A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species
Abstract Background Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide associati...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | deu |
| Published: |
BMC
2021-01-01
|
| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-020-00599-7 |
| _version_ | 1818844910927740928 |
|---|---|
| author | Wim Gorssen Roel Meyermans Steven Janssens Nadine Buys |
| author_facet | Wim Gorssen Roel Meyermans Steven Janssens Nadine Buys |
| author_sort | Wim Gorssen |
| collection | DOAJ |
| description | Abstract Background Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. Results The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep). Conclusions We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository. |
| first_indexed | 2024-12-19T05:21:17Z |
| format | Article |
| id | doaj.art-c95c71b65cf144c68ed25d53a6e1f800 |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-12-19T05:21:17Z |
| publishDate | 2021-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-c95c71b65cf144c68ed25d53a6e1f8002022-12-21T20:34:30ZdeuBMCGenetics Selection Evolution1297-96862021-01-0153111010.1186/s12711-020-00599-7A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet speciesWim Gorssen0Roel Meyermans1Steven Janssens2Nadine Buys3Livestock Genetics, Department of Biosystems, KU LeuvenLivestock Genetics, Department of Biosystems, KU LeuvenLivestock Genetics, Department of Biosystems, KU LeuvenLivestock Genetics, Department of Biosystems, KU LeuvenAbstract Background Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. Results The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep). Conclusions We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.https://doi.org/10.1186/s12711-020-00599-7 |
| spellingShingle | Wim Gorssen Roel Meyermans Steven Janssens Nadine Buys A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species Genetics Selection Evolution |
| title | A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species |
| title_full | A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species |
| title_fullStr | A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species |
| title_full_unstemmed | A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species |
| title_short | A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species |
| title_sort | publicly available repository of roh islands reveals signatures of selection in different livestock and pet species |
| url | https://doi.org/10.1186/s12711-020-00599-7 |
| work_keys_str_mv | AT wimgorssen apubliclyavailablerepositoryofrohislandsrevealssignaturesofselectionindifferentlivestockandpetspecies AT roelmeyermans apubliclyavailablerepositoryofrohislandsrevealssignaturesofselectionindifferentlivestockandpetspecies AT stevenjanssens apubliclyavailablerepositoryofrohislandsrevealssignaturesofselectionindifferentlivestockandpetspecies AT nadinebuys apubliclyavailablerepositoryofrohislandsrevealssignaturesofselectionindifferentlivestockandpetspecies AT wimgorssen publiclyavailablerepositoryofrohislandsrevealssignaturesofselectionindifferentlivestockandpetspecies AT roelmeyermans publiclyavailablerepositoryofrohislandsrevealssignaturesofselectionindifferentlivestockandpetspecies AT stevenjanssens publiclyavailablerepositoryofrohislandsrevealssignaturesofselectionindifferentlivestockandpetspecies AT nadinebuys publiclyavailablerepositoryofrohislandsrevealssignaturesofselectionindifferentlivestockandpetspecies |