Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops

For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism data. Although we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased toward nonsynonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome. Finally, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. Although the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.

种群若要维持最优适合度，需从基因组中高效清除有害突变。然而，在削弱自然选择有效性的情境中——例如动植物驯化过程——有害突变预计会发生积累。本研究借助全转录组单核苷酸多态性（single nucleotide polymorphism, SNP）数据，对普通向日葵的21份自然种群种质材料与19份驯化种质材料的有害突变负荷展开了比较分析。尽管研究发现驯化过程中遗传多样性已大幅降低，但剩余突变却显著偏向非同义替换；其中，经生物信息学预测的、影响蛋白质功能的有害突变的富集程度尤为显著。我们在向日葵科另外两个驯化物种——洋蓟（globe artichoke）和菜蓟（cardoon）——中也观测到了类似模式，表明该现象并非源于向日葵驯化或向日葵基因组的特异性。最后，本研究提供了确凿证据：由于纯化选择（purifying selection）有效性降低，有害突变会在基因组低重组区域发生积累。上述结果给作物改良工作带来了一道困境：尽管清除有害突变理应成为动植物育种计划的长期目标，但受限于有限的重组，剔除这类突变将极具挑战性。