Genomic profiling of selective sweeps through haplotype differentiation unravelled genes associated with production and reproduction traits in Indian goat breeds
A comprehensive genomic scan of selective sweeps was conducted in autochthonous Attappady Black and improved dual-purpose Malabari goat breeds in south India. High-throughput single nucleotide polymorphism (SNP) marker data, obtained through Illumina goat SNP50 BeadChip genotyping of 48 goats (24 ea...
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| Veröffentlicht in: | Tropical animal health and production 2024-11, Vol.56 (8), p.296-296, Article 296 |
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| creator | Thomas, Marykutty G., Radhika V., R. Thirupathy V., Aravindakshan T. |
| description | A comprehensive genomic scan of selective sweeps was conducted in autochthonous Attappady Black and improved dual-purpose Malabari goat breeds in south India. High-throughput single nucleotide polymorphism (SNP) marker data, obtained through Illumina goat SNP50 BeadChip genotyping of 48 goats (24 each of Attappady Black and Malabari goats), were utilized for the analysis. Selection signature analysis, employing hapFLK analysis based on haplotype differentiation, identified seven significant sweep regions (
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| doi_str_mv | 10.1007/s11250-024-04136-2 |
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p
< 0.005). Notably, one of these regions encompassed the genomic area housing the casein cluster and quantitative trait loci associated with milk production on chromosome 6. Gene ontology enrichment analysis of 166 putative selective genes associated with these sweep regions revealed 13 significantly over-represented Panther pathways (
p
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p
< 0.005). Notably, one of these regions encompassed the genomic area housing the casein cluster and quantitative trait loci associated with milk production on chromosome 6. Gene ontology enrichment analysis of 166 putative selective genes associated with these sweep regions revealed 13 significantly over-represented Panther pathways (
p
≤ 0.05), including the TGF-beta signalling pathway and GNRHR pathway. 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Thirupathy ; V., Aravindakshan T.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c289t-c681b61a55db6dc662be6f21e39da778dc8f7f3133a8072b8f0ef778ecef26f93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Animals</topic><topic>Biomedical and Life Sciences</topic><topic>Breeding</topic><topic>Casein</topic><topic>Chromosome 6</topic><topic>chromosomes</topic><topic>Comparative analysis</topic><topic>Differentiation</topic><topic>Female</topic><topic>Gene mapping</topic><topic>gene ontology</topic><topic>Gene polymorphism</topic><topic>Genes</topic><topic>Genomic analysis</topic><topic>Genomics</topic><topic>Genotype</topic><topic>Genotype & phenotype</topic><topic>Genotyping</topic><topic>Goats</topic><topic>Goats - genetics</topic><topic>Goats - physiology</topic><topic>Haplotypes</topic><topic>India</topic><topic>Life Sciences</topic><topic>Livestock</topic><topic>Milk</topic><topic>Milk production</topic><topic>Nucleotides</topic><topic>phenotypic variation</topic><topic>Polymorphism</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Quantitative Trait Loci</topic><topic>quantitative traits</topic><topic>Regular Articles</topic><topic>Reproduction</topic><topic>Selection, Genetic</topic><topic>Signal transduction</topic><topic>Signature analysis</topic><topic>Single-nucleotide polymorphism</topic><topic>transforming growth factor beta</topic><topic>Veterinary Medicine/Veterinary Science</topic><topic>Zoology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Thomas, Marykutty</creatorcontrib><creatorcontrib>G., Radhika</creatorcontrib><creatorcontrib>V., R. 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Thirupathy</au><au>V., Aravindakshan T.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomic profiling of selective sweeps through haplotype differentiation unravelled genes associated with production and reproduction traits in Indian goat breeds</atitle><jtitle>Tropical animal health and production</jtitle><stitle>Trop Anim Health Prod</stitle><addtitle>Trop Anim Health Prod</addtitle><date>2024-11-01</date><risdate>2024</risdate><volume>56</volume><issue>8</issue><spage>296</spage><epage>296</epage><pages>296-296</pages><artnum>296</artnum><issn>0049-4747</issn><issn>1573-7438</issn><eissn>1573-7438</eissn><abstract>A comprehensive genomic scan of selective sweeps was conducted in autochthonous Attappady Black and improved dual-purpose Malabari goat breeds in south India. High-throughput single nucleotide polymorphism (SNP) marker data, obtained through Illumina goat SNP50 BeadChip genotyping of 48 goats (24 each of Attappady Black and Malabari goats), were utilized for the analysis. Selection signature analysis, employing hapFLK analysis based on haplotype differentiation, identified seven significant sweep regions (
p
< 0.005). Notably, one of these regions encompassed the genomic area housing the casein cluster and quantitative trait loci associated with milk production on chromosome 6. Gene ontology enrichment analysis of 166 putative selective genes associated with these sweep regions revealed 13 significantly over-represented Panther pathways (
p
≤ 0.05), including the TGF-beta signalling pathway and GNRHR pathway. The selective sweeps detected in this study contributed significantly to the phenotypic divergence observed between Attappady Black and Malabari goats in south India.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>39340615</pmid><doi>10.1007/s11250-024-04136-2</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0001-7679-3420</orcidid></addata></record> |
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| subjects | Animals Biomedical and Life Sciences Breeding Casein Chromosome 6 chromosomes Comparative analysis Differentiation Female Gene mapping gene ontology Gene polymorphism Genes Genomic analysis Genomics Genotype Genotype & phenotype Genotyping Goats Goats - genetics Goats - physiology Haplotypes India Life Sciences Livestock Milk Milk production Nucleotides phenotypic variation Polymorphism Polymorphism, Single Nucleotide Quantitative Trait Loci quantitative traits Regular Articles Reproduction Selection, Genetic Signal transduction Signature analysis Single-nucleotide polymorphism transforming growth factor beta Veterinary Medicine/Veterinary Science Zoology |
| title | Genomic profiling of selective sweeps through haplotype differentiation unravelled genes associated with production and reproduction traits in Indian goat breeds |
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