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

Waseem Hussain,Ahmed Sallam,Jorge P Venegas,Amanda Easterly,Jesse Poland,Mary J Guttieri,P Stephen Baenziger,Vikas Belamkar

doi:10.1038/s41598-017-16006-z

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.

Highlights

Bread wheat (Triticum aestivum L.) is the staple food crop for more than 35% of the global human population and accounts for 20% of all calories consumed by humans throughout the world[1]
The heat map that combines the estimates of pairwise recombination fraction between markers as well as logarithm of the odds (LOD) scores reflects the strength of linkage between markers and can be used to find marker ordering errors
We used a GBS approach for genome-wide identification of SNPs and their utilization for the development of high-density linkage map in recombinant inbred lines (RILs) population of bread wheat derived from highly different parents Harry and Wesley[22,23]

Summary

Introduction

Bread wheat (Triticum aestivum L.) is the staple food crop for more than 35% of the global human population and accounts for 20% of all calories consumed by humans throughout the world[1]. In the construction of high-density linkage map based on high-throughput SNP markers, genotyping errors including heterozygosity, excessive single cross events, unexpected double recombinants, segregation distortion and allele switching are common[14]. These genotyping errors can distort the linkage maps, especially by expanding the map distance due to overestimation of recombination frequencies[15]. In the construction of high-density linkage maps in various crop researchers have mainly focused on missing data percentage and heterozygosity as the main contributors to genotyping errors and largely ignore the errors arising due to excessive single cross events or double recombinants. Only one study has investigated flag leaf-related traits using high-density linkage map based on high-throughput SNP markers[21]

Methods

Results

Conclusion