Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

doi:10.1016/j.pld.2024.03.006

Plant Diversity ›› 2024, Vol. 46 ›› Issue (03): 294-308.DOI: 10.1016/j.pld.2024.03.006

• Articles • 上一篇

Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

Zhen Yang^a, Lisong Liang^a, Weibo Xiang^b,c, Lujun Wang^d, Qinghua Ma^a, Zhaoshan Wang^a

a. Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
b. National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing 100083, China;
c. Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang 443133, China;
d. Research Institute of Economic Forest Cultivation and Processing, Anhui Academy of Forestry, Hefei 230031, China

收稿日期:2024-01-20 修回日期:2024-03-23 发布日期:2024-05-20
通讯作者: Qinghua Ma,E-mail:mqhmary@caf.ac.cn;Zhaoshan Wang,E-mail:w@caf.ac.cn
基金资助:
We sincerely thank Guowei Chen (Institute of Microbiology, Chinese Academy of Sciences) and Liya Dou (Beijing University of Chemical Technology) for their helpful discussions and guidance. This work was supported by the National Natural Science Foundation of China (Grant No. 32101541) and the National Key R&D Program of China (Grant No. 2022YFD2200400).

Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

Zhen Yang^a, Lisong Liang^a, Weibo Xiang^b,c, Lujun Wang^d, Qinghua Ma^a, Zhaoshan Wang^a

a. Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
b. National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing 100083, China;
c. Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang 443133, China;
d. Research Institute of Economic Forest Cultivation and Processing, Anhui Academy of Forestry, Hefei 230031, China

Received:2024-01-20 Revised:2024-03-23 Published:2024-05-20
Contact: Qinghua Ma,E-mail:mqhmary@caf.ac.cn;Zhaoshan Wang,E-mail:w@caf.ac.cn
Supported by:
We sincerely thank Guowei Chen (Institute of Microbiology, Chinese Academy of Sciences) and Liya Dou (Beijing University of Chemical Technology) for their helpful discussions and guidance. This work was supported by the National Natural Science Foundation of China (Grant No. 32101541) and the National Key R&D Program of China (Grant No. 2022YFD2200400).

摘要/Abstract

摘要： Global climate change has increased concerns regarding biodiversity loss. However, many key conservation issues still required further research, including demographic history, deleterious mutation load, adaptive evolution, and putative introgression. Here we generated the first chromosome-level genome of the endangered Chinese hazelnut, Corylus chinensis, and compared the genomic signatures with its sympatric widespread C. kwechowensis-C. yunnanensis complex. We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation. Population genomics revealed that both C. chinensis and the C. kwechowensis-C. yunnanensis complex had diverged into two genetic lineages, forming a consistent pattern of southwestern-northern differentiation. Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene, whereas the widespread northern lineages have remained stable (C. chinensis) or have even recovered from population bottlenecks (C. kwechowensis-C. yunnanensis complex) during the Quaternary. Compared with C. kwechowensis-C. yunnanensis complex, C. chinensis showed significantly lower genomic diversity and higher inbreeding level. However, C. chinensis carried significantly fewer deleterious mutations than C. kwechowensis-C. yunnanensis complex, as more effective purging selection reduced the accumulation of homozygous variants. We also detected signals of positive selection and adaptive introgression in different lineages, which facilitated the accumulation of favorable variants and formation of local adaptation. Hence, both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C. chinensis. Overall, our study provides critical insights into lineage differentiation, local adaptation, and the potential for future recovery of endangered trees.

关键词: Conservation genomics, Demographic history, Inbreeding, Genetic load, Runs of homozygosity, Local adaptation

Abstract: Global climate change has increased concerns regarding biodiversity loss. However, many key conservation issues still required further research, including demographic history, deleterious mutation load, adaptive evolution, and putative introgression. Here we generated the first chromosome-level genome of the endangered Chinese hazelnut, Corylus chinensis, and compared the genomic signatures with its sympatric widespread C. kwechowensis-C. yunnanensis complex. We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation. Population genomics revealed that both C. chinensis and the C. kwechowensis-C. yunnanensis complex had diverged into two genetic lineages, forming a consistent pattern of southwestern-northern differentiation. Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene, whereas the widespread northern lineages have remained stable (C. chinensis) or have even recovered from population bottlenecks (C. kwechowensis-C. yunnanensis complex) during the Quaternary. Compared with C. kwechowensis-C. yunnanensis complex, C. chinensis showed significantly lower genomic diversity and higher inbreeding level. However, C. chinensis carried significantly fewer deleterious mutations than C. kwechowensis-C. yunnanensis complex, as more effective purging selection reduced the accumulation of homozygous variants. We also detected signals of positive selection and adaptive introgression in different lineages, which facilitated the accumulation of favorable variants and formation of local adaptation. Hence, both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C. chinensis. Overall, our study provides critical insights into lineage differentiation, local adaptation, and the potential for future recovery of endangered trees.

Key words: Conservation genomics, Demographic history, Inbreeding, Genetic load, Runs of homozygosity, Local adaptation

Zhen Yang, Lisong Liang, Weibo Xiang, Lujun Wang, Qinghua Ma, Zhaoshan Wang. Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis[J]. Plant Diversity, 2024, 46(03): 294-308.

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Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

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