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

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

doi:10.1016/j.molp.2025.01.016

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

Mol Plant. 2025 Jan 23:S1674-2052(25)00037-1. doi: 10.1016/j.molp.2025.01.016. Online ahead of print.

Authors

Qun Lian¹, Yingying Zhang², Jinzhe Zhang³, Zhen Peng⁴, Weilun Wang², Miru Du², Hongbo Li⁵, Xinyan Zhang⁶, Lin Cheng⁶, Ran Du⁶, Zijian Zhou², Zhenqiang Yang², Guohui Xin², Yuanyuan Pu², Zhiwen Feng², Qian Wu², Guochao Xuanyuan², Shunbuer Bai², Rong Hu², Sónia Negrão⁷, Glenn J Bryan⁸, Christian W B Bachem⁹, Yongfeng Zhou⁶, Ruofang Zhang², Yi Shang¹⁰, Sanwen Huang¹¹, Tao Lin¹², Jianjian Qi¹³

Affiliations

¹ Inner Mongolia Potato Engineering and Technology Research Centre, Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China; National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
² Inner Mongolia Potato Engineering and Technology Research Centre, Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
³ State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
⁴ College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
⁵ National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, the Netherlands.
⁶ National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
⁷ School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
⁸ Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD25DA, UK.
⁹ Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, the Netherlands.
¹⁰ Yunnan Key Laboratory of Potato Biology, CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, China.
¹¹ National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. Electronic address: qijj@imu.edu.cn.
¹² College of Horticulture, China Agricultural University, Beijing, 100193, China. Electronic address: qijj@imu.edu.cn.
¹³ Inner Mongolia Potato Engineering and Technology Research Centre, Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China. Electronic address: qijj@imu.edu.cn.

PMID: 39861948
DOI: 10.1016/j.molp.2025.01.016

Abstract

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. Here, 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, and identified a jasmonic acid biosynthetic gene possibly affecting tuber dormancy period. Genome-wide association studies revealed a UDP-glycosyltransferase gene for biosynthesis of antinutritional 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 tetraploid potatoes originated from the diploid S. 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.

Keywords: average tuber weight; differentiation; domestication; potato; steroidal glycoalkaloids; tuber dormancy.