National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China.
State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
PLoS Genet. 2023 Jun 20;19(6):e1010811. doi: 10.1371/journal.pgen.1010811. eCollection 2023 Jun.
Conservation of crop wild relatives is critical for plant breeding and food security. The lack of clarity on the genetic factors that lead to endangered status or extinction create difficulties when attempting to develop concrete recommendations for conserving a citrus wild relative: the wild relatives of crops. Here, we evaluate the conservation of wild kumquat (Fortunella hindsii) using genomic, geographical, environmental, and phenotypic data, and forward simulations. Genome resequencing data from 73 accessions from the Fortunella genus were combined to investigate population structure, demography, inbreeding, introgression, and genetic load. Population structure was correlated with reproductive type (i.e., sexual and apomictic) and with a significant differentiation within the sexually reproducing population. The effective population size for one of the sexually reproducing subpopulations has recently declined to ~1,000, resulting in high levels of inbreeding. In particular, we found that 58% of the ecological niche overlapped between wild and cultivated populations and that there was extensive introgression into wild samples from cultivated populations. Interestingly, the introgression pattern and accumulation of genetic load may be influenced by the type of reproduction. In wild apomictic samples, the introgressed regions were primarily heterozygous, and genome-wide deleterious variants were hidden in the heterozygous state. In contrast, wild sexually reproducing samples carried a higher recessive deleterious burden. Furthermore, we also found that sexually reproducing samples were self-incompatible, which prevented the reduction of genetic diversity by selfing. Our population genomic analyses provide specific recommendations for distinct reproductive types and monitoring during conservation. This study highlights the genomic landscape of a wild relative of citrus and provides recommendations for the conservation of crop wild relatives.
保护作物野生近缘种对于植物育种和粮食安全至关重要。由于缺乏明确的遗传因素导致濒危或灭绝，因此在尝试制定保护柑橘野生近缘种（即作物野生近缘种）的具体建议时会遇到困难。在这里，我们使用基因组学、地理、环境和表型数据以及正向模拟来评估野生金桔（ Fortunella hindsii）的保护状况。对来自 Fortunella 属的 73 个样本的基因组重测序数据进行了组合分析，以研究种群结构、人口动态、近亲繁殖、基因渗入和遗传负荷。种群结构与繁殖类型（即有性和无融合生殖）相关，并且在有性繁殖种群内存在明显的分化。其中一个有性繁殖亚种群的有效种群数量最近下降到约 1000 个，导致近亲繁殖程度很高。特别是，我们发现野生和栽培种群的生态位有 58%重叠，并且在野生样本中存在广泛的基因渗入来自栽培种群。有趣的是，基因渗入模式和遗传负荷的积累可能受到繁殖类型的影响。在野生无融合生殖样本中，渗入的区域主要是杂合的，并且全基因组有害变异隐藏在杂合状态下。相比之下，野生有性繁殖样本携带更高的隐性有害负担。此外，我们还发现有性繁殖样本是自交不亲和的，这阻止了通过自交降低遗传多样性。我们的群体基因组分析为不同的繁殖类型提供了具体的保护建议和监测建议。这项研究突出了柑橘野生近缘种的基因组景观，并为作物野生近缘种的保护提供了建议。
