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Genomic insights into the genetic basis of cotton breeding in China

Molecular Plant 2023年第4期16卷 662-677页

作者： Yiqian Li Zhanfeng Si Guoping Wang Zhuolin Shi Jinwen Chen Guoan Qi Shangkun Jin Zegang Han Wenhao Gao Yue Tian Yun Mao Lei Fang Yan Hu Hong Chen Xiefei Zhu Tianzhen Zhang zhejiang Provincial Key Laboratory of Crop Genetic Resources the Advanced Seed InstitutePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina xinjang production and construction corps seventh division agricultural research institute KuintunChina state Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricutural UniversityNanjingChina College of Biotechnology Jiangsu University of Science and TechnologyZhenjiangChina Key Laboratory of China Northwestern Inland Region Ministry of AgricultureCotton Research InstituteXinjiang Academy of Agricultural and Reclamation ScienceShiheziChina

The excellent Upland cotton(Gossypium hirsutum)cultivars developed since 1949 have made a huge contribution to cotton production in China,the world's largest producer and consumer of cotton.However,the genetic and genomic basis for the improvements of these cotton cultivars remains largely unclear.In this study,we selected 16 Upland cotton cultivars with important historical status in Chinese cotton breeding and constructed a multiparent,advanced generation,intercross(MAGiC)population comprising 920 recombinant inbred lines.A genome-wide association study using the MAGIC population identified 54 genomic loci associated with lint yield and fiber quality.Of them,25(46.30%)pleiotropic genomic loci cause simultaneous changes of lint yield and/or fiber quality traits,revealing complex trade-offs and linkage drags in Upland cotton agronomic traits.Deep sequencing data of 11 introduced ancestor cultivars and publicly available resequencing datasets of 839 cultivars developed in China during the past 70 years were integrated to explore the historical distribution and origin of the elite or selected alleles.Interestingly,85%oftheseelitealleles were selectedandfixed fromdifferent Americanancestors,consistentwithcotton breeding practices in China.However,seven elite alleles of native origin that are responsible for Fusarium wilt resistance,early maturing,good-quality fiber,and other characteristics were not found in American an-cestors but have greatly contributed to Chinese cotton breeding and wide cultivation.Taken together,these results provide a genetic basis for further improving cotton cultivars and reveal that the genetic composition of Chinese cotton cultivars is narrow and mainly derived from early introduced American varieties.

关键词： cotton MAGiC population GWAS whole-genome sequencing pleiotropic loci breeding history

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