Association Mapping and Validation of QTLs for Flour Yield in the Soft Winter Wheat Variety Kitahonami

Abstract

The winter wheat variety Kitahonami shows a superior flour yield in comparison to other Japanese soft wheat varieties. To map the quantitative trait loci (QTL) associated with this trait, association mapping was performed using a panel of lines from Kitahonami’s pedigree, along with leading Japanese varieties and advanced breeding lines. Using a mixed linear model corrected for kernel types and familial relatedness, 62 marker-trait associations for flour yield were identified and classified into 21 QTLs. In eighteen of these, Kitahonami alleles showed positive effects. Pedigree analysis demonstrated that a continuous pyramiding of QTLs had occurred throughout the breeding history of Kitahonami. Linkage analyses using three sets of doubled haploid populations from crosses in which Kitahonami was used as a parent were performed, leading to the validation of five of the eight QTLs tested. Among these, QTLs on chromosomes 3B and 7A showed highly significant and consistent effects across the three populations. This study shows that pedigree-based association mapping using breeding materials can be a useful method for QTL identification at the early stages of breeding programs.

Tracking haplotype for QTLs associated with Fusarium head blight resistance in Japanese wheat (Triticum aestivum L.) lineage

“…In addition, previous pedigree analysis identified that pyramiding QTLs for flour yields through ancestors ('Hokushin' and 'Kitamoe' , etc.) led to the release of 'Kitahonami' as the highest flour yield cultivar [33]. They also reported that a QTL for flour yield on 6B was common in 'Hokushin' and 'Kitahonami' [33], while both cultivars harboured 'Gamenya' haplotype based on our results (Fig.…”

Identification of milling and baking quality QTL in multiple soft wheat mapping populations

“…The genetic architecture of wheat quality traits has been frequently studied through classical linkage mapping in bi-parental populations Elangovan et al 2008;Li et al 2013;McCartney et al 2006;Nelson et al 2006;Parker et al 1999;Prasad et al 2003;Reif et al 2011b;Schmidt et al 2004;Sun et al 2008Sun et al , 2010. Despite, higher probability of type I errors due to population structure (Yu et al 2006), insufficient marker coverage due to low LD, and the inability to identify the parental source of the desired alleles (Sneller et al 2009), association analysis takes advantage of populations already developed within a breeding program to identify QTL (Ishikawa et al 2014). However, time and resources are required to develop these populations, which often still have extensive linkage disequilibrium (LD) resulting in identification of marker loci distant from the functional loci.…”

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

“…Generally, during long-term breeding programs, favorable QTLs are expected to accumulate in most breeding materials. Our previous study revealed that ongoing pyramiding of flour yield QTLs occurred during the history of wheat breeding [22]. Based on these results, pyramiding of favorable alleles from various donors into an elite variety will be continued in future breeding.…”

“…High-density genotyping platforms for wheat, such as 90K iSelect [19] and 660K Axiom arrays (http://wheat.pw.usda.gov/ggpages/topics/Wheat660_SNP_array_developed_by_ CAAS.pdf), enable us to perform genome-wide association studies (GWASs) using a set of germplasms or advanced breeding lines. GWASs of wheat quality traits have drastically emerged within the last five years and revealed many significant marker-trait associations (MTAs) across the wheat genome [20][21][22][23][24][25]. These MTAs would be useful for improving wheat quality.…”