A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cotton

Abdelraheem, Abdelraheem; Elassbli, Hanan; Kuraparthy, Vasu; Hinze, Lori L.; Stelly, David M.; Wedegaertner, Tom; Zhang, Jinfa

doi:10.1007/s00122-019-03487-x

Cited by 66 publications

(50 citation statements)

References 60 publications

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“…vasinfectum race 4 (FOV4) has become a major threat to cotton production. Recent studies have been undertaken to understand its epidemiology and identify resistance (Ulloa et al 2013;Wang et al 2018a;Abdelraheem et al 2020;Srivastava et al 2021). The transgenic analysis of charcoal rot presented by Lawaju et al (2018), through the use of the pRAP plasmids, provides a model for understanding and developing resistance for FOV4.…”

Section: Future Applications Of the Prap System Of Plant Transformation Vectorsmentioning

confidence: 99%

The impact of pRAP vectors on plant genetic transformation and pathogenesis studies including an analysis of BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-mediated resistance

Klink

Darwish

Alkharouf

et al. 2021

Journal of Plant Interactions

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Section: Future Applications Of the Prap System Of Plant Transformation Vectorsmentioning

confidence: 99%

The impact of pRAP vectors on plant genetic transformation and pathogenesis studies including an analysis of BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-mediated resistance

Klink

Darwish

Alkharouf

et al. 2021

Journal of Plant Interactions

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“…The putative E3 ubiquitin-protein ligase LIN gene may also be effective in the regulation of mechanisms against stress factors, so it can be involved in regulation and develop as a response to Verticillium wilt disease. On the other hand, regarding Verticillium wilt resistance, QTL were determined on chromosomes 4, 9, and 11, with the majority on 16 [32], 4, 22, 24, and 26 [33], 26 and 21 [34]. It has been determined that the markers we have determined are on the same chromosomes previously determined by different researchers.…”

Section: Markers Associated With Resistance/tolerance To Verticillium Wilt Dsi On Leaves At the 50-60% Boll Opening Periodmentioning

confidence: 63%

Association Mapping of Verticillium Wilt Disease in a Worldwide Collection of Cotton (Gossypium hirsutum L.)

Bardak

Çelik

Erdoğan

et al. 2021

Plants

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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.

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“…We compared our GWAS results to previous studies and found that the significantly associated signal (A10_98704568) on A10 was overlapped to the reported SNP loci (Li et al ., 2017a ), supporting the reliability of our results. Although previously reported VW resistance QTLs or GWAS signals were not overlapped with the region of D11 that identified in the present study (Abdelraheem, et al ., 2020 ; Fang et al ., 2017 ; Li et al ., 2017a ), the SNPs identified in the region of D11 were repeatedly associated and exhibited clusters of resistance gene analogues (RGAs) (Holub, 2001 ) via bioinformatics analysis (Table S7 ). Thus, the significant SNPs that we identified on D11 were novel.…”

Section: Resultsmentioning

confidence: 99%

A large‐scale genomic association analysis identifies a fragment in Dt11 chromosome conferring cotton Verticillium wilt resistance

Zhang

Chen

Sun

et al. 2021

Plant Biotechnology Journal

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Verticillium wilt (VW) is a destructive disease that results in great losses in cotton yield and quality. Identifying genetic variation that enhances crop disease resistance is a primary objective in plant breeding. Here we reported a GWAS of cotton VW resistance in a natural-variation population, challenged by different pathogenicity stains and different environments, and found 382 SNPs significantly associated with VW resistance. The associated signal repeatedly peaked in chromosome Dt11 (68 798 494-69 212 808) containing 13 core elite alleles undescribed previously. The core SNPs can make the disease reaction type from susceptible to tolerant or resistant in accessions with alternate genotype compared to reference genotype. Of the genes associated with the Dt11 signal, 25 genes differentially expressed upon Verticillium dahliae stress, with 21 genes verified in VW resistance via gene knockdown and/or overexpression experiments. We firstly discovered that a gene cluster of L-type lectin-domain containing receptor kinase (GhLecRKs-V.9) played an important role in VW resistance. These results proved that the associated Dt11 region was a major genetic locus responsible for VW resistance. The frequency of the core elite alleles (FEA) in modern varieties was significantly higher than the early/middle varieties (12.55% vs 4.29%), indicating that the FEA increased during artificial selection breeding. The current developmental resistant cultivars, JND23 and JND24, had fixed these core elite alleles during breeding without yield penalty. These findings unprecedentedly provided genomic variations and promising alleles for promoting cotton VW resistance improvement.

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A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cotton

Cited by 66 publications

References 60 publications

The impact of pRAP vectors on plant genetic transformation and pathogenesis studies including an analysis of BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-mediated resistance

The impact of pRAP vectors on plant genetic transformation and pathogenesis studies including an analysis of BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-mediated resistance

Association Mapping of Verticillium Wilt Disease in a Worldwide Collection of Cotton (Gossypium hirsutum L.)

A large‐scale genomic association analysis identifies a fragment in Dt11 chromosome conferring cotton Verticillium wilt resistance

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