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

<b>Abstract</b><br/>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.

<b>摘要</b><br/>种群要维持最优适合度，需从基因组中高效清除有害突变。然而，在自然选择效力减弱的情境下——比如动植物驯化过程——有害突变预计会发生积累。本研究依托全转录组单核苷酸多态性（whole-transcriptome single nucleotide polymorphism, SNP）数据，比对了普通向日葵21份自然种群种质与19份驯化种质的有害突变负荷。尽管研究发现驯化过程中遗传多样性已大幅降低，但剩余突变却不成比例地偏向非同义替换。经生物信息学预测、会影响蛋白质功能的有害突变，其富集程度尤为显著。我们还在菊科另外两个驯化物种——朝鲜蓟（globe artichoke）与刺菜蓟（cardoon）——中发现了相似的模式，表明该现象并非由向日葵驯化的特异性或向日葵基因组的独有特征所导致。最后，本研究提供了确凿证据：由于纯化选择（purifying selection）效力减弱，有害突变会在基因组低重组区域发生积累。上述结果为作物改良工作带来了两难困境：尽管清除有害突变理应成为动植物育种项目的长期目标，但由于重组受限，想要剔除这些突变将困难重重。