Mapping QTL for agronomic traits in breeding populations

Quantitative Trait Loci Mapping for Spike Characteristics in Hexaploid Wheat

Wheat ( L.) spike characteristics determine the number of grains produced on each spike and constitute key components of grain yield. Understanding of the genetic basis of spike characteristics in wheat, however, is limited. In this study, genotyping-by-sequencing (GBS) and the iSelect 9K assay were used on a doubled-haploid (DH) soft red winter wheat population that showed a wide range of phenotypic variation for spike traits. A genetic map spanning 2934.1 cM with an average interval length of 3.4 cM was constructed. Quantitative trait loci (QTL) analysis involving additive effects, epistasis (QQ) and QTL × environment (QE), and epistasis × environment (QQE) interactions detected a total of 109 QTL, 13 QE, and 20 QQ interactions in five environments. Spike characteristics were mainly determined by additive effects and were fine-tuned by QQ, QE, and QQE. Major QTL / explained up to 30.9% of the phenotypic variation for spike length (SL) and fertile spikelet number, .1 explained up to 15.6% of the phenotypic variation of grain number per spikelet, and explained up to 80.2% of the phenotypic variation for spike compactness. Additionally, QTL for correlated spike characteristics formed QTL clusters on chromosomes 1A, 5A, 2B, 3B, 5B, 1D, and 5D. This study expands the understanding of the genetic basis of spike characteristics in hexaploid wheat. A number of stable QTL detected in this study have potential to be used in marker-assisted selection. Additionally, the genetic map generated in this study could be used to study other traits of economic importance.

Genome-Wide Mapping of Spike-Related and Agronomic Traits in a Common Wheat Population Derived from a Supernumerary Spikelet Parent and an Elite Parent

In wheat, exotic genotypes harbor a broad range of spike-related traits, and can be used as a source of new genes for germplasm enhancement in wheat breeding programs. In the present study, a population of 163 recombinant inbred lines was derived from a cross between an elite line (WCB414) and an exotic line (WCB617) with branched spike (supernumerary spikelet; SS) head morphology. The population was evaluated over four to six environments to identify quantitative trait loci (QTL) associated with nine spike-related traits and 10 agronomic traits. A genetic map consisting of 939 diversity arrays technology (DArT) markers was constructed. Composite interval mapping identified a total of 143 QTL located on 17 different wheat chromosomes and included 33 consistent and definitive QTL. The amount of phenotype variation explained (PVE) by individual QTL ranged from 0.61 to 91.8%. One major QTL for glume pubescence was located in a QTL-rich region on the short arm of chromosome 1A, where loci for other traits such as for kernels per spike (KS) and spike length (SL) were also identified. Similarly, a cluster of QTL associated with yield-related, agronomic and spike-related traits contributing up to 40.3% of PVE was found on the short arm of chromosome 2D, in the vicinity of a major QTL for SS-related traits. Consistent and major QTL identified in the present study may be useful in marker-assisted breeding programs to facilitate transfer of desirable alleles into other germplasm. Desirable QTL alleles were also contributed by the exotic line, suggesting the possibility of enriching the breeding germplasm with alleles from SS genotypes.