Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication
Abstract Background Persian walnut, Juglans regia, occurs naturally from Greece to western China, while its closest relative, the iron walnut, Juglans sigillata, is endemic in southwest China; both species are cultivated for their nuts and wood. Here, we infer their demographic histories and the tim...
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| Format: | Article |
| Language: | English |
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BMC
2022-07-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-022-02720-z |
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| author | Ya-Mei Ding Yu Cao Wei-Ping Zhang Jun Chen Jie Liu Pan Li Susanne S. Renner Da-Yong Zhang Wei-Ning Bai |
| author_facet | Ya-Mei Ding Yu Cao Wei-Ping Zhang Jun Chen Jie Liu Pan Li Susanne S. Renner Da-Yong Zhang Wei-Ning Bai |
| author_sort | Ya-Mei Ding |
| collection | DOAJ |
| description | Abstract Background Persian walnut, Juglans regia, occurs naturally from Greece to western China, while its closest relative, the iron walnut, Juglans sigillata, is endemic in southwest China; both species are cultivated for their nuts and wood. Here, we infer their demographic histories and the time and direction of possible hybridization and introgression between them. Results We use whole-genome resequencing data, different population-genetic approaches (PSMC and GONE), and isolation-with-migration models (IMa3) on individuals from Europe, Iran, Kazakhstan, Pakistan, and China. IMa3 analyses indicate that the two species diverged from each other by 0.85 million years ago, with unidirectional gene flow from eastern J. regia and its ancestor into J. sigillata, including the shell-thickness gene. Within J. regia, a western group, located from Europe to Iran, and an eastern group with individuals from northern China, experienced dramatically declining population sizes about 80 generations ago (roughly 2400 to 4000 years), followed by an expansion at about 40 generations, while J. sigillata had a constant population size from about 100 to 20 generations ago, followed by a rapid decline. Conclusions Both J. regia and J. sigillata appear to have suffered sudden population declines during their domestication, suggesting that the bottleneck scenario of plant domestication may well apply in at least some perennial crop species. Introgression from introduced J. regia appears to have played a role in the domestication of J. sigillata. |
| first_indexed | 2024-04-13T13:56:27Z |
| format | Article |
| id | doaj.art-391f0a1b57c040f8b89274ec57224e05 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-04-13T13:56:27Z |
| publishDate | 2022-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-391f0a1b57c040f8b89274ec57224e052022-12-22T02:44:11ZengBMCGenome Biology1474-760X2022-07-0123111810.1186/s13059-022-02720-zPopulation-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domesticationYa-Mei Ding0Yu Cao1Wei-Ping Zhang2Jun Chen3Jie Liu4Pan Li5Susanne S. Renner6Da-Yong Zhang7Wei-Ning Bai8State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal UniversityState Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal UniversityState Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal UniversityState Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal UniversityCAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesThe Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang UniversityDepartment of Biology, Washington UniversityState Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal UniversityState Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal UniversityAbstract Background Persian walnut, Juglans regia, occurs naturally from Greece to western China, while its closest relative, the iron walnut, Juglans sigillata, is endemic in southwest China; both species are cultivated for their nuts and wood. Here, we infer their demographic histories and the time and direction of possible hybridization and introgression between them. Results We use whole-genome resequencing data, different population-genetic approaches (PSMC and GONE), and isolation-with-migration models (IMa3) on individuals from Europe, Iran, Kazakhstan, Pakistan, and China. IMa3 analyses indicate that the two species diverged from each other by 0.85 million years ago, with unidirectional gene flow from eastern J. regia and its ancestor into J. sigillata, including the shell-thickness gene. Within J. regia, a western group, located from Europe to Iran, and an eastern group with individuals from northern China, experienced dramatically declining population sizes about 80 generations ago (roughly 2400 to 4000 years), followed by an expansion at about 40 generations, while J. sigillata had a constant population size from about 100 to 20 generations ago, followed by a rapid decline. Conclusions Both J. regia and J. sigillata appear to have suffered sudden population declines during their domestication, suggesting that the bottleneck scenario of plant domestication may well apply in at least some perennial crop species. Introgression from introduced J. regia appears to have played a role in the domestication of J. sigillata.https://doi.org/10.1186/s13059-022-02720-zDomestication bottleneckIntrogressionIron walnutPersian walnutShell-thickness gene |
| spellingShingle | Ya-Mei Ding Yu Cao Wei-Ping Zhang Jun Chen Jie Liu Pan Li Susanne S. Renner Da-Yong Zhang Wei-Ning Bai Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication Genome Biology Domestication bottleneck Introgression Iron walnut Persian walnut Shell-thickness gene |
| title | Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication |
| title_full | Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication |
| title_fullStr | Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication |
| title_full_unstemmed | Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication |
| title_short | Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication |
| title_sort | population genomic analyses reveal bottlenecks and asymmetric introgression from persian into iron walnut during domestication |
| topic | Domestication bottleneck Introgression Iron walnut Persian walnut Shell-thickness gene |
| url | https://doi.org/10.1186/s13059-022-02720-z |
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