Genome-wide association study discovered candidate genes of Verticillium wilt resistance in upland cotton (Gossypium hirsutum L.)

Summary 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 ( SNP s) detected using the specific‐locus amplified fragment sequencing ( SLAF ‐seq) approach. Trait– SNP association analysis detected a total of 17 significant SNP s at P < 1.17 × 10 –5 ( P = 1/85 630, –log 10 P = 4.93); the peaks of SNP s associated with VW resistance on A10 were continuous and common in three environments ( RDIG 2015, RDIF 2015 and RDIF 2016). Haplotype block structure analysis predicted 22 candidate genes for VW resistance based on A10_99672586 with a minimum P ‐value (–log 10 P = 6.21). One of these genes ( CG 02) was near the significant SNP A10_99672586 (0.26 Mb), located in a 372‐kb haplotype block, and its Arabidopsis AT 3G25510 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 CG 02 was specific to up‐regulation in the resistant (R) genotype Zhongzhimian2 ( ZZM 2) and that silenced plants were more susceptible to V. dahliae . These results indicate that CG 02 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.