Introgression leads to genetic divergence for maturity and fiber quality in upland cotton

Understanding the genetic diversity and genetic divergence in population structure of germplasms is important when selecting parents for crop breeding. The genomic changes that occurred during the domestication and improvement of upland cotton remain poorly understood, and the available genetic resources from improved cotton cultivars are very limited. By applying restriction site-associated DNA marker sequencing (RAD-seq) technology to 582 tetraploid cotton accessions, we detected two distinct genomic signatures had the highest divergence on chromosomes A06 and A08 which dramaticly affect the population structure and genetic diversity in modern improved upland cotton populations. Based on integrating the pedigree of the accessions with previously reported QTLs, genome-wide association study (GWAS) and introgression analyses, we suggest that the two divergent regions resulted from the introgression of exotic lineages from G. hirsutum races and wild relatives. Genetic divergence of these regions were the typical genomic characteristic might be responsible for maturity in central Asia ecotype cotton population (Group-2) A06 and fiber quality for offspring resulting from interspecific hybridization developing mainly in southern China (Group-1) (A08), and several candidate genes were screened by integrating transcriptome data. Additionally, both genomic regions are located in putative pericentromere regions, implying that their application will be challenging. In the study, based on high-density SNP markers, we firstly reported two genomic signatures on chromosome A06 and A08 which could both distinguish ecotypes and be responsible for important agronomic traits in upland cotton. These results provides new insights for understanding the genomic basis of exotic introgressions in modern cotton cultivars.