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Phylogenomic discovery of deleterious mutations facilitates hybrid potato

文献类型: 外文期刊

作者: Wu, Yaoyao 1 ; Li, Dawei 1 ; Hu, Yong 1 ; Li, Hongbo 1 ; Ramstein, Guillaume P. 5 ; Zhou, Shaoqun 1 ; Zhang, Xinyan 1 ; Bao, Zhigui 1 ; Zhang, Yu 1 ; Song, Baoxing 8 ; Zhou, Yao 1 ; Zhou, Yongfeng 1 ; Gagnon, Edeline 11 ; Sarkinen, Tiina 12 ; Knapp, Sandra 13 ; Zhang, Chunzhi 1 ; Stadler, Thomas 14 ; Buckler, Edward S. 2 ; Huang, Sanwen 1 ;

作者机构: 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen,Minist Agr & Rural Affair, Shenzhen Branch,Genome Anal Lab, State Key Lab Trop Crop Breeding,Guandong Lab Lin, Shenzhen 518120, Guangdong, Peoples R China

2.Cornell Univ, Inst Genom Divers, Ithaca, NY 14853 USA

3.Chinese Acad Trop Agr Sci, State Key Lab Trop Crop Breeding, Haikou 571101, Hainan, Peoples R China

4.Yunnan Normal Univ, AGISCAAS YNNU Joint Acad Potato Sci, Kunming 650500, Yunnan, Peoples R China

5.Aarhus Univ, Ctr Quantitat Genet & Genom, DK-8000 Aarhus, Denmark

6.Max Planck Inst Biol Tubingen, Dept Mol Biol, D-72076 Tubingen, Germany

7.Sun Yat Sen Univ, Sch Agr, Shenzhen 518107, Guangdong, Peoples R China

8.Peking Univ, Inst Adv Agr Sci, Weifang 261000, Shandong, Peoples R China

9.Chinese Acad Sci, Inst Bot, Beijing 100093, Peoples R China

10.Univ Chinese Acad Sci, Coll Life Sci, Beijing 100094, Peoples R China

11.Tech Univ Munich, TUM Sch Life Sci, Emil Ramann Str 2, D-85354 Freising Weihenstephan, Germany

12.Royal Bot Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland

13.Nat Hist Museum, Cromwell Rd, London SW7 5BD, England

14.Swiss Fed Inst Technol, Inst Integrat Biol, CH-8092 Zurich, Switzerland

15.Swiss Fed Inst Technol, Zurich Basel Plant Sci Ctr, CH-8092 Zurich, Switzerland

16.USDA ARS, Ithaca, NY 14853 USA

期刊名称:CELL ( 影响因子:64.5; 五年影响因子:57.5 )

ISSN: 0092-8674

年卷期: 2023 年 186 卷 11 期

页码:

收录情况: SCI

摘要: Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising-2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.

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