Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding
Abstract Background Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a significant decrease in gen...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | deu |
| Published: |
BMC
2019-06-01
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| Series: | Genetics Selection Evolution |
| Online Access: | http://link.springer.com/article/10.1186/s12711-019-0468-4 |
| _version_ | 1819169005846396928 |
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| author | Jonathan D’Ambrosio Florence Phocas Pierrick Haffray Anastasia Bestin Sophie Brard-Fudulea Charles Poncet Edwige Quillet Nicolas Dechamp Clémence Fraslin Mathieu Charles Mathilde Dupont-Nivet |
| author_facet | Jonathan D’Ambrosio Florence Phocas Pierrick Haffray Anastasia Bestin Sophie Brard-Fudulea Charles Poncet Edwige Quillet Nicolas Dechamp Clémence Fraslin Mathieu Charles Mathilde Dupont-Nivet |
| author_sort | Jonathan D’Ambrosio |
| collection | DOAJ |
| description | Abstract Background Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a significant decrease in genetic variability due to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacities of populations facing change(s) in the environment. Thus, it is important to evaluate the impact of selection practices on genetic diversity to limit future inbreeding. The current study presents an analysis of genetic diversity within and between six French rainbow trout (Oncorhynchus mykiss) experimental or commercial lines based on a medium-density single nucleotide polymorphism (SNP) chip and various molecular genetic indicators: fixation index (F ST), linkage disequilibrium (LD), effective population size (N e ) and inbreeding coefficient derived from runs of homozygosity (ROH). Results Our results showed a moderate level of genetic differentiation between selected lines (F ST ranging from 0.08 to 0.15). LD declined rapidly over the first 100 kb, but then remained quite high at long distances, leading to low estimates of N e in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreeding estimates that varied from 10.0% in an unselected experimental line to 19.5% in a commercial line, and which are clearly higher than corresponding estimates in ruminants or pigs. In addition, strong variations in LD and inbreeding were observed along the genome that may be due to differences in local rates of recombination or due to key genes that tended to have fixed favorable alleles for domestication or production. Conclusions This is the first report on ROH for any aquaculture species. Inbreeding appeared to be moderate to high in the six French rainbow trout lines, due to founder effects at the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efficient management of inbreeding is a major goal in breeding programs to ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreeding builds up in the fish genome. |
| first_indexed | 2024-12-22T19:12:38Z |
| format | Article |
| id | doaj.art-41a8f239d3c040648f6ef42e302ff903 |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-12-22T19:12:38Z |
| publishDate | 2019-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-41a8f239d3c040648f6ef42e302ff9032022-12-21T18:15:37ZdeuBMCGenetics Selection Evolution1297-96862019-06-0151111510.1186/s12711-019-0468-4Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breedingJonathan D’Ambrosio0Florence Phocas1Pierrick Haffray2Anastasia Bestin3Sophie Brard-Fudulea4Charles Poncet5Edwige Quillet6Nicolas Dechamp7Clémence Fraslin8Mathieu Charles9Mathilde Dupont-Nivet10GABI, INRA, AgroParisTech, Université Paris-SaclayGABI, INRA, AgroParisTech, Université Paris-SaclaySYSAAF Section AquacoleSYSAAF Section AquacoleSYSAAF Section Avicole, Centre INRA Val de LoireGDEC, INRA, Université Clermont-AuvergneGABI, INRA, AgroParisTech, Université Paris-SaclayGABI, INRA, AgroParisTech, Université Paris-SaclayGABI, INRA, AgroParisTech, Université Paris-SaclayGABI, INRA, AgroParisTech, Université Paris-SaclayGABI, INRA, AgroParisTech, Université Paris-SaclayAbstract Background Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a significant decrease in genetic variability due to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacities of populations facing change(s) in the environment. Thus, it is important to evaluate the impact of selection practices on genetic diversity to limit future inbreeding. The current study presents an analysis of genetic diversity within and between six French rainbow trout (Oncorhynchus mykiss) experimental or commercial lines based on a medium-density single nucleotide polymorphism (SNP) chip and various molecular genetic indicators: fixation index (F ST), linkage disequilibrium (LD), effective population size (N e ) and inbreeding coefficient derived from runs of homozygosity (ROH). Results Our results showed a moderate level of genetic differentiation between selected lines (F ST ranging from 0.08 to 0.15). LD declined rapidly over the first 100 kb, but then remained quite high at long distances, leading to low estimates of N e in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreeding estimates that varied from 10.0% in an unselected experimental line to 19.5% in a commercial line, and which are clearly higher than corresponding estimates in ruminants or pigs. In addition, strong variations in LD and inbreeding were observed along the genome that may be due to differences in local rates of recombination or due to key genes that tended to have fixed favorable alleles for domestication or production. Conclusions This is the first report on ROH for any aquaculture species. Inbreeding appeared to be moderate to high in the six French rainbow trout lines, due to founder effects at the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efficient management of inbreeding is a major goal in breeding programs to ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreeding builds up in the fish genome.http://link.springer.com/article/10.1186/s12711-019-0468-4 |
| spellingShingle | Jonathan D’Ambrosio Florence Phocas Pierrick Haffray Anastasia Bestin Sophie Brard-Fudulea Charles Poncet Edwige Quillet Nicolas Dechamp Clémence Fraslin Mathieu Charles Mathilde Dupont-Nivet Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding Genetics Selection Evolution |
| title | Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding |
| title_full | Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding |
| title_fullStr | Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding |
| title_full_unstemmed | Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding |
| title_short | Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding |
| title_sort | genome wide estimates of genetic diversity inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding |
| url | http://link.springer.com/article/10.1186/s12711-019-0468-4 |
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