title: Genome-wide association study discovered candidate genes of Verticillium wilt resistance in upland cotton (Gossypium hirsutum L.).
abstract: Verticillium wilt (VW), caused by infection by Verticillium dahliae, is considered one of the most yield-limiting diseases in cotton. To examine the genetic architecture of cotton VW resistance, we performed a genome-wide association study (GWAS) using a panel of 299 accessions and 85 630 single nucleotide polymorphisms (SNPs) detected using the specific-locus amplified fragment sequencing (SLAF-seq) approach. Trait-SNP association analysis detected a total of 17 significant SNPs at P < 1.17 × 10-5(P = 1/85 630, -log10P = 4.93); the peaks of SNPs associated with VW resistance on A10 were continuous and common in three environments (RDIG2015, RDIF2015 and RDIF2016). Haplotype block structure analysis predicted 22 candidate genes for VW resistance based on A10_99672586 with a minimum P-value (-log10P = 6.21). One of these genes (CG02) was near the significant SNP A10_99672586 (0.26 Mb), located in a 372-kb haplotype block, and its Arabidopsis AT3G25510 homologues contain TIR-NBS-LRR domains that may be involved in disease resistance response. Real-time quantitative PCR and virus-induced gene silencing (VIGS) analysis showed that CG02 was specific to up-regulation in the resistant (R) genotype Zhongzhimian2 (ZZM2) and that silenced plants were more susceptible to V. dahliae. These results indicate that CG02 is likely the candidate gene for resistance against V. dahliae in cotton. The identified locus or gene may serve as a promising target for genetic engineering and selection for improving resistance to VW in cotton.
authors.affiliation: Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Tinggang
authors.initials: T
authors.lastname: Li
authors.affiliation: Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Ma
authors.affiliation: Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Nanyang
authors.initials: N
authors.lastname: Li
authors.affiliation: Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhou
authors.affiliation: Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang, China.
authors.forename: Huanyong
authors.initials: H
authors.lastname: Han
authors.affiliation: Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Yuejing
authors.initials: Y
authors.lastname: Gui
authors.affiliation: Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Yuming
authors.initials: Y
authors.lastname: Bao
authors.affiliation: Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Jieyin
authors.initials: J
authors.lastname: Chen
authors.affiliation: Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Dai
mesh_terms: D002681:China; D060467:Disease Resistance / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D003368:Gossypium / Q000235:genetics* / Q000382:microbiology*; D015810:Linkage Disequilibrium; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D020172:Verticillium / Q000472:pathogenicity*
chemical_list: D010940:Plant Proteins
keywords: Verticillium wilt; candidate gene; cotton; genome-wide association; virus-induced gene silencing (VIGS)