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.

杂交马铃薯育种将把作物从克隆繁殖的四倍体转变为种子繁殖的二倍体。马铃薯基因组有害突变的历史积累阻碍了优良近交系和杂交种的发展。利用 92 种茄科及其姐妹进化枝物种的全基因组系统发育，我们采用进化策略来识别有害突变。深层系统发育揭示了高度受限位点的全基因组景观，占基因组的 ~2.4%。基于二倍体马铃薯多样性面板，我们推断出 367,499 个有害变异，其中 50% 出现在非编码位点，15% 出现在同义位点。与直觉相反，具有相对较高纯合有害负担的二倍体品系可能是近交系开发的更好起始材料，尽管其生长活力较低。包含推断的有害突变可使基因组预测产量的准确性提高 24.7%。我们的研究深入了解了有害突变的全基因组发生率和特性及其对育种的深远影响。