InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus
Citrus collections from extreme growing regions can be an important source of tolerant germplasms for the breeding of cold-tolerant varieties. However, the efficient utilization of these germplasms requires their genetic background information. Thus, efficient marker systems are necessary for the ch...
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MDPI AG
2023-05-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/9/8276 |
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| author | Raisa Kulyan Lidiia Samarina Ruset Shkhalakhova Alexandr Kuleshov Yulia Ukhatova Olga Antonova Natalia Koninskaya Alexandra Matskiv Valentina Malyarovskaya Alexey Ryndin |
| author_facet | Raisa Kulyan Lidiia Samarina Ruset Shkhalakhova Alexandr Kuleshov Yulia Ukhatova Olga Antonova Natalia Koninskaya Alexandra Matskiv Valentina Malyarovskaya Alexey Ryndin |
| author_sort | Raisa Kulyan |
| collection | DOAJ |
| description | Citrus collections from extreme growing regions can be an important source of tolerant germplasms for the breeding of cold-tolerant varieties. However, the efficient utilization of these germplasms requires their genetic background information. Thus, efficient marker systems are necessary for the characterization and identification of valuable accessions. In this study, the efficiency of 36 SCoT markers and 60 InDel markers were evaluated as part of the broad citrus collection of the Western Caucasus. The interspecific and intraspecific genetic diversity and genetic structures were analyzed for 172 accessions, including 31 species and sets of the locally derived cultivars. Single markers, such as SCoT18 (0.84), SCoT20 (0.93), SCoT23 (0.87), SCoT31 (0.88), SCoT36 (0.87) и LG 1-4 (0.94), LG 4-3 (0.86), LG 7-11 (0.98), and LG 8-10 (0.83), showed a high discriminating power, indicating the good applicability of these markers to assess intraspecific diversity of the genus <i>Citrus</i>. Overall, SCoT markers showed a higher level of polymorphism than InDel markers. According to analysis of population structure, SCoT and InDel markers showed K = 9 and K = 5 genetic clusters, respectively. The lowest levels of genetic admixtures and diversity were observed among the locally derived satsumas and lemons. The highest level of genetic admixtures was observed in the lime group. Phylogenetic relationships indicated a high level of interspecific genetic diversity but a low level of intraspecific diversity in locally derived satsumas and lemons. The results provide new insight into the origin of citrus germplasms and their distribution in colder regions. Furthermore, they are important for implementing conservation measures, controlling genetic erosion, developing breeding strategies, and improving breeding efficiency. |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T04:16:41Z |
| publishDate | 2023-05-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-f297d7e1b04548e7a58b8f3a9b2007552023-11-17T23:07:21ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-05-01249827610.3390/ijms24098276InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western CaucasusRaisa Kulyan0Lidiia Samarina1Ruset Shkhalakhova2Alexandr Kuleshov3Yulia Ukhatova4Olga Antonova5Natalia Koninskaya6Alexandra Matskiv7Valentina Malyarovskaya8Alexey Ryndin9Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, RussiaFederal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, RussiaFederal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, RussiaFederal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia“Sirius University of Science and Technology”, Olimpiyskiy Ave. b.1, 354340 Sirius, Kransnodar Region, Russia“Sirius University of Science and Technology”, Olimpiyskiy Ave. b.1, 354340 Sirius, Kransnodar Region, RussiaFederal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, RussiaFederal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, RussiaFederal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, RussiaFederal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, RussiaCitrus collections from extreme growing regions can be an important source of tolerant germplasms for the breeding of cold-tolerant varieties. However, the efficient utilization of these germplasms requires their genetic background information. Thus, efficient marker systems are necessary for the characterization and identification of valuable accessions. In this study, the efficiency of 36 SCoT markers and 60 InDel markers were evaluated as part of the broad citrus collection of the Western Caucasus. The interspecific and intraspecific genetic diversity and genetic structures were analyzed for 172 accessions, including 31 species and sets of the locally derived cultivars. Single markers, such as SCoT18 (0.84), SCoT20 (0.93), SCoT23 (0.87), SCoT31 (0.88), SCoT36 (0.87) и LG 1-4 (0.94), LG 4-3 (0.86), LG 7-11 (0.98), and LG 8-10 (0.83), showed a high discriminating power, indicating the good applicability of these markers to assess intraspecific diversity of the genus <i>Citrus</i>. Overall, SCoT markers showed a higher level of polymorphism than InDel markers. According to analysis of population structure, SCoT and InDel markers showed K = 9 and K = 5 genetic clusters, respectively. The lowest levels of genetic admixtures and diversity were observed among the locally derived satsumas and lemons. The highest level of genetic admixtures was observed in the lime group. Phylogenetic relationships indicated a high level of interspecific genetic diversity but a low level of intraspecific diversity in locally derived satsumas and lemons. The results provide new insight into the origin of citrus germplasms and their distribution in colder regions. Furthermore, they are important for implementing conservation measures, controlling genetic erosion, developing breeding strategies, and improving breeding efficiency.https://www.mdpi.com/1422-0067/24/9/8276citruscold tolerancegermplasm collectionsSCoT markersInDel markersgenetic diversity |
| spellingShingle | Raisa Kulyan Lidiia Samarina Ruset Shkhalakhova Alexandr Kuleshov Yulia Ukhatova Olga Antonova Natalia Koninskaya Alexandra Matskiv Valentina Malyarovskaya Alexey Ryndin InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus International Journal of Molecular Sciences citrus cold tolerance germplasm collections SCoT markers InDel markers genetic diversity |
| title | InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus |
| title_full | InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus |
| title_fullStr | InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus |
| title_full_unstemmed | InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus |
| title_short | InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus |
| title_sort | indel and scot markers for genetic diversity analysis in a citrus collection from the western caucasus |
| topic | citrus cold tolerance germplasm collections SCoT markers InDel markers genetic diversity |
| url | https://www.mdpi.com/1422-0067/24/9/8276 |
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