Transcriptome Comparison Reveals Patterns of Selection in Domesticated and Wild Cotton

Cotton genomic resources and nucleotide polymorphism information is useful to understand germplasm diversity, crop domestication, and crop improvement. There are many publicly available resources of cotton; however most resources of gene expression are from fiber tissue and roots have been less studied. In this study, we report individual transcriptome of 108 G. hirsutum accessions of root tissue, including 41 improved (domesticated) and 67 wild accessions from the USDA Germplasm collection. More than 3.0 billion clean reads were generated. Of the 37,505 genes in the diploid cotton G. raimondii reference genome, 61.4% were expressed in root tissue. Of these, 1,648 and 1,487 genes in improved and wild accessions respectively which were differentially expressed between the two subgenomes. The RNA-seq data was mined for alleles that were polymorphic among the diverse germplasm. The A_T-genome had 234,266 SNPs in 25,993 genes, while the D_T-genome had 169,123 SNPs in 25,836 genes (5x coverage). After a stricter filtering (<50% missing; 5% MAF), 31,513 and 23,585 high-confidence SNPs were used for population genomics analyses of A_T and D_T-genomes, respectively. Germplasm diversity, population structure and domestication sweeps were analyzed in each genome of polyploid cotton. These genic SNPs from root tissue will complement with the expanding genomic resources of cotton and provides a valuable resource to future genetic analyses and breeding programs.