From STRs to SNPs via ddRAD‐seq: Geographic assignment of confiscated tortoises at reduced costs
Abstract Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving ar...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2022-09-01
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| Series: | Evolutionary Applications |
| Subjects: | |
| Online Access: | https://doi.org/10.1111/eva.13431 |
| _version_ | 1811183457702772736 |
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| author | Roberto Biello Mauro Zampiglia Silvia Fuselli Giulia Fabbri Roberta Bisconti Andrea Chiocchio Stefano Mazzotti Emiliano Trucchi Daniele Canestrelli Giorgio Bertorelle |
| author_facet | Roberto Biello Mauro Zampiglia Silvia Fuselli Giulia Fabbri Roberta Bisconti Andrea Chiocchio Stefano Mazzotti Emiliano Trucchi Daniele Canestrelli Giorgio Bertorelle |
| author_sort | Roberto Biello |
| collection | DOAJ |
| description | Abstract Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost‐effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD‐seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro‐area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re‐assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than €15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in‐situ of confiscated animals and their possible re‐allocation in the wild. Our methodological pipeline can easily be extended to other species. |
| first_indexed | 2024-04-11T09:47:25Z |
| format | Article |
| id | doaj.art-793ac26fbc7742a9b95e076ae3b026b2 |
| institution | Directory Open Access Journal |
| issn | 1752-4571 |
| language | English |
| last_indexed | 2024-04-11T09:47:25Z |
| publishDate | 2022-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | Evolutionary Applications |
| spelling | doaj.art-793ac26fbc7742a9b95e076ae3b026b22022-12-22T04:30:56ZengWileyEvolutionary Applications1752-45712022-09-011591344135910.1111/eva.13431From STRs to SNPs via ddRAD‐seq: Geographic assignment of confiscated tortoises at reduced costsRoberto Biello0Mauro Zampiglia1Silvia Fuselli2Giulia Fabbri3Roberta Bisconti4Andrea Chiocchio5Stefano Mazzotti6Emiliano Trucchi7Daniele Canestrelli8Giorgio Bertorelle9Department of Life Sciences and Biotechnology University of Ferrara Ferrara ItalyDepartment of Ecological and Biological Science Tuscia University Viterbo ItalyDepartment of Life Sciences and Biotechnology University of Ferrara Ferrara ItalyDepartment of Life Sciences and Biotechnology University of Ferrara Ferrara ItalyDepartment of Ecological and Biological Science Tuscia University Viterbo ItalyDepartment of Ecological and Biological Science Tuscia University Viterbo ItalyNatural History Museum Ferrara ItalyDepartment of Life Sciences and Biotechnology University of Ferrara Ferrara ItalyDepartment of Ecological and Biological Science Tuscia University Viterbo ItalyDepartment of Life Sciences and Biotechnology University of Ferrara Ferrara ItalyAbstract Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost‐effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD‐seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro‐area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re‐assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than €15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in‐situ of confiscated animals and their possible re‐allocation in the wild. Our methodological pipeline can easily be extended to other species.https://doi.org/10.1111/eva.13431assignmentinformative SNPsMediterranean tortoisesRAD sequencingreduced SNP panelTestudo hermanni |
| spellingShingle | Roberto Biello Mauro Zampiglia Silvia Fuselli Giulia Fabbri Roberta Bisconti Andrea Chiocchio Stefano Mazzotti Emiliano Trucchi Daniele Canestrelli Giorgio Bertorelle From STRs to SNPs via ddRAD‐seq: Geographic assignment of confiscated tortoises at reduced costs Evolutionary Applications assignment informative SNPs Mediterranean tortoises RAD sequencing reduced SNP panel Testudo hermanni |
| title | From STRs to SNPs via ddRAD‐seq: Geographic assignment of confiscated tortoises at reduced costs |
| title_full | From STRs to SNPs via ddRAD‐seq: Geographic assignment of confiscated tortoises at reduced costs |
| title_fullStr | From STRs to SNPs via ddRAD‐seq: Geographic assignment of confiscated tortoises at reduced costs |
| title_full_unstemmed | From STRs to SNPs via ddRAD‐seq: Geographic assignment of confiscated tortoises at reduced costs |
| title_short | From STRs to SNPs via ddRAD‐seq: Geographic assignment of confiscated tortoises at reduced costs |
| title_sort | from strs to snps via ddrad seq geographic assignment of confiscated tortoises at reduced costs |
| topic | assignment informative SNPs Mediterranean tortoises RAD sequencing reduced SNP panel Testudo hermanni |
| url | https://doi.org/10.1111/eva.13431 |
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