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.

Figure 1

Linkage map constructed from genotyping-by-sequencing derived SNPs in a recombinant inbred population derived from a cross between Harry and Wesley.

Figure 2

Distribution of marker bins on 21 chromosomes of the linkage map. The x-axis shows the position of bin on each chromosome and y-axis shows the number of markers in each bin.

Figure 3

The proportion of contributing alleles Harry (AA) and Wesley (BB) for each marker. Parental allele contributed by Harry and Wesley is represented in red and blue. Chromosome name is given on top and x-axis represents the position of distorted markers.

Figure 4

Distribution of genotyping-by-sequencing derived normal (blue) and segregation distorted regions (SDRs) on 21 chromosomes of the linkage map. For better visualization, SDRs are colored as green (3–30 markers clustered together) and red (>30 markers clustered together) depending upon the number of markers clustered together to form SDRs.

Figure 5

Dot plot depicting the marker order collinearity between Harry x Wesley map (cM) and POPSEQ-based on high-density linkage map (cM) for 21 chromosomes of hexaploid wheat.

Figure 6

Graphical display of significant QTL for chaff color (CC) and leaf cuticular wax (CW) on chromosome 1B and 2D. Phenotypic variance explained (PVE), additive effect (AE) and confidence interval (CI) for identified QTL is shown on top of the figure for both traits. The dashed dark-red horizontal line indicates the threshold LOD score of 3 to declare significant QTL.

Figure 7

Graphical display of significant QTL detected in 4 environments for (a) flag leaf length (FLL), (b) flag leaf width (FLW) and (c) flag leaf area (FLA). Red, green, blue and violet represent the four environments (L15, L16, M15, and M16). The dashed dark-red horizontal line indicates the threshold LOD score of 3 to declare significant QTL.