Population Genomics of Cotton

Cotton (Gossypium) is a fiber-producing oil seed crop with significant economic and scientific importance in natural textile fiber and edible oil industries. Cotton is an ideal crop model system for studying polyploidy, evolution, population genomics, and domestication, due to the presence of several species, wild relatives, and progenitors. Population genomics studies can provide key insights into genetic diversity, population structure, evolution, and domestication as well as genotype-phenotype associations and genomics-assisted breeding of Gossypium species. Population genomics research in cotton is lagging behind when compared to other crops with simple genomes due to its large complex genome size and polyploidy. However, modern genomics technologies such as sequencing, resequencing, comparative genomics, and whole-genome sequencing (WGS) have generated reference genomes of diploid and tetraploid cotton, which have addressed key questions about the role of polyploidy in the evolution of cotton. Population genomics studies and reference genomes have advanced understanding of genomic variation across species, gene expression changes, domestication, and evolutionary history of several species of Gossypium, and genetic variation underlying different traits of cotton such as fiber yield, fiber quality, biotic, and abiotic stress resistance/tolerance. These advances are facilitating selection and breeding of cotton for improved traits through genome-wide association studies (GWAS) and genomic selection. GWAS has discovered candidate genes for different quantitative trait loci (QTLs). Hence, population genomics approach will be a key component in studying genetic history of cotton domestication, improvement of different agronomic traits such as fiber quality, oil yield, disease resistance, and tolerance to extreme environmental conditions. This chapter discusses the recent advances made in cotton population genomics and its future perspectives.