Rapid Mining of Candidate Genes for Verticillium Wilt Resistance in Cotton Based on BSA-Seq Analysis.

Yanli Cui,Quanjia Chen,Hongmei Wang,Qun Ge,Pei Zhao,Wei Chen,Xiaohui Sang,Yunlei Zhao

doi:10.3389/fpls.2021.703011

Abstract

Cotton is a globally important cash crop. Verticillium wilt (VW) is commonly known as “cancer” of cotton and causes serious loss of yield and fiber quality in cotton production around the world. Here, we performed a BSA-seq analysis using an F2:3 segregation population to identify the candidate loci involved in VW resistance. Two QTLs (qvw-D05-1 and qvw-D05-2) related to VW resistance in cotton were identified using two resistant/susceptible bulks from the F2 segregation population constructed by crossing the resistant cultivar ZZM2 with the susceptible cultivar J11. A total of 30stop-lost SNPs and 42 stop-gained SNPs, which included 17 genes, were screened in the qvw-D05-2 region by SnpEff analysis. Further analysis of the transcriptome data and qRT-PCR revealed that the expression level of Ghir_D05G037630 (designated as GhDRP) varied significantly at certain time points after infection with V. dahliae. The virus-induced gene silencing of GhDRP resulted in higher susceptibility of the plants to V. dahliae than the control, suggesting that GhDRP is involved in the resistance to V. dahlia infection. This study provides a method for rapid mining of quantitative trait loci and screening of candidate genes, as well as enriches the genomic information and gene resources for the molecular breeding of disease resistance in cotton.

Highlights

As a globally important cash crop, cotton provides approximately 35% of total fiber used worldwide (Zhang et al, 2014a) and is an important source of oilseed (Hulse-Kemp et al, 2015)
Assessment of Verticillium wilt (VW) severity showed that the relative disease index (RDI) of the parent ZZM2 was 18.71 in the field and 21.25 in the greenhouse, respectively; and that of J11 was adjusted to 50 in both environments, which was used as a susceptible control (Figure 1F)
Correlation analysis showed that the RDI value in the greenhouse was strongly correlated with that in the field (r = 0.628, p < 0.001), which revealed that RDI investigated in seedling and adult stages could reflect the resistance of cotton to VW

Summary

Introduction

As a globally important cash crop, cotton provides approximately 35% of total fiber used worldwide (Zhang et al, 2014a) and is an important source of oilseed (Hulse-Kemp et al, 2015). VW reduces the yield of cotton and causes significant degradation of the fiber quality (Zhang et al, 2014a). Development of new cotton varieties resistant to VW has been considered as the most effective and feasible way to control VW (Zhao et al, 2017). It has been widely recognized that VW is a quantitative trait controlled by multiple genes (Devey and Roose, 1987; Wang et al, 2004, 2010). The quantitative trait loci (QTL) related to VW in cotton have been located using F2 or recombinant inbred line (RIL) populations

Methods

Results

Conclusion