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Genomic conservation of crop wild relatives: A case study of citrus

文献类型： 外文期刊

作者： Wang, Nan 1 ; Cao, Shuo 1 ; Liu, Zhongjie 2 ; Xiao, Hua 2 ; Hu, Jianbing 1 ; Xu, Xiaodong 2 ; Chen, Peng 4 ; Ma, Zhiyao 2 ; Ye, Junli 1 ; Chai, Lijun 1 ; Guo, Wenwu 1 ; Larkin, Robert M. M. 1 ; Xu, Qiang 1 ; Morrell, Peter L. L. 5 ; Zhou, Yongfeng 2 ; Deng, Xiuxin 1 ;

作者机构： 1.Huazhong Agr Univ, Natl Key Lab Germplasm Innovat & Utilizat Hort Cro, Wuhan, Peoples R China

2.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch, Minist Agr & Rural Affairs,Key Lab Synthet Biol,Gu, Shenzhen, Peoples R China

3.Hubei Hongshan Lab, Wuhan, Peoples R China

4.Hunan Acad Agr Sci, Inst Hort Res, Changsha, Peoples R China

5.Univ Minnesota, Dept Agron & Plant Genet, St Paul, MN USA

6.Chinese Acad Trop Agr Sci, Trop Crops Genet Resources Inst, State Key Lab Trop Crop Breeding, Haikou, Peoples R China

期刊名称：PLOS GENETICS （ 影响因子：4.5； 五年影响因子：5.5 ）

ISSN： 1553-7404

年卷期： 2023 年 19 卷 6 期

页码：

收录情况： SCI

摘要： 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 similar 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.

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