results of this study can be used in developing high‐quality SRWW varieties for the eastern region of the United States.

Transferability of Marker Trait Associations in Wheat Is Disturbed Mainly by Genotype × Year Interaction

“…Figure S2). Consistent with the reports of Gaire et al [33] and Huang et al [42], PCs separated two distinct groups, which were previously attributed to whether germplasm is progeny, close relative, or descendants of the soft red winter wheat variety "Truman" or not [42].…”

“…Marker-trait associations for this population have been previously identified for Fusarium head blight [65], days to heading [66], and grain quality [33] from plants grown in Ohio and Virginia. We dissected the genetic architecture of grain yield and related traits based on phenotypes observed in Indiana.…”

“…In this study, our goal was to identify MTAs for yield and yield component traits in an elite SRW wheat population developed by eastern and midwestern public breeding programs. Previous work by Gaire et al [33] in this population identified MTAs concerning SRW wheat end use quality traits in this population, but no work to date has explored yield related traits in the context of GWAS. We achieve this goal by field-based phenotyping and high-throughput genotyping.…”

“…GWAS has been used previously to study wheat kernel size and milling quality [31][32][33], spike traits [30], root traits [34], and grain yield and yield components traits [35,36]. These studies implemented the various GWAS mapping approaches such as mixed linear model (MLM) [37] and compressed mixed linear model (CMLM) [38] to appropriately account for the underlying population structure and kinship.…”

Multifamily QTL analysis and comprehensive design of genotypes for high-quality soft wheat

“…For example, 15, 28, 25 and 32 MTAs for flour color L � , a � , and b � and yellow pigment content, respectively, were detected [25]. Recently, using soft winter wheat from the eastern region of the United States, significant MTAs for flour yield were found on chromosomes 1B, 2A and 2B [42]. Our previous association mapping approach revealed approximately 20 QTLs related to flour yield that accumulated during the process of breeding [22].…”