Integrative genomics analysis highlights functionally relevant genes for equine behaviour
Behavioural plasticity enables horses entering an exercise training programme to adapt with reduced stress. We characterised SNPs associated with behaviour in yearling Thoroughbred horses using genomics analyses for two phenotypes: (1) handler‐assessed coping with early training events [coping] (n =...
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| Veröffentlicht in: | Animal genetics 2023-08, Vol.54 (4), p.457-469 |
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| creator | Holtby, Amy R. Hall, Thomas J. McGivney, Beatrice A. Han, Haige Murphy, Keith J. MacHugh, David E. Katz, Lisa M. Hill, Emmeline W. |
| description | Behavioural plasticity enables horses entering an exercise training programme to adapt with reduced stress. We characterised SNPs associated with behaviour in yearling Thoroughbred horses using genomics analyses for two phenotypes: (1) handler‐assessed coping with early training events [coping] (n = 96); and (2) variation in salivary cortisol concentration at the first backing event [cortisol] (n = 34). Using RNA‐seq derived gene expression data for amygdala and hippocampus tissues from n = 2 Thoroughbred stallions, we refined the SNPs to those with functional relevance to behaviour by cross‐referencing to the 500 most highly expressed genes in each tissue. The SNPs of high significance (q |
| doi_str_mv | 10.1111/age.13320 |
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We characterised SNPs associated with behaviour in yearling Thoroughbred horses using genomics analyses for two phenotypes: (1) handler‐assessed coping with early training events [coping] (n = 96); and (2) variation in salivary cortisol concentration at the first backing event [cortisol] (n = 34). Using RNA‐seq derived gene expression data for amygdala and hippocampus tissues from n = 2 Thoroughbred stallions, we refined the SNPs to those with functional relevance to behaviour by cross‐referencing to the 500 most highly expressed genes in each tissue. The SNPs of high significance (q < 0.01) were in proximity to genes (coping – GABARAP, NDM, OAZ1, RPS15A, SPARCL1, VAMP2; cortisol – CEBPA, COA3, DUSP1, HNRNPH1, RACK1) with biological functions in social behaviour, autism spectrum disorder, suicide, stress‐induced anxiety and depression, Alzheimer's disease, neurodevelopmental disorders, neuroinflammatory disease, fear‐induced behaviours and alcohol and cocaine addiction. The strongest association (q = 0.0002) was with NDN, a gene previously associated with temperament in cattle. This approach highlights functionally relevant genes in the behavioural adaptation of Thoroughbred horses that will contribute to the development of genetic markers to improve racehorse welfare.</description><identifier>ISSN: 0268-9146</identifier><identifier>EISSN: 1365-2052</identifier><identifier>DOI: 10.1111/age.13320</identifier><identifier>PMID: 36971191</identifier><language>eng</language><publisher>England: Wiley Subscription Services, Inc</publisher><subject>Alzheimer's disease ; Amygdala ; Animals ; Autism ; Autism Spectrum Disorder ; Cattle ; Cocaine ; Coping ; Cortisol ; Drug abuse ; Drug addiction ; FAANG ; functional genomics ; GABARAP protein ; Gene expression ; Genes ; genetic association ; Genetic markers ; genetic variation ; Genomics ; Hormones ; horse ; Horses ; Horses - genetics ; Hydrocortisone ; Inflammation ; Male ; Narcotics ; Neurodegenerative diseases ; Neurodevelopmental disorders ; Phenotype ; Phenotypes ; Physical training ; population genomics ; Racehorses ; RNA‐seq ; Single-nucleotide polymorphism ; SNP ; Social behavior ; Suicide ; temperament ; thoroughbred ; Training ; transcriptomics</subject><ispartof>Animal genetics, 2023-08, Vol.54 (4), p.457-469</ispartof><rights>2023 The Authors. published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.</rights><rights>2023 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.</rights><rights>2023. This article is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). 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We characterised SNPs associated with behaviour in yearling Thoroughbred horses using genomics analyses for two phenotypes: (1) handler‐assessed coping with early training events [coping] (n = 96); and (2) variation in salivary cortisol concentration at the first backing event [cortisol] (n = 34). Using RNA‐seq derived gene expression data for amygdala and hippocampus tissues from n = 2 Thoroughbred stallions, we refined the SNPs to those with functional relevance to behaviour by cross‐referencing to the 500 most highly expressed genes in each tissue. The SNPs of high significance (q < 0.01) were in proximity to genes (coping – GABARAP, NDM, OAZ1, RPS15A, SPARCL1, VAMP2; cortisol – CEBPA, COA3, DUSP1, HNRNPH1, RACK1) with biological functions in social behaviour, autism spectrum disorder, suicide, stress‐induced anxiety and depression, Alzheimer's disease, neurodevelopmental disorders, neuroinflammatory disease, fear‐induced behaviours and alcohol and cocaine addiction. The strongest association (q = 0.0002) was with NDN, a gene previously associated with temperament in cattle. This approach highlights functionally relevant genes in the behavioural adaptation of Thoroughbred horses that will contribute to the development of genetic markers to improve racehorse welfare.</description><subject>Alzheimer's disease</subject><subject>Amygdala</subject><subject>Animals</subject><subject>Autism</subject><subject>Autism Spectrum Disorder</subject><subject>Cattle</subject><subject>Cocaine</subject><subject>Coping</subject><subject>Cortisol</subject><subject>Drug abuse</subject><subject>Drug addiction</subject><subject>FAANG</subject><subject>functional genomics</subject><subject>GABARAP protein</subject><subject>Gene expression</subject><subject>Genes</subject><subject>genetic association</subject><subject>Genetic markers</subject><subject>genetic variation</subject><subject>Genomics</subject><subject>Hormones</subject><subject>horse</subject><subject>Horses</subject><subject>Horses - genetics</subject><subject>Hydrocortisone</subject><subject>Inflammation</subject><subject>Male</subject><subject>Narcotics</subject><subject>Neurodegenerative diseases</subject><subject>Neurodevelopmental disorders</subject><subject>Phenotype</subject><subject>Phenotypes</subject><subject>Physical training</subject><subject>population genomics</subject><subject>Racehorses</subject><subject>RNA‐seq</subject><subject>Single-nucleotide polymorphism</subject><subject>SNP</subject><subject>Social behavior</subject><subject>Suicide</subject><subject>temperament</subject><subject>thoroughbred</subject><subject>Training</subject><subject>transcriptomics</subject><issn>0268-9146</issn><issn>1365-2052</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><sourceid>EIF</sourceid><recordid>eNp10EFPwjAYBuDGaATRg3_ALPGih0G_lnXdkRBEExIvevC0dN03KBkbtBtm_94i6MHEJk0P39M37UvILdAh-DVSSxwC54yekT5wEYWMRuyc9CkTMkxgLHrkyrk1pVRCDJekx0USAyTQJx8vVYNLqxqzx2CJVb0x2gWqUmXnjAtWZrkq_W5cULSVbkztJ2UXWCxxr6rmcAX9rLYB7lpTYZDhSu1N3dprclGo0uHN6RyQ96fZ2_Q5XLzOX6aTRai5lDTM8ryIKC90ksUiinIlqJQgdQKaFjrLJYuE1kpLyaGI8xyEUjxG5CzRgDLjA_JwzN3aeteia9KNcRrLUlVYty5lcQIxHY8F9_T-D137h_ofeSU5kwmwiHn1eFTa1s5ZLNKtNRtluxRoeug79X2n3317e3dKbLMN5r_yp2APRkfwaUrs_k9KJ_PZMfILtcWKzg</recordid><startdate>202308</startdate><enddate>202308</enddate><creator>Holtby, Amy R.</creator><creator>Hall, Thomas J.</creator><creator>McGivney, Beatrice A.</creator><creator>Han, Haige</creator><creator>Murphy, Keith J.</creator><creator>MacHugh, David E.</creator><creator>Katz, Lisa M.</creator><creator>Hill, Emmeline W.</creator><general>Wiley Subscription Services, Inc</general><scope>24P</scope><scope>WIN</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TK</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-1805-2250</orcidid></search><sort><creationdate>202308</creationdate><title>Integrative genomics analysis highlights functionally relevant genes for equine behaviour</title><author>Holtby, Amy R. ; Hall, Thomas J. ; McGivney, Beatrice A. ; Han, Haige ; Murphy, Keith J. ; MacHugh, David E. ; Katz, Lisa M. ; Hill, Emmeline W.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3880-bddf503fc9b7655da608818c91c0fcbd8256ccac8831f7dd16aa37ee329c1e8b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Alzheimer's disease</topic><topic>Amygdala</topic><topic>Animals</topic><topic>Autism</topic><topic>Autism Spectrum Disorder</topic><topic>Cattle</topic><topic>Cocaine</topic><topic>Coping</topic><topic>Cortisol</topic><topic>Drug abuse</topic><topic>Drug addiction</topic><topic>FAANG</topic><topic>functional genomics</topic><topic>GABARAP protein</topic><topic>Gene expression</topic><topic>Genes</topic><topic>genetic association</topic><topic>Genetic markers</topic><topic>genetic variation</topic><topic>Genomics</topic><topic>Hormones</topic><topic>horse</topic><topic>Horses</topic><topic>Horses - genetics</topic><topic>Hydrocortisone</topic><topic>Inflammation</topic><topic>Male</topic><topic>Narcotics</topic><topic>Neurodegenerative diseases</topic><topic>Neurodevelopmental disorders</topic><topic>Phenotype</topic><topic>Phenotypes</topic><topic>Physical training</topic><topic>population genomics</topic><topic>Racehorses</topic><topic>RNA‐seq</topic><topic>Single-nucleotide polymorphism</topic><topic>SNP</topic><topic>Social behavior</topic><topic>Suicide</topic><topic>temperament</topic><topic>thoroughbred</topic><topic>Training</topic><topic>transcriptomics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Holtby, Amy R.</creatorcontrib><creatorcontrib>Hall, Thomas J.</creatorcontrib><creatorcontrib>McGivney, Beatrice A.</creatorcontrib><creatorcontrib>Han, Haige</creatorcontrib><creatorcontrib>Murphy, Keith J.</creatorcontrib><creatorcontrib>MacHugh, David E.</creatorcontrib><creatorcontrib>Katz, Lisa M.</creatorcontrib><creatorcontrib>Hill, Emmeline W.</creatorcontrib><collection>Wiley Online Library (Open Access Collection)</collection><collection>Wiley Online Library (Open Access Collection)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Animal genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Holtby, Amy R.</au><au>Hall, Thomas J.</au><au>McGivney, Beatrice A.</au><au>Han, Haige</au><au>Murphy, Keith J.</au><au>MacHugh, David E.</au><au>Katz, Lisa M.</au><au>Hill, Emmeline W.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Integrative genomics analysis highlights functionally relevant genes for equine behaviour</atitle><jtitle>Animal genetics</jtitle><addtitle>Anim Genet</addtitle><date>2023-08</date><risdate>2023</risdate><volume>54</volume><issue>4</issue><spage>457</spage><epage>469</epage><pages>457-469</pages><issn>0268-9146</issn><eissn>1365-2052</eissn><abstract>Behavioural plasticity enables horses entering an exercise training programme to adapt with reduced stress. We characterised SNPs associated with behaviour in yearling Thoroughbred horses using genomics analyses for two phenotypes: (1) handler‐assessed coping with early training events [coping] (n = 96); and (2) variation in salivary cortisol concentration at the first backing event [cortisol] (n = 34). Using RNA‐seq derived gene expression data for amygdala and hippocampus tissues from n = 2 Thoroughbred stallions, we refined the SNPs to those with functional relevance to behaviour by cross‐referencing to the 500 most highly expressed genes in each tissue. The SNPs of high significance (q < 0.01) were in proximity to genes (coping – GABARAP, NDM, OAZ1, RPS15A, SPARCL1, VAMP2; cortisol – CEBPA, COA3, DUSP1, HNRNPH1, RACK1) with biological functions in social behaviour, autism spectrum disorder, suicide, stress‐induced anxiety and depression, Alzheimer's disease, neurodevelopmental disorders, neuroinflammatory disease, fear‐induced behaviours and alcohol and cocaine addiction. The strongest association (q = 0.0002) was with NDN, a gene previously associated with temperament in cattle. This approach highlights functionally relevant genes in the behavioural adaptation of Thoroughbred horses that will contribute to the development of genetic markers to improve racehorse welfare.</abstract><cop>England</cop><pub>Wiley Subscription Services, Inc</pub><pmid>36971191</pmid><doi>10.1111/age.13320</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0002-1805-2250</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Animal genetics, 2023-08, Vol.54 (4), p.457-469 |
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| subjects | Alzheimer's disease Amygdala Animals Autism Autism Spectrum Disorder Cattle Cocaine Coping Cortisol Drug abuse Drug addiction FAANG functional genomics GABARAP protein Gene expression Genes genetic association Genetic markers genetic variation Genomics Hormones horse Horses Horses - genetics Hydrocortisone Inflammation Male Narcotics Neurodegenerative diseases Neurodevelopmental disorders Phenotype Phenotypes Physical training population genomics Racehorses RNA‐seq Single-nucleotide polymorphism SNP Social behavior Suicide temperament thoroughbred Training transcriptomics |
| title | Integrative genomics analysis highlights functionally relevant genes for equine behaviour |
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