Identification of new genetic sources of resistance to bacterial blight race 18 in diploid Asiatic cotton and resistance transfer to tetraploid Upland cotton (Gossypium hirsutum)

Bacterial blight (BB) caused by Xanthomonas citri pv. malvacearum (Xcm), poses a significant threat to Upland cotton (Gossypium hirsutum L.) production worldwide, and Xcm race 18 is the most virulent and widespread and can cause serious yield loss. Understanding the genetic basis of resistance in diploid Asiatic cotton (G. arboreum) and successfully transferring the resistance to tetraploid Upland cotton are crucial for developing resistant cotton cultivars. This study aimed to identify chromosomal regions for BB resistance through a genome-wide association study (GWAS) using 245 G. arboreum accessions evaluated in two replicated greenhouse tests and to evaluate an introgression BC2F7 population derived from a tri-species hybrid (G. arboreum/G. aridum/G. hirsutum). In response to Xcm race 18 infections after artificial inoculation, 80% of the accessions exhibited a high level of resistance, including 151 accessions showing immunity with no visible foliar water-soaked lesions. A GWAS based on 7009 polymorphic SNP markers detected 9 major BB resistance QTLs on chromosomes A01, A02, A05, A06, A10, A12 and A13 in the Asiatic cotton. The tri-species introgression population showed segregation in BB resistance with significantly lower disease incidence of BB than the susceptible check Acala 1517-18 GLS (30.2 vs. 100%), suggesting that the resistance in the diploid species has been successfully transferred into Upland cotton. The identification of Xcm race 18 resistant diploid Asiatic cotton germplasm and specific chromosomal regions and candidate genes delineated by SNPs for resistance for the first time provides strong evidence that the Asiatic cotton is a new genetic source of resistance to Xcm race 18. The results will facilitate further genetic and genomic studies toward the eventual identification of resistance genes in Asiatic cotton and their transfer into tetraploid cotton through marker-assisted selection.