Genomic reconstruction of upland cotton domestication uncovers staged selection, gene flow, and flowering-time adaptation
Abstract
Upland cotton ( Gossypium hirsutum L.) makes up about 90% of global cotton farming. Despite its importance, the origins and domestication history of upland cotton remain poorly understood. Here, we present a high-density pan-genome variation map constructed from 2,910 cotton accessions, including 440 newly sequenced G. hirsutum landraces. Our pan-genome analysis indicates that modern upland cotton most probably originated from a single domestication and underwent three major stages. We also identified several genomic signatures associated with agriculturally important traits, including photoperiod sensitivity, fiber properties, and seed yield, which map to candidate loci GhTOFD06 , GhFLD11, and GhSID05, respectively, through a genome-wide association study (GWAS) and VIGS knockdown. During the third domestication stage (D3), selective pressures favored genes, such as GhTOFD06, a homolog of Arabidopsis COP9 signalosome complex subunit 5b (CSN5B), that control photoperiod-regulated flowering, thereby accelerating cotton domestication and facilitating upland cotton’s latitudinal expansion. Notably, functional validation via gene silencing showed that knockdown of GhSID05 reduced single seed weight by 11.41%, confirming its pivotal role in seed yield regulation. Additionally, we revealed natural gene flow between G. hirsutum and G. barbadense , which has significantly enriched the genetic diversity of the G. hirsutum gene pool and may have contributed favorable alleles for improving modern upland cotton. Our study provides a comprehensive understanding of the genomic evolution of G. hirsutum and valuable genetic resources for future breeding programs.
Article Details
Journal Info
Proceedings of the National Academy of Sciences
National Academy of Sciences
Authors (26)
Yanchao Xu
Department of Industrial and Systems Engineering
Xiaoyan Cai
State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences
Zhongli Zhou
State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences
Damar Lopez-Arredondo
Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University
Yuqing Hou
Institute of Chemistry, Chinese Academy of Sciences , , ,
Jie Zheng
Key Laboratory of Radiation Physics and Technology, Ministry of Education, Institute of Nuclear Science and Technology
Hongge Li
State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences
Gaofei Sun
Anyang Institute of Technology
Dingsha Jin
Sanya Research Institute, Hainan Academy of Agricultural Sciences
Panhong Dai
Anyang Institute of Technology
Yangyang Wei
Anyang Institute of Technology
Yuling Liu
Anyang Institute of Technology
Pengtao Li
Anyang Institute of Technology
Qiankun Liu
State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences
Heng Wang
Runrun Sun
Department of Biology, East Carolina University
Lijie Li
Department of Biology, East Carolina University
Xiaoping Pan
Department of Biology, East Carolina University
Kunbo Wang
State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences
Xiongming Du
State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences
Guoli Song
State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences
Baohong Zhang
Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University
Luis Rafael Herrera-Estrella
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Department of Plant Nutrition, College of Resources and Environmental Sciences, Nanjing Agricultural University
Shoupu He
State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences
Fang Liu
Renhai Peng
State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences