Genomic resequencing reveals genetic diversity, population structure, and core collection of durian germplasm
Abstract Durio zibethinus Murr. is a tropical fruit crop of growing global importance, prized for its unique flavor and nutritional value. Yet only a narrow genetic base has been utilized in breeding efforts. We performed whole-genome resequencing of 114 diverse durian accessions collected in China,...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-08-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08715-3 |
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| _version_ | 1849226001565876224 |
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| author | Yiwang Zhong Liying Feng Huidong Deng Xiaohao Ji Jing Zhang Yangyang Sun Peifan Lin Yang Qiao Shenghua Xie Haibo Wang Lijun Guo Xuejie Feng |
| author_facet | Yiwang Zhong Liying Feng Huidong Deng Xiaohao Ji Jing Zhang Yangyang Sun Peifan Lin Yang Qiao Shenghua Xie Haibo Wang Lijun Guo Xuejie Feng |
| author_sort | Yiwang Zhong |
| collection | DOAJ |
| description | Abstract Durio zibethinus Murr. is a tropical fruit crop of growing global importance, prized for its unique flavor and nutritional value. Yet only a narrow genetic base has been utilized in breeding efforts. We performed whole-genome resequencing of 114 diverse durian accessions collected in China, identifying over 39 million high-quality SNPs across the genome, revealing genome-wide patterns of diversity. Population structure analysis revealed three major genetic clusters, supported by PCA, phylogenetic analysis, and STRUCTURE modeling. Genome-wide scans identified candidate selective sweeps, and several genes potentially under selection. From the 114 accessions, we further identified a core collection of representative durian germplasms capturing the majority of the species’ genetic diversity. This subset includes both elite cultivars and genetically distinct individuals. Our study provides insights into the genetic diversity and population structure of cultivated durian. The defined core collection and genomic variation map establish a valuable resource for durian breeding and germplasm conservation. These findings will facilitate the identification of superior alleles for important traits and guide future durian improvement programs. |
| format | Article |
| id | doaj-art-941d9fde62c349f480ad788ab05ab2c8 |
| institution | Kabale University |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-941d9fde62c349f480ad788ab05ab2c82025-08-24T11:46:12ZengNature PortfolioCommunications Biology2399-36422025-08-018111110.1038/s42003-025-08715-3Genomic resequencing reveals genetic diversity, population structure, and core collection of durian germplasmYiwang Zhong0Liying Feng1Huidong Deng2Xiaohao Ji3Jing Zhang4Yangyang Sun5Peifan Lin6Yang Qiao7Shenghua Xie8Haibo Wang9Lijun Guo10Xuejie Feng11Sanya Institute, Hainan Academy of Agricultural SciencesYazhouwan National LaboratoryInstitute of Tropical Fruit Trees, Hainan Academy of Agricultural SciencesResearch Institute of Pomology, Chinese Academy of Agricultural SciencesSanya Institute, Hainan Academy of Agricultural SciencesSanya Institute, Hainan Academy of Agricultural SciencesKey Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of SciencesInstitute of Tropical Fruit Trees, Hainan Academy of Agricultural SciencesSanya Institute, Hainan Academy of Agricultural SciencesResearch Institute of Pomology, Chinese Academy of Agricultural SciencesInstitute of Tropical Fruit Trees, Hainan Academy of Agricultural SciencesSanya Institute, Hainan Academy of Agricultural SciencesAbstract Durio zibethinus Murr. is a tropical fruit crop of growing global importance, prized for its unique flavor and nutritional value. Yet only a narrow genetic base has been utilized in breeding efforts. We performed whole-genome resequencing of 114 diverse durian accessions collected in China, identifying over 39 million high-quality SNPs across the genome, revealing genome-wide patterns of diversity. Population structure analysis revealed three major genetic clusters, supported by PCA, phylogenetic analysis, and STRUCTURE modeling. Genome-wide scans identified candidate selective sweeps, and several genes potentially under selection. From the 114 accessions, we further identified a core collection of representative durian germplasms capturing the majority of the species’ genetic diversity. This subset includes both elite cultivars and genetically distinct individuals. Our study provides insights into the genetic diversity and population structure of cultivated durian. The defined core collection and genomic variation map establish a valuable resource for durian breeding and germplasm conservation. These findings will facilitate the identification of superior alleles for important traits and guide future durian improvement programs.https://doi.org/10.1038/s42003-025-08715-3 |
| spellingShingle | Yiwang Zhong Liying Feng Huidong Deng Xiaohao Ji Jing Zhang Yangyang Sun Peifan Lin Yang Qiao Shenghua Xie Haibo Wang Lijun Guo Xuejie Feng Genomic resequencing reveals genetic diversity, population structure, and core collection of durian germplasm Communications Biology |
| title | Genomic resequencing reveals genetic diversity, population structure, and core collection of durian germplasm |
| title_full | Genomic resequencing reveals genetic diversity, population structure, and core collection of durian germplasm |
| title_fullStr | Genomic resequencing reveals genetic diversity, population structure, and core collection of durian germplasm |
| title_full_unstemmed | Genomic resequencing reveals genetic diversity, population structure, and core collection of durian germplasm |
| title_short | Genomic resequencing reveals genetic diversity, population structure, and core collection of durian germplasm |
| title_sort | genomic resequencing reveals genetic diversity population structure and core collection of durian germplasm |
| url | https://doi.org/10.1038/s42003-025-08715-3 |
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