Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding

作者：Yaoyao Wu, Dawei Li, Yong Hu, Hongbo Li, Guillaume P. Ramstein, Shaoqun Zhou, Xinyan Zhang, Zhigui Bao, Yu Zhang, Baoxing Song, Yao Zhou, Yongfeng Zhou, Edeline Gagnon, Tiina Särkinen, Sandra Knapp, Chunzhi Zhang, Thomas Städler, Edward S. Buckler, Sanwen Huang · 发表于：Cell · 年份：2023 · DOI：10.1016/j.cell.2023.04.008 · 被引用次数：138 · 研究领域：Plant Pathogens and Resistance、Plant Disease Resistance and Genetics、Chromosomal and Genetic Variations

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.