Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed
Gene banks, framed within the efforts for conserving animal genetic resources to ensure the adaptability of livestock production systems to population growth, income, and climate change challenges, have emerged as invaluable resources for biodiversity and scientific research. Allele frequency trajec...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.575405/full |
| _version_ | 1829531891506610176 |
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| author | Simon Boitard Cyriel Paris Natalia Sevane Bertrand Servin Kenza Bazi-Kabbaj Kenza Bazi-Kabbaj Susana Dunner |
| author_facet | Simon Boitard Cyriel Paris Natalia Sevane Bertrand Servin Kenza Bazi-Kabbaj Kenza Bazi-Kabbaj Susana Dunner |
| author_sort | Simon Boitard |
| collection | DOAJ |
| description | Gene banks, framed within the efforts for conserving animal genetic resources to ensure the adaptability of livestock production systems to population growth, income, and climate change challenges, have emerged as invaluable resources for biodiversity and scientific research. Allele frequency trajectories over the few last generations contain rich information about the selection history of populations, which cannot be obtained from classical selection scan approaches based on present time data only. Here we apply a new statistical approach taking advantage of genomic time series and a state of the art statistic (nSL) based on present time data to disentangle both old and recent signatures of selection in the Asturiana de los Valles cattle breed. This local Spanish originally multipurpose breed native to Asturias has been selected for beef production over the last few generations. With the use of SNP chip and whole-genome sequencing (WGS) data, we detect candidate regions under selection reflecting the effort of breeders to produce economically valuable beef individuals, e.g., by improving carcass and meat traits with genes such as MSTN, FLRT2, CRABP2, ZNF215, RBPMS2, OAZ2, or ZNF609, while maintaining the ability to thrive under a semi-intensive production system, with the selection of immune (GIMAP7, GIMAP4, GIMAP8, and TICAM1) or olfactory receptor (OR2D2, OR2D3, OR10A4, and 0R6A2) genes. This kind of information will allow us to take advantage of the invaluable resources provided by gene bank collections from local less competitive breeds, enabling the livestock industry to exploit the different mechanisms fine-tuned by natural and human-driven selection on different populations to improve productivity. |
| first_indexed | 2024-12-16T18:29:59Z |
| format | Article |
| id | doaj.art-7621896da7cf417a961a1c5e07fa2873 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-16T18:29:59Z |
| publishDate | 2021-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-7621896da7cf417a961a1c5e07fa28732022-12-21T22:21:19ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-02-011210.3389/fgene.2021.575405575405Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine BreedSimon Boitard0Cyriel Paris1Natalia Sevane2Bertrand Servin3Kenza Bazi-Kabbaj4Kenza Bazi-Kabbaj5Susana Dunner6GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet-Tolosan, FranceGenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet-Tolosan, FranceDpto. Animal Production, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, SpainGenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet-Tolosan, FranceGABI, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, FranceSIGENAE, INRA, Jouy-en-Josas, FranceDpto. Animal Production, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, SpainGene banks, framed within the efforts for conserving animal genetic resources to ensure the adaptability of livestock production systems to population growth, income, and climate change challenges, have emerged as invaluable resources for biodiversity and scientific research. Allele frequency trajectories over the few last generations contain rich information about the selection history of populations, which cannot be obtained from classical selection scan approaches based on present time data only. Here we apply a new statistical approach taking advantage of genomic time series and a state of the art statistic (nSL) based on present time data to disentangle both old and recent signatures of selection in the Asturiana de los Valles cattle breed. This local Spanish originally multipurpose breed native to Asturias has been selected for beef production over the last few generations. With the use of SNP chip and whole-genome sequencing (WGS) data, we detect candidate regions under selection reflecting the effort of breeders to produce economically valuable beef individuals, e.g., by improving carcass and meat traits with genes such as MSTN, FLRT2, CRABP2, ZNF215, RBPMS2, OAZ2, or ZNF609, while maintaining the ability to thrive under a semi-intensive production system, with the selection of immune (GIMAP7, GIMAP4, GIMAP8, and TICAM1) or olfactory receptor (OR2D2, OR2D3, OR10A4, and 0R6A2) genes. This kind of information will allow us to take advantage of the invaluable resources provided by gene bank collections from local less competitive breeds, enabling the livestock industry to exploit the different mechanisms fine-tuned by natural and human-driven selection on different populations to improve productivity.https://www.frontiersin.org/articles/10.3389/fgene.2021.575405/fullcattlegene bankstime seriesnSLselection signatures |
| spellingShingle | Simon Boitard Cyriel Paris Natalia Sevane Bertrand Servin Kenza Bazi-Kabbaj Kenza Bazi-Kabbaj Susana Dunner Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed Frontiers in Genetics cattle gene banks time series nSL selection signatures |
| title | Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed |
| title_full | Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed |
| title_fullStr | Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed |
| title_full_unstemmed | Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed |
| title_short | Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed |
| title_sort | gene banks as reservoirs to detect recent selection the example of the asturiana de los valles bovine breed |
| topic | cattle gene banks time series nSL selection signatures |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.575405/full |
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