Gossypium arboreum Raw sequence reads

As the only cultivated diploid cotton, G. arboreum and G. herbaceum provide excellent genetic resources for functional research. Here we reported the genome variation map of 230 G. arboreum and 15 G. herbaceum accessions. A total of ~18 million high quality SNPs and ~2 million indels were obtained by average 6-fold coverage whole-genome resequencing. Based-on SNP genotypes, we found the great genomic difference existed between G. arboreum and G. herbaceum, as well as the obvious population differentiation among Chinese G. arboreum accessions owing to the geographical divergence. Moreover, we identified abundant of candidate genes using genome-wide association study (GWAS) for 20 agronomically important traits in G. arboreum, including variations affecting oil components, seed fuzz and disease resistance. Our study provides fundamental resources for cotton genetics improvements, and molecular breeding in future.