Publications

A genomic variation map provides insights into potato evolution and key agronomic traits

Lian, Qun; Zhang, Yingying; Zhang, Jinzhe; Peng, Zhen; Wang, Weilun; Du, Miru; Li, Hongbo; Zhang, Xinyan; Cheng, Lin; Du, Ran; Zhou, Zijian; Yang, Zhenqiang; Xin, Guohui; Pu, Yuanyuan; Feng, Zhiwen; Wu, Qian; Xuanyuan, Guochao; Bai, Shunbuer; Hu, Rong; Negrão, Sónia; Bryan, Glenn J.; Bachem, Christian W.B.; Zhou, Yongfeng; Zhang, Ruofang; Shang, Yi; Huang, Sanwen; Lin, Tao; Qi, Jianjian

Summary

Hybrid potato breeding based on diploid inbred lines is transforming the way of genetic improvement of this staple food crop, which requires a deep understanding of potato domestication and differentiation. In the present study, we resequenced 314 diploid wild and landrace accessions to generate a variome map of 47,203,407 variants. Using the variome map, we discovered the reshaping of tuber transcriptome during potato domestication, characterized genome-wide differentiation between landrace groups Stenotomum and Phureja. We identified a jasmonic acid biosynthetic gene possibly affecting the tuber dormancy period. Genome-wide association studies revealed a UDP-glycosyltransferase gene for the biosynthesis of anti-nutritional steroidal glycoalkaloids (SGAs), and a Dehydration Responsive Element Binding (DREB) transcription factor conferring increased average tuber weight. In addition, genome similarity and group-specific SNP analyses indicated that tetraploid potatoes originated from the diploid Solanum tuberosum group Stenotomum. These findings shed light on the evolutionary trajectory of potato domestication and improvement, providing a solid foundation for advancing hybrid potato-breeding practices.