Gossypium arboreum Raw sequence reads. Gossypium arboreum

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.

作为仅有的两类栽培二倍体棉花，亚洲棉（G. arboreum）与草棉（G. herbaceum）为功能研究提供了优异的遗传资源。本研究报道了230份亚洲棉及15份草棉种质的基因组变异图谱。通过平均6倍覆盖度的全基因组重测序，共获得约1800万个高质量单核苷酸多态性（Single Nucleotide Polymorphism, SNP）与约200万个插入缺失变异（Insertion-Deletion, indel）。基于单核苷酸多态性基因型，本研究发现亚洲棉与草棉间存在显著基因组差异，同时中国境内的亚洲棉种质因地理分化呈现出明显的群体分化特征。此外，本研究针对亚洲棉的20个重要农艺性状开展全基因组关联分析（Genome-Wide Association Study, GWAS），鉴定得到大量候选基因，相关变异涉及油脂组分、种子短绒与抗病性等性状。本研究为棉花遗传改良与未来分子育种提供了基础性资源。