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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...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10179493/ https://www.ncbi.nlm.nih.gov/pubmed/37175981 http://dx.doi.org/10.3390/ijms24098276 |
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author | Kulyan, Raisa Samarina, Lidiia Shkhalakhova, Ruset Kuleshov, Alexandr Ukhatova, Yulia Antonova, Olga Koninskaya, Natalia Matskiv, Alexandra Malyarovskaya, Valentina Ryndin, Alexey |
author_facet | Kulyan, Raisa Samarina, Lidiia Shkhalakhova, Ruset Kuleshov, Alexandr Ukhatova, Yulia Antonova, Olga Koninskaya, Natalia Matskiv, Alexandra Malyarovskaya, Valentina Ryndin, Alexey |
author_sort | Kulyan, Raisa |
collection | PubMed |
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 Citrus. 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. |
format | Online Article Text |
id | pubmed-10179493 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-101794932023-05-13 InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus Kulyan, Raisa Samarina, Lidiia Shkhalakhova, Ruset Kuleshov, Alexandr Ukhatova, Yulia Antonova, Olga Koninskaya, Natalia Matskiv, Alexandra Malyarovskaya, Valentina Ryndin, Alexey Int J Mol Sci Article 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 Citrus. 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. MDPI 2023-05-05 /pmc/articles/PMC10179493/ /pubmed/37175981 http://dx.doi.org/10.3390/ijms24098276 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Kulyan, Raisa Samarina, Lidiia Shkhalakhova, Ruset Kuleshov, Alexandr Ukhatova, Yulia Antonova, Olga Koninskaya, Natalia Matskiv, Alexandra Malyarovskaya, Valentina Ryndin, Alexey InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus |
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 | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10179493/ https://www.ncbi.nlm.nih.gov/pubmed/37175981 http://dx.doi.org/10.3390/ijms24098276 |
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