QTL Mapping Using a High-Density Genetic Map to Identify Candidate Genes Associated With Metribuzin Tolerance in Hexaploid Wheat (Triticum aestivum L.).

Ling Xu,Weijun Zhou,Jian Wang,Roopali Bhoite,Guannan Liu,Andrzej Kilian,Ping Si,Hui Liu,Guijun Yan

doi:10.3389/fpls.2020.573439

Abstract

Tolerance to metribuzin, a broad-spectrum herbicide, is an important trait for weed control in wheat breeding. However, the genetics of metribuzin tolerance in relation to the underlying quantitative trait loci (QTL) and genes is limited. This study developed F8 recombinant inbred lines (RILs) from a cross between a highly resistant genotype (Chuan Mai 25) and highly susceptible genotype (Ritchie), which were used for QTL mapping of metribuzin tolerance. Genotyping was done using a diversity arrays technology sequencing (DArTseq) platform, and phenotyping was done in controlled environments. Herbicide tolerance was measured using three traits, visual score (VS), reduction of chlorophyll content (RCC), and mean value of chlorophyll content for metribuzin-treated plants (MCC). A high-density genetic linkage map was constructed using 2,129 DArTseq markers. Inclusive composite interval mapping (ICIM) identified seven QTL, one each on chromosomes 2A, 2D, 3A, 3B, 4A, 5A, and 6A. Three major QTL—Qrcc.uwa.2AS, Qrcc.uwa.5AL, and Qrcc.uwa.6AL—explained 11.39%, 11.06%, and 11.45% of the phenotypic variation, respectively. The 5A QTL was further validated using kompetitive allele-specific PCR (KASP) assays in an F3 validation population developed from Chuan Mai 25 × Dagger. Blasting the single-nucleotide polymorphisms (SNPs) flanking the QTL in the wheat reference genome RefV1.0 revealed SNP markers within or very close to annotated genes which could be candidate genes responsible for metribuzin tolerance. Most of the candidate genes were related to metabolic detoxification, especially those of P450 pathway and xenobiotic transmembrane transporter activity, which are reportedly key molecules responsible for herbicide tolerance. This study is the first to use specially developed populations to conduct QTL mapping on the metribuzin tolerance trait. The three major QTL and candidate genes identified in this study could facilitate marker-assisted metribuzin breeding in wheat. The QTL could be fine-mapped to locate the genes responsible for metribuzin tolerance, which could be introgressed into elite wheat cultivars.

Highlights

Wheat (Triticum aestivum L.) is a major food crop worldwide, providing approximately 20% of the global daily consumption of calories and proteins (Monneveux et al, 2012; Shiferaw et al, 2013)
This study aimed to 1) use the specially developed F8 recombinant inbred lines (RILs) populations to conduct quantitative trait loci (QTL) mapping on metribuzin tolerance; 2) develop a high-density genetic linkage map of hexaploid wheat with diversity arrays technology sequencing (DArTseq) markers; 3) identify QTL for metribuzin tolerance traits, including visual score (VS), reduction of chlorophyll content (RCC), and mean value of chlorophyll content for metribuzin-treated plants [mean chlorophyll content (MCC)]; and 4) identify candidate genes associated with the QTL for metribuzin tolerance
Following the QTL mapping, crosses were made between Chuan Mai 25 and two susceptible genotypes (Spear and Dagger) to develop populations to validate the phenotypic effects of the identified QTL in different genetic backgrounds

Summary

Introduction

Wheat (Triticum aestivum L.) is a major food crop worldwide, providing approximately 20% of the global daily consumption of calories and proteins (Monneveux et al, 2012; Shiferaw et al, 2013). Breeding wheat cultivars with high tolerance to herbicides will improve weed control efficiency and crop production. Most wheat cultivars lack tolerance to this broad-spectrum herbicide. Our previous study identified cultivar Chuan Mai 25 with superior metribuzintolerance using a pre-emergence selection method (Bhoite et al, 2018); this cultivar is a valuable resource for increasing wheat tolerance to metribuzin. Bhoite et al (2019) further reported that the inheritance of pre-emergent metribuzin tolerance acted as an additive-dominance model in wheat and proposed putative genes through 90k SNP array analysis of seven cultivars with contrasting responses to metribuzin. No studies have constructed a genetic linkage map for metribuzin tolerance in wheat using a specially developed mapping population

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