Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat

Abstract

Winter wheat parents ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) were used to develop a recombinant inbred population with future goals of identifying genomic regions associated with drought tolerance. To precisely map genomic regions, high-density linkage maps are a prerequisite. In this study genotyping-by- sequencing (GBS) was used to construct the high-density linkage map. The map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. The constructed linkage map revealed strong collinearity in marker order across 21 chromosomes with POPSEQ-v2.0, which was based on a high-density linkage map. The reliability of the linkage map for QTL mapping was demonstrated by co-localizing the genes to previously mapped genomic regions for two highly heritable traits, chaff color, and leaf cuticular wax. Applicability of linkage map for QTL mapping of three quantitative traits, flag leaf length, width, and area, identified 21 QTLs in four environments, and QTL expression varied across the environments. Two major stable QTLs, one each for flag leaf length (Qfll.hww-7A) and flag leaf width (Qflw.hww-5A) were identified. The map constructed will facilitate QTL and fine mapping of quantitative traits, map-based cloning, comparative mapping, and in marker-assisted wheat breeding endeavors.

QTL mapping for flag leaf-related traits and genetic effect of QFLW-6A on flag leaf width using two related introgression line populations in wheat

“…The qFL1 for FLL and qFLW4 and qFSR4 for FLW have been fine-mapped, and even two genes related to FLW, Nal1 and Nal7 have been cloned in rice [24][25][26][27][28]. In wheat, QTLs controlling flag leaf-related traits have been identified on almost all 21 chromosomes [16,[29][30][31]. For example, using recombinant inbred line (RIL) population, 12 QTLs for chlorophyll content-related traits were mapped on chromosomes 1A, 3A, 3B, 3D, 4A, 5A, 6A, 6D, 7A and 7D [32].…”

Registration of a Bread Wheat Recombinant Inbred Line Mapping Population Derived from a Cross Between ‘Harry’ and ‘Wesley’

“…Genotyping of the RIL mapping population was done using the genotyping‐by‐sequencing (GBS) approach as per protocol described by Poland et al (2012). A high‐density linkage map based on GBS‐derived SNPs was developed (Hussain et al, 2017).…”

“…The HW RIL population was genotyped using GBS, and the high‐density linkage map was developed based on GBS‐derived SNP markers (Hussain et al, 2017). Briefly, the linkage map has 3641 markers distributed across 21 chromosomes.…”

“…The HW RIL population is an important germplasm resource that will facilitate the genetic dissection of important agronomic traits in response to drought and in the development of wheat cultivars with drought tolerance and broader adaptation. The value of the population was recently shown by Kariyawasam et al (2016) and Hussain et al (2017), as the HW RIL population was used to map tan spot [incited by Pyrenophora tritici‐repentis (Died.) Drechs.]…”

A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa

“…Genotyping-by-sequencing (GBS) is a simple, robust multiplex method that generates large numbers of SNPs at very low cost (Elshire et al, 2011). GBS has been mostly used to study host plants (Torkamaneh et al, 2017; Fernandez-Mazuecos et al, 2017; Hussain et al, 2017) because of the emphasis on resistance, however this technique can equally be applied to a pathogen. There are several combinatorial factors that can complicate the characterization of virulence in plant-pathogenic fungi, including genetic diversity present in natural populations, difficulty in conducting controlled crosses among genotypes, complexity of inheritance, inaccessibility to genomic information and the high costs associated with whole genome sequencing (Leboldus et al, 2015).…”