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.
Bibliographical noteFunding Information:
This work was funded by the National Key Research and Development Program of China (Nos. 2021YFD1200202) to L.J.C., the Special Project for External Science and Technology Cooperation of Science and Technology Department of Yunnan Province (202003AD150014) to X.X.D., the Fund of the Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations (PSESP2021F10) to Y.F.Z. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank the Chinese Virtual Herbarium for providing the collection information for Fortunella. We would also like to thank Dr. Sanwen Huang (Chinese Academy of Tropical Agricultural Sciences) and Dr. Li Lei (Joint Genome Institute) for comments and discussions during the project.
© 2023 Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.