Assessment of Genetic Diversity and Discovery of Molecular Markers in Durian (<i>Durio zibethinus</i> L.) in China
Durian (<i>Durio zibethinus</i> L.) is a crop of economic and health importance globally. Efforts are being made to revamp China’s only successful commercial-scale durian plantations in Hainan; however, their genetic base is unknown. Therefore, the present study was undertaken to assess...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-09-01
|
| Series: | Diversity |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1424-2818/14/9/769 |
| _version_ | 1797489293140164608 |
|---|---|
| author | Xinge Lin Xiaodi Liu Meigu Chen Hongmao Gao Zhenzhong Zhu Zheli Ding Zhaoxi Zhou |
| author_facet | Xinge Lin Xiaodi Liu Meigu Chen Hongmao Gao Zhenzhong Zhu Zheli Ding Zhaoxi Zhou |
| author_sort | Xinge Lin |
| collection | DOAJ |
| description | Durian (<i>Durio zibethinus</i> L.) is a crop of economic and health importance globally. Efforts are being made to revamp China’s only successful commercial-scale durian plantations in Hainan; however, their genetic base is unknown. Therefore, the present study was undertaken to assess the genetic base and population structure of 32 genotypes in durian plantation sites in Hainan, China, and develop simple sequence repeat (SSR) markers by whole genome sequencing through restriction site-associated DNA sequencing technology to facilitate germplasm conservation and breeding. The results from identity by state (IBS), phylogenetic tree, population structure, and principal component analysis grouped the 32 genotypes into two clusters/sub-populations. Based on IBS, genotypes in Cluster I are largely duplicated genotypes; however, results from the model-based population structure demonstrated that most of the genotypes in Sub-population II shared a common genetic background with those in Sub-population I/Cluster I. The results revealed that the core durian collection in the plantation sites in Hainan include D24, D101, MSW, JH, D163, HFH, and NLX-5. In addition, we developed a total of 79,178 SSR markers with varied lengths and amplicon sizes. The genetic diversity and population structure reported in this study will be useful for durian conservation and utilization. In addition, the discovered and developed SSR markers will lay the foundation for molecular breeding via marker-assisted selection, quantitative trait loci mapping, and candidate gene discovery and validation. |
| first_indexed | 2024-03-10T00:15:24Z |
| format | Article |
| id | doaj.art-dafa63fddb744fe0bdaa756184dbd4df |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-10T00:15:24Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diversity |
| spelling | doaj.art-dafa63fddb744fe0bdaa756184dbd4df2023-11-23T15:53:18ZengMDPI AGDiversity1424-28182022-09-0114976910.3390/d14090769Assessment of Genetic Diversity and Discovery of Molecular Markers in Durian (<i>Durio zibethinus</i> L.) in ChinaXinge Lin0Xiaodi Liu1Meigu Chen2Hongmao Gao3Zhenzhong Zhu4Zheli Ding5Zhaoxi Zhou6Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaHaikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaHaikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaHaikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaHaikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaHaikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaHaikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaDurian (<i>Durio zibethinus</i> L.) is a crop of economic and health importance globally. Efforts are being made to revamp China’s only successful commercial-scale durian plantations in Hainan; however, their genetic base is unknown. Therefore, the present study was undertaken to assess the genetic base and population structure of 32 genotypes in durian plantation sites in Hainan, China, and develop simple sequence repeat (SSR) markers by whole genome sequencing through restriction site-associated DNA sequencing technology to facilitate germplasm conservation and breeding. The results from identity by state (IBS), phylogenetic tree, population structure, and principal component analysis grouped the 32 genotypes into two clusters/sub-populations. Based on IBS, genotypes in Cluster I are largely duplicated genotypes; however, results from the model-based population structure demonstrated that most of the genotypes in Sub-population II shared a common genetic background with those in Sub-population I/Cluster I. The results revealed that the core durian collection in the plantation sites in Hainan include D24, D101, MSW, JH, D163, HFH, and NLX-5. In addition, we developed a total of 79,178 SSR markers with varied lengths and amplicon sizes. The genetic diversity and population structure reported in this study will be useful for durian conservation and utilization. In addition, the discovered and developed SSR markers will lay the foundation for molecular breeding via marker-assisted selection, quantitative trait loci mapping, and candidate gene discovery and validation.https://www.mdpi.com/1424-2818/14/9/769crop improvementgenomicsmarker-assisted selectionsingle nucleotide polymorphismsimple sequence repeats |
| spellingShingle | Xinge Lin Xiaodi Liu Meigu Chen Hongmao Gao Zhenzhong Zhu Zheli Ding Zhaoxi Zhou Assessment of Genetic Diversity and Discovery of Molecular Markers in Durian (<i>Durio zibethinus</i> L.) in China Diversity crop improvement genomics marker-assisted selection single nucleotide polymorphism simple sequence repeats |
| title | Assessment of Genetic Diversity and Discovery of Molecular Markers in Durian (<i>Durio zibethinus</i> L.) in China |
| title_full | Assessment of Genetic Diversity and Discovery of Molecular Markers in Durian (<i>Durio zibethinus</i> L.) in China |
| title_fullStr | Assessment of Genetic Diversity and Discovery of Molecular Markers in Durian (<i>Durio zibethinus</i> L.) in China |
| title_full_unstemmed | Assessment of Genetic Diversity and Discovery of Molecular Markers in Durian (<i>Durio zibethinus</i> L.) in China |
| title_short | Assessment of Genetic Diversity and Discovery of Molecular Markers in Durian (<i>Durio zibethinus</i> L.) in China |
| title_sort | assessment of genetic diversity and discovery of molecular markers in durian i durio zibethinus i l in china |
| topic | crop improvement genomics marker-assisted selection single nucleotide polymorphism simple sequence repeats |
| url | https://www.mdpi.com/1424-2818/14/9/769 |
| work_keys_str_mv | AT xingelin assessmentofgeneticdiversityanddiscoveryofmolecularmarkersindurianiduriozibethinusilinchina AT xiaodiliu assessmentofgeneticdiversityanddiscoveryofmolecularmarkersindurianiduriozibethinusilinchina AT meiguchen assessmentofgeneticdiversityanddiscoveryofmolecularmarkersindurianiduriozibethinusilinchina AT hongmaogao assessmentofgeneticdiversityanddiscoveryofmolecularmarkersindurianiduriozibethinusilinchina AT zhenzhongzhu assessmentofgeneticdiversityanddiscoveryofmolecularmarkersindurianiduriozibethinusilinchina AT zheliding assessmentofgeneticdiversityanddiscoveryofmolecularmarkersindurianiduriozibethinusilinchina AT zhaoxizhou assessmentofgeneticdiversityanddiscoveryofmolecularmarkersindurianiduriozibethinusilinchina |