Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case of <i>Seriola lalandi</i>
Developing sound breeding programs for aquaculture species may be challenging when matings cannot be controlled due to communal spawning. We developed a genotyping-by-sequencing marker panel of 300 SNPs for parentage testing and sex determination by using data from an in-house reference genome as we...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/13/5/913 |
| _version_ | 1797615894208184320 |
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| author | Víctor Martinez Nicolas Galarce Alvin Setiawan |
| author_facet | Víctor Martinez Nicolas Galarce Alvin Setiawan |
| author_sort | Víctor Martinez |
| collection | DOAJ |
| description | Developing sound breeding programs for aquaculture species may be challenging when matings cannot be controlled due to communal spawning. We developed a genotyping-by-sequencing marker panel of 300 SNPs for parentage testing and sex determination by using data from an in-house reference genome as well as a 90 K SNP genotyping array based on different populations of yellowtail kingfish (<i>Seriola lalandi</i>). The minimum and maximum distance between adjacent marker pairs were 0.7 Mb and 13 Mb, respectively, with an average marker spacing of 2 Mb. Weak evidence of the linkage disequilibrium between adjacent marker pairs was found. The results showed high panel performance for parental assignment, with probability exclusion values equaling 1. The rate of false positives when using cross-population data was null. A skewed distribution of genetic contributions by dominant females was observed, thus increasing the risk of higher rates of inbreeding in subsequent captive generations when no parentage data are used. All these results are discussed in the context of breeding program design, using this marker panel to increase the sustainability of this aquaculture resource. |
| first_indexed | 2024-03-11T07:32:24Z |
| format | Article |
| id | doaj.art-f4b505223d224b47b9f4363f5cd0dc1a |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-11T07:32:24Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-f4b505223d224b47b9f4363f5cd0dc1a2023-11-17T07:14:01ZengMDPI AGAnimals2076-26152023-03-0113591310.3390/ani13050913Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case of <i>Seriola lalandi</i>Víctor Martinez0Nicolas Galarce1Alvin Setiawan2INBIOGEN, Department of Animal Production, Faculty of Veterinary Sciences, Universidad de Chile, Avda. Santa Rosa 11735, Santiago 8820808, ChileEscuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, ChileNorthland Aquaculture Centre, National Institute of Water and Atmospheric Research, Ruakaka 0116, New ZealandDeveloping sound breeding programs for aquaculture species may be challenging when matings cannot be controlled due to communal spawning. We developed a genotyping-by-sequencing marker panel of 300 SNPs for parentage testing and sex determination by using data from an in-house reference genome as well as a 90 K SNP genotyping array based on different populations of yellowtail kingfish (<i>Seriola lalandi</i>). The minimum and maximum distance between adjacent marker pairs were 0.7 Mb and 13 Mb, respectively, with an average marker spacing of 2 Mb. Weak evidence of the linkage disequilibrium between adjacent marker pairs was found. The results showed high panel performance for parental assignment, with probability exclusion values equaling 1. The rate of false positives when using cross-population data was null. A skewed distribution of genetic contributions by dominant females was observed, thus increasing the risk of higher rates of inbreeding in subsequent captive generations when no parentage data are used. All these results are discussed in the context of breeding program design, using this marker panel to increase the sustainability of this aquaculture resource.https://www.mdpi.com/2076-2615/13/5/913<i>seriola</i>inbreedinggenotyping-by-sequencing |
| spellingShingle | Víctor Martinez Nicolas Galarce Alvin Setiawan Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case of <i>Seriola lalandi</i> Animals <i>seriola</i> inbreeding genotyping-by-sequencing |
| title | Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case of <i>Seriola lalandi</i> |
| title_full | Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case of <i>Seriola lalandi</i> |
| title_fullStr | Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case of <i>Seriola lalandi</i> |
| title_full_unstemmed | Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case of <i>Seriola lalandi</i> |
| title_short | Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case of <i>Seriola lalandi</i> |
| title_sort | developing methods for maintaining genetic diversity in novel aquaculture species the case of i seriola lalandi i |
| topic | <i>seriola</i> inbreeding genotyping-by-sequencing |
| url | https://www.mdpi.com/2076-2615/13/5/913 |
| work_keys_str_mv | AT victormartinez developingmethodsformaintaininggeneticdiversityinnovelaquaculturespeciesthecaseofiseriolalalandii AT nicolasgalarce developingmethodsformaintaininggeneticdiversityinnovelaquaculturespeciesthecaseofiseriolalalandii AT alvinsetiawan developingmethodsformaintaininggeneticdiversityinnovelaquaculturespeciesthecaseofiseriolalalandii |