Development of Polymorphic Microsatellite Markers and Identification of Applications for Wild Walnut (<i>Juglans regia</i> L.) in Middle Asia
The common walnut (<i>Juglans regia</i> L.), a species of significant economic and ecological importance, along with its variant, holds developmental value. Simple sequence repeat (SSR) markers are used as an effective method for material identification due to their co-dominant inheritan...
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MDPI AG
2023-10-01
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| Online Access: | https://www.mdpi.com/1424-2818/15/10/1073 |
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| author | Xuerong Li Xiyong Wang Zhijun Cui Wei Shi Junhua Huang Jiancheng Wang |
| author_facet | Xuerong Li Xiyong Wang Zhijun Cui Wei Shi Junhua Huang Jiancheng Wang |
| author_sort | Xuerong Li |
| collection | DOAJ |
| description | The common walnut (<i>Juglans regia</i> L.), a species of significant economic and ecological importance, along with its variant, holds developmental value. Simple sequence repeat (SSR) markers are used as an effective method for material identification due to their co-dominant inheritance. In this work, a total of 357629 SSR loci were searched based on previously published walnut genome sequences, with a density of 662.28 (SSRs/Mb). The majority of all these loci were found to be single nucleotide A/T (58.49%), followed by the dinucleotide AT (19.48%). Based on the results of genome-wide SSR site design, 22 effective primer pairs were designed and screened to analyze the genetic diversity of 48 wild walnut samples from three countries. Each locus had an average of 5.17 effective alleles (Ne), with an average polymorphism information content (PIC) of 0.71, average heterozygosity (He) of 0.52, and average genetic differentiation index (Fst) of 0.09. The analysis of 48 wild walnut samples from three countries (Kyrgyzstan, Tajikistan, and China) using the unweighted pairwise clustering method and arithmetic mean (UPGMA) along with principal coordinate analysis revealed the division of all samples into three groups. In summary, these novel SSR markers serve as a reference for the identification of wild walnut germplasm in Central Asia and for the development and utilization of wild walnut seed resources. |
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| id | doaj.art-8bd0965d6cd04e21b36c1fae87794564 |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-10T21:18:43Z |
| publishDate | 2023-10-01 |
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| series | Diversity |
| spelling | doaj.art-8bd0965d6cd04e21b36c1fae877945642023-11-19T16:14:41ZengMDPI AGDiversity1424-28182023-10-011510107310.3390/d15101073Development of Polymorphic Microsatellite Markers and Identification of Applications for Wild Walnut (<i>Juglans regia</i> L.) in Middle AsiaXuerong Li0Xiyong Wang1Zhijun Cui2Wei Shi3Junhua Huang4Jiancheng Wang5College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830052, ChinaState Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, ChinaGongliu County Forestry and Steppe Bureau, Gongliu 835400, ChinaCollege of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830052, ChinaCollege of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830052, ChinaState Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, ChinaThe common walnut (<i>Juglans regia</i> L.), a species of significant economic and ecological importance, along with its variant, holds developmental value. Simple sequence repeat (SSR) markers are used as an effective method for material identification due to their co-dominant inheritance. In this work, a total of 357629 SSR loci were searched based on previously published walnut genome sequences, with a density of 662.28 (SSRs/Mb). The majority of all these loci were found to be single nucleotide A/T (58.49%), followed by the dinucleotide AT (19.48%). Based on the results of genome-wide SSR site design, 22 effective primer pairs were designed and screened to analyze the genetic diversity of 48 wild walnut samples from three countries. Each locus had an average of 5.17 effective alleles (Ne), with an average polymorphism information content (PIC) of 0.71, average heterozygosity (He) of 0.52, and average genetic differentiation index (Fst) of 0.09. The analysis of 48 wild walnut samples from three countries (Kyrgyzstan, Tajikistan, and China) using the unweighted pairwise clustering method and arithmetic mean (UPGMA) along with principal coordinate analysis revealed the division of all samples into three groups. In summary, these novel SSR markers serve as a reference for the identification of wild walnut germplasm in Central Asia and for the development and utilization of wild walnut seed resources.https://www.mdpi.com/1424-2818/15/10/1073<i>Juglans regia</i>SSR markersspecies identificationwhole genomegenetic diversity |
| spellingShingle | Xuerong Li Xiyong Wang Zhijun Cui Wei Shi Junhua Huang Jiancheng Wang Development of Polymorphic Microsatellite Markers and Identification of Applications for Wild Walnut (<i>Juglans regia</i> L.) in Middle Asia Diversity <i>Juglans regia</i> SSR markers species identification whole genome genetic diversity |
| title | Development of Polymorphic Microsatellite Markers and Identification of Applications for Wild Walnut (<i>Juglans regia</i> L.) in Middle Asia |
| title_full | Development of Polymorphic Microsatellite Markers and Identification of Applications for Wild Walnut (<i>Juglans regia</i> L.) in Middle Asia |
| title_fullStr | Development of Polymorphic Microsatellite Markers and Identification of Applications for Wild Walnut (<i>Juglans regia</i> L.) in Middle Asia |
| title_full_unstemmed | Development of Polymorphic Microsatellite Markers and Identification of Applications for Wild Walnut (<i>Juglans regia</i> L.) in Middle Asia |
| title_short | Development of Polymorphic Microsatellite Markers and Identification of Applications for Wild Walnut (<i>Juglans regia</i> L.) in Middle Asia |
| title_sort | development of polymorphic microsatellite markers and identification of applications for wild walnut i juglans regia i l in middle asia |
| topic | <i>Juglans regia</i> SSR markers species identification whole genome genetic diversity |
| url | https://www.mdpi.com/1424-2818/15/10/1073 |
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