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Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer
Deer genera around the globe are threatened by anthropogenic interference. The translocation of alien species and their subsequent genetic introgression into indigenous deer populations is particularly harmful to the species of greatest conservation concern. Products derived from deer, including ven...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8975116/ https://www.ncbi.nlm.nih.gov/pubmed/35363791 http://dx.doi.org/10.1371/journal.pone.0265311 |
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author | Hsiao, Chen Lin, Hsin-Hung Kang, Shann-Ren Hung, Chien-Yi Sun, Pei-Yu Yu, Chieh-Cheng Toh, Kok-Lin Yu, Pei-Ju Ju, Yu-Ten |
author_facet | Hsiao, Chen Lin, Hsin-Hung Kang, Shann-Ren Hung, Chien-Yi Sun, Pei-Yu Yu, Chieh-Cheng Toh, Kok-Lin Yu, Pei-Ju Ju, Yu-Ten |
author_sort | Hsiao, Chen |
collection | PubMed |
description | Deer genera around the globe are threatened by anthropogenic interference. The translocation of alien species and their subsequent genetic introgression into indigenous deer populations is particularly harmful to the species of greatest conservation concern. Products derived from deer, including venison and antler velvet, are also at risk of fraudulent labeling. The current molecular markers used to genetically identify deer species were developed from genome sequences and have limited applicability for cross-species amplification. The absence of efficacious diagnostic techniques for identifying deer species has hampered conservation and wildlife crime investigation efforts. Expressed sequence tag-simple sequence repeat (EST-SSR) markers are reliable tools for individual and species identification, especially in terms of cross-species genotyping. We conducted transcriptome sequencing of sambar (Rusa unicolor) antler velvet and acquired 11,190 EST-SSRs from 65,074 newly assembled unigenes. We identified a total of 55 unambiguous amplicons in sambar (n = 45), which were selected as markers to evaluate cross-species genotyping in sika deer (Cervus nippon, n = 30) and red deer (Cervus elaphus, n = 46), resulting in cross-species amplification rates of 94.5% and 89.1%, respectively. Based on polymorphic information content (>0.25) and genotyping fidelity, we selected 16 of these EST-SSRs for species identification. This marker set revealed significant genetic differentiation based on the fixation index and genetic distance values. Principal coordinate analysis and STRUCTURE analysis revealed distinct clusters of species and clearly identified red-sika hybrids. These markers showed applicability across different genera and proved suitable for identification and phylogenetic analyses across deer species. |
format | Online Article Text |
id | pubmed-8975116 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-89751162022-04-02 Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer Hsiao, Chen Lin, Hsin-Hung Kang, Shann-Ren Hung, Chien-Yi Sun, Pei-Yu Yu, Chieh-Cheng Toh, Kok-Lin Yu, Pei-Ju Ju, Yu-Ten PLoS One Research Article Deer genera around the globe are threatened by anthropogenic interference. The translocation of alien species and their subsequent genetic introgression into indigenous deer populations is particularly harmful to the species of greatest conservation concern. Products derived from deer, including venison and antler velvet, are also at risk of fraudulent labeling. The current molecular markers used to genetically identify deer species were developed from genome sequences and have limited applicability for cross-species amplification. The absence of efficacious diagnostic techniques for identifying deer species has hampered conservation and wildlife crime investigation efforts. Expressed sequence tag-simple sequence repeat (EST-SSR) markers are reliable tools for individual and species identification, especially in terms of cross-species genotyping. We conducted transcriptome sequencing of sambar (Rusa unicolor) antler velvet and acquired 11,190 EST-SSRs from 65,074 newly assembled unigenes. We identified a total of 55 unambiguous amplicons in sambar (n = 45), which were selected as markers to evaluate cross-species genotyping in sika deer (Cervus nippon, n = 30) and red deer (Cervus elaphus, n = 46), resulting in cross-species amplification rates of 94.5% and 89.1%, respectively. Based on polymorphic information content (>0.25) and genotyping fidelity, we selected 16 of these EST-SSRs for species identification. This marker set revealed significant genetic differentiation based on the fixation index and genetic distance values. Principal coordinate analysis and STRUCTURE analysis revealed distinct clusters of species and clearly identified red-sika hybrids. These markers showed applicability across different genera and proved suitable for identification and phylogenetic analyses across deer species. Public Library of Science 2022-04-01 /pmc/articles/PMC8975116/ /pubmed/35363791 http://dx.doi.org/10.1371/journal.pone.0265311 Text en © 2022 Hsiao et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Hsiao, Chen Lin, Hsin-Hung Kang, Shann-Ren Hung, Chien-Yi Sun, Pei-Yu Yu, Chieh-Cheng Toh, Kok-Lin Yu, Pei-Ju Ju, Yu-Ten Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer |
title | Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer |
title_full | Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer |
title_fullStr | Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer |
title_full_unstemmed | Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer |
title_short | Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer |
title_sort | development of 16 novel est-ssr markers for species identification and cross-genus amplification in sambar, sika, and red deer |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8975116/ https://www.ncbi.nlm.nih.gov/pubmed/35363791 http://dx.doi.org/10.1371/journal.pone.0265311 |
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