Data from: What causes mating system shifts in plants? Arabidopsis lyrata as a case study

The genetic breakdown of self-incompatibility (SI) and subsequent mating system shifts to inbreeding has intrigued evolutionary geneticists for decades. Most of our knowledge is derived from interspecific comparisons between inbreeding species and their outcrossing relatives, where inferences may be confounded by secondary mutations that arose after the initial loss of SI. Here, we study an intraspecific breakdown of SI and its consequences in North American Arabidopsis lyrata to test whether: (1) particular S-locus haplotypes are associated with the loss of SI and/or the shift to inbreeding; (2) a population bottleneck may have played a role in driving the transition to inbreeding; and (3) the mutation(s) underlying the loss of SI are likely to have occurred at the S-locus. Combining multiple approaches for genotyping, we found that outcrossing populations on average harbour 5 to 9 S-locus receptor kinase (SRK) alleles, but only two, S1 and S19, are shared by most inbreeding populations. Self-compatibility (SC) behaved genetically as a recessive trait, as expected from a loss-of-function mutation. Bulked segregant analysis in SC × SI F2 individuals using deep sequencing confirmed that all SC plants were S1 homozygotes but not all S1 homozygotes were SC. This was also revealed in population surveys, where only a few S1 homozygotes were SC. Together with crossing data, this suggests that there is a recessive factor that causes SC that is physically unlinked to the S-locus. Overall, our results emphasise the value of combining classical genetics with advanced sequencing approaches to resolve long outstanding questions in evolutionary biology.

自交不亲和（self-incompatibility, SI）的遗传衰退以及随后交配系统向近交方向的转变，数十年来一直令进化遗传学家们着迷。目前我们的相关认知大多源自近交物种与其异交近缘类群之间的种间比较，但这类研究的推论可能会受到自交不亲和初始丧失后产生的次级突变的干扰。本研究以北美 lyrate拟南芥（Arabidopsis lyrata）为对象，探究其种内自交不亲和衰退现象及其后果，以验证以下三个推测：（1）特定S位点单倍型是否与自交不亲和的丧失及/或向近交的转变相关；（2）种群瓶颈是否可能在推动向近交的过渡中发挥了作用；（3）导致自交不亲和丧失的突变是否大概率发生于S位点。结合多种基因分型方法，我们发现异交种群平均携带5至9个S位点受体激酶（S-locus receptor kinase, SRK）等位基因，但近交种群中仅S1和S19这两个等位基因在多数类群中共享。自交亲和（self-compatibility, SC）的遗传行为符合功能丧失突变的预期，表现为隐性性状。对自交亲和×自交不亲和F2个体开展的深度测序集群分离分析证实，所有自交亲和植株均为S1纯合子，但并非所有S1纯合子均表现出自交亲和性。种群调查结果也印证了这一结论：仅少数S1纯合子为自交亲和型。结合杂交实验数据，该结果表明存在一个与S位点物理上不连锁的隐性因子，可引发自交亲和性。总体而言，本研究结果凸显了将经典遗传学与先进测序技术相结合，以解析进化生物学领域长期悬而未决的科学问题的重要价值。