Abstract
Cotton (Gossypium spp.) is the best plant fiber source in the world and provides the raw material for industry. Verticillium wilt caused by Verticillium dahliae Kleb. is accepted as a major disease of cotton production. The most practical way to deal with verticillium wilt is to develop resistant/tolerant varieties after cultural practices. One of the effective selections in plant breeding is the use of marker-assisted selection (MAS) via quantitative trait loci (QTL). Therefore, in this study, we aimed to discover the genetic markers associated with the disease. Through the association mapping analysis, common single nucleotide polymorphism (SNP) markers were obtained using 4730 SNP alleles. As a result, twenty-three markers were associated with defoliating (PYDV6 isolate) pathotype, twenty-one markers with non-defoliating (Vd11 isolate) pathotype, ten QTL with Disease Severity Index (DSI) of the leaves at the 50–60% boll opening period and eight markers were associated with DSI in the stem section. Some of the markers that show significant associations are located on protein coding genes such as protein Mpv17-like, 21 kDa protein-like, transcription factor MYB113-like, protein dehydration-induced 19 homolog 3-like, F-box protein CPR30-like, extracellular ribonuclease LE-like, putative E3 ubiquitin-protein ligase LIN, pentatricopeptide repeat-containing protein At3g62890-like, fructose-1,6-bisphosphatase, tubby-like F-box protein 8, endoglucanase 16-like, glucose-6-phosphate/phosphate translocator 2, metal tolerance protein 11-like, VAN3-binding protein-like, transformation/transcription domain-associated protein-like, pyruvate kinase isozyme A, ethylene-responsive transcription factor CRF2-like, molybdate transporter 2-like, IRK-interacting protein-like, glycosylphosphatidylinositol anchor attachment 1 protein, U3 small nucleolar RNA-associated protein 4-like, microtubule-associated protein futsch-like, transport and Golgi organization 2 homolog, splicing factor 3B subunit 3-like, mediator of RNA polymerase II transcription subunit 15a-like, putative ankyrin repeat protein, and protein networked 1D-like. It has been reported in previous studies that most of these genes are associated with biotic and abiotic stress factors. As a result, once validated, it would be possible to use the markers obtained in the study in Marker Assisted Selection (MAS) breeding.
Highlights
Cotton (Gossypium spp.) is an important plant that provides raw materials to the textile, food and feed industries [1]
Minor allele frequency (MAF) filtering was performed for 10,173 single nucleotide polymorphism (SNP) data obtained from Beijing Genome Institute (BGI) to determine the markers related to Verticillium wilt disease and 4370 SNP markers used in association mapping analysis
Marker trait relationship was determined through the general linear model (GLM)
Summary
Cotton (Gossypium spp.) is an important plant that provides raw materials to the textile, food and feed industries [1]. Biotic and abiotic stress factors in cotton cause a decrease in yield and quality. As a biotic stress factor, Wilt disease is caused by Verticillium dahliae Kleb., which is known as the most disruptive and destructive one in the world [2,3,4]. The pathogen can cause wilting in more than 400 plant species other than cotton, such as vegetables, legumes, ornamental plants, industrial plants, fruit trees and weeds [5]. Worldwide estimated crop loss of Verticillium wilt is reported as 1.5 million bales [6]. It has been reported that Verticillium wilt caused approximately 148 thousand cotton bale losses in the 2010 production season in the USA [7] and 480 million bales from 1990–2014 [8]
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