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

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 NegrãoGlenn J. Bryan, Christian W.B. Bachem, Yongfeng Zhou, Ruofang Zhang, Yi Shang, Sanwen Huang^*, Tao Lin^*, Jianjian Qi^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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. 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.

Original language	English
Number of pages	20
Journal	Molecular Plant
DOIs	https://doi.org/10.1016/j.molp.2025.01.016
Publication status	E-pub ahead of print - 23 Jan 2025

Keywords

average tuber weight
differentiation
domestication
potato
steroidal glycoalkaloids
tuber dormancy

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10.1016/j.molp.2025.01.016

https://edepot.wur.nl/689244Licence: Taverne

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Lian, Q., Zhang, Y., Zhang, J., Peng, Z., Wang, W., Du, M., Li, H., Zhang, X., Cheng, L., Du, R., Zhou, Z., Yang, Z., Xin, G., Pu, Y., Feng, Z., Wu, Q., Xuanyuan, G., Bai, S., Hu, R., ... Qi, J. (2025). A genomic variation map provides insights into potato evolution and key agronomic traits. Molecular Plant. Advance online publication. https://doi.org/10.1016/j.molp.2025.01.016

@article{df561568f1a94158a3cf6ac47540c5ea,

title = "A genomic variation map provides insights into potato evolution and key agronomic traits",

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. 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.",

keywords = "average tuber weight, differentiation, domestication, potato, steroidal glycoalkaloids, tuber dormancy",

author = "Qun Lian and Yingying Zhang and Jinzhe Zhang and Zhen Peng and Weilun Wang and Miru Du and Hongbo Li and Xinyan Zhang and Lin Cheng and Ran Du and Zijian Zhou and Zhenqiang Yang and Guohui Xin and Yuanyuan Pu and Zhiwen Feng and Qian Wu and Guochao Xuanyuan and Shunbuer Bai and Rong Hu and S{\'o}nia Negr{\~a}o and Bryan, {Glenn J.} and Bachem, {Christian W.B.} and Yongfeng Zhou and Ruofang Zhang and Yi Shang and Sanwen Huang and Tao Lin and Jianjian Qi",

year = "2025",

month = jan,

day = "23",

doi = "10.1016/j.molp.2025.01.016",

language = "English",

journal = "Molecular Plant",

issn = "1674-2052",

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Lian, Q, Zhang, Y, Zhang, J, Peng, Z, Wang, W, Du, M, Li, H, Zhang, X, Cheng, L, Du, R, Zhou, Z, Yang, Z, Xin, G, Pu, Y, Feng, Z, Wu, Q, Xuanyuan, G, Bai, S, Hu, R, Negrão, S, Bryan, GJ, Bachem, CWB, Zhou, Y, Zhang, R, Shang, Y, Huang, S, Lin, T & Qi, J 2025, 'A genomic variation map provides insights into potato evolution and key agronomic traits', Molecular Plant. https://doi.org/10.1016/j.molp.2025.01.016

TY - JOUR

T1 - A genomic variation map provides insights into potato evolution and key agronomic traits

AU - Lian, Qun

AU - Zhang, Yingying

AU - Zhang, Jinzhe

AU - Peng, Zhen

AU - Wang, Weilun

AU - Du, Miru

AU - Li, Hongbo

AU - Zhang, Xinyan

AU - Cheng, Lin

AU - Du, Ran

AU - Zhou, Zijian

AU - Yang, Zhenqiang

AU - Xin, Guohui

AU - Pu, Yuanyuan

AU - Feng, Zhiwen

AU - Wu, Qian

AU - Xuanyuan, Guochao

AU - Bai, Shunbuer

AU - Hu, Rong

AU - Negrão, Sónia

AU - Bryan, Glenn J.

AU - Bachem, Christian W.B.

AU - Zhou, Yongfeng

AU - Zhang, Ruofang

AU - Shang, Yi

AU - Huang, Sanwen

AU - Lin, Tao

AU - Qi, Jianjian

PY - 2025/1/23

Y1 - 2025/1/23

N2 - 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.

AB - 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.

KW - average tuber weight

KW - differentiation

KW - domestication

KW - potato

KW - steroidal glycoalkaloids

KW - tuber dormancy

U2 - 10.1016/j.molp.2025.01.016

DO - 10.1016/j.molp.2025.01.016

M3 - Article

AN - SCOPUS:85218915164

SN - 1674-2052

JO - Molecular Plant

JF - Molecular Plant

ER -

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

Abstract

Keywords

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