A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes
Genome-wide association studies (GWAS) were used to discover genomic regions explaining variation in dairy production and fertility traits. Associations were detected with either single nucleotide polymorphism (SNP) markers or haplotypes of SNP alleles. An across-breed validation strategy was used t...
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| Veröffentlicht in: | Journal of dairy science 2010-07, Vol.93 (7), p.3331-3345 |
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| container_title | Journal of dairy science |
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| creator | Pryce, J.E. Bolormaa, S. Chamberlain, A.J. Bowman, P.J. Savin, K. Goddard, M.E. Hayes, B.J. |
| description | Genome-wide association studies (GWAS) were used to discover genomic regions explaining variation in dairy production and fertility traits. Associations were detected with either single nucleotide polymorphism (SNP) markers or haplotypes of SNP alleles. An across-breed validation strategy was used to narrow the genomic interval containing causative mutations. There were 39,048 SNP tested in a discovery population of 780 Holstein sires and validated in 386 Holsteins and 364 Jersey sires. Previously identified mutations affecting milk production traits were confirmed. In addition, several novel regions were identified, including a putative quantitative trait loci for fertility on chromosome 18 that was detected only using haplotypes greater than 3 SNP long. It was found that the precision of quantitative trait loci mapping increased with haplotype length as did the number of validated haplotypes discovered, especially across breed. Promising candidate genes have been identified in several of the validated regions. |
| doi_str_mv | 10.3168/jds.2009-2893 |
| format | Article |
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Associations were detected with either single nucleotide polymorphism (SNP) markers or haplotypes of SNP alleles. An across-breed validation strategy was used to narrow the genomic interval containing causative mutations. There were 39,048 SNP tested in a discovery population of 780 Holstein sires and validated in 386 Holsteins and 364 Jersey sires. Previously identified mutations affecting milk production traits were confirmed. In addition, several novel regions were identified, including a putative quantitative trait loci for fertility on chromosome 18 that was detected only using haplotypes greater than 3 SNP long. It was found that the precision of quantitative trait loci mapping increased with haplotype length as did the number of validated haplotypes discovered, especially across breed. Promising candidate genes have been identified in several of the validated regions.</description><identifier>ISSN: 0022-0302</identifier><identifier>EISSN: 1525-3198</identifier><identifier>DOI: 10.3168/jds.2009-2893</identifier><identifier>PMID: 20630249</identifier><identifier>CODEN: JDSCAE</identifier><language>eng</language><publisher>New York, NY: Elsevier Inc</publisher><subject>animal fertility ; Animal productions ; Animals ; Biological and medical sciences ; Breeding - methods ; Cattle ; chromosome mapping ; chromosomes ; dairy cattle ; Dairying - methods ; Female ; Fertility - genetics ; fertility traits ; Food industries ; Fundamental and applied biological sciences. Psychology ; genes ; genetic marker ; genome-wide association study ; Genome-Wide Association Study - methods ; Genome-Wide Association Study - standards ; Genome-Wide Association Study - veterinary ; genomics ; haplotype ; haplotypes ; Haplotypes - genetics ; Holstein ; Jersey ; Lactation - genetics ; Male ; Milk - secretion ; Milk and cheese industries. Ice creams ; milk production ; mutation ; Polymorphism, Single Nucleotide - genetics ; quantitative trait loci ; single nucleotide polymorphism ; sires ; Terrestrial animal productions ; traits ; validity ; variable length haplotypes ; Vertebrates</subject><ispartof>Journal of dairy science, 2010-07, Vol.93 (7), p.3331-3345</ispartof><rights>2010 American Dairy Science Association</rights><rights>2015 INIST-CNRS</rights><rights>Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.</rights><rights>Copyright American Dairy Science Association Jul 2010</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c460t-a4b73e8699b76fde89c3243c4b988d78349cf7964617588b4976235dd0c01e533</citedby><cites>FETCH-LOGICAL-c460t-a4b73e8699b76fde89c3243c4b988d78349cf7964617588b4976235dd0c01e533</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.3168/jds.2009-2893$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=22962813$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20630249$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Pryce, J.E.</creatorcontrib><creatorcontrib>Bolormaa, S.</creatorcontrib><creatorcontrib>Chamberlain, A.J.</creatorcontrib><creatorcontrib>Bowman, P.J.</creatorcontrib><creatorcontrib>Savin, K.</creatorcontrib><creatorcontrib>Goddard, M.E.</creatorcontrib><creatorcontrib>Hayes, B.J.</creatorcontrib><title>A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes</title><title>Journal of dairy science</title><addtitle>J Dairy Sci</addtitle><description>Genome-wide association studies (GWAS) were used to discover genomic regions explaining variation in dairy production and fertility traits. Associations were detected with either single nucleotide polymorphism (SNP) markers or haplotypes of SNP alleles. An across-breed validation strategy was used to narrow the genomic interval containing causative mutations. There were 39,048 SNP tested in a discovery population of 780 Holstein sires and validated in 386 Holsteins and 364 Jersey sires. Previously identified mutations affecting milk production traits were confirmed. In addition, several novel regions were identified, including a putative quantitative trait loci for fertility on chromosome 18 that was detected only using haplotypes greater than 3 SNP long. It was found that the precision of quantitative trait loci mapping increased with haplotype length as did the number of validated haplotypes discovered, especially across breed. Promising candidate genes have been identified in several of the validated regions.</description><subject>animal fertility</subject><subject>Animal productions</subject><subject>Animals</subject><subject>Biological and medical sciences</subject><subject>Breeding - methods</subject><subject>Cattle</subject><subject>chromosome mapping</subject><subject>chromosomes</subject><subject>dairy cattle</subject><subject>Dairying - methods</subject><subject>Female</subject><subject>Fertility - genetics</subject><subject>fertility traits</subject><subject>Food industries</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>genes</subject><subject>genetic marker</subject><subject>genome-wide association study</subject><subject>Genome-Wide Association Study - methods</subject><subject>Genome-Wide Association Study - standards</subject><subject>Genome-Wide Association Study - veterinary</subject><subject>genomics</subject><subject>haplotype</subject><subject>haplotypes</subject><subject>Haplotypes - genetics</subject><subject>Holstein</subject><subject>Jersey</subject><subject>Lactation - genetics</subject><subject>Male</subject><subject>Milk - secretion</subject><subject>Milk and cheese industries. Ice creams</subject><subject>milk production</subject><subject>mutation</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>quantitative trait loci</subject><subject>single nucleotide polymorphism</subject><subject>sires</subject><subject>Terrestrial animal productions</subject><subject>traits</subject><subject>validity</subject><subject>variable length haplotypes</subject><subject>Vertebrates</subject><issn>0022-0302</issn><issn>1525-3198</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp10U1vFCEYB_CJ0di1evSqxMR4msrLDAPHpvEtaeJBeyYMPLNlZWAFps18Bz-0rLtqYuKJQH48_MO_aZ4TfMEIF293Nl9QjGVLhWQPmg3pad8yIsXDZoMxpS1mmJ41T3Le1S2huH_cnFHM62knN82PS3SnvbO6gEVbCHGG9t5ZQDrnaJwuLgaUy2JX5AKiyGqXVmR0KR7QmABsRlNMaHb-G9qnaBfz64oOFk2QivOurKgk7UpGS3ZhW99LTo_1uoewLbfoVu99LOse8tPm0aR9hmen9by5ef_u69XH9vrzh09Xl9et6Tgure7GgYHgUo4DnywIaRjtmOlGKYQdBOukmQbJO06GXoixkwOnrLcWG0ygZ-y8eXOcWwN_XyAXNbtswHsdIC5ZDYxJSYUgVb76R-7ikkINp4Y6nnCOu4raIzIp5pxgUvvkZp1WRbA6lKRqSepQkjqUVP2L09BlnMH-0b9bqeD1CehstJ-SDsblv45KTmu46l4e3aSj0ttUzc0XignDRHAhJK1iOAqo33nnIKlsHAQD1iUwRdno_hPyJ-V4tu4</recordid><startdate>20100701</startdate><enddate>20100701</enddate><creator>Pryce, J.E.</creator><creator>Bolormaa, S.</creator><creator>Chamberlain, A.J.</creator><creator>Bowman, P.J.</creator><creator>Savin, K.</creator><creator>Goddard, M.E.</creator><creator>Hayes, B.J.</creator><general>Elsevier Inc</general><general>Elsevier</general><general>American Dairy Science Association</general><scope>6I.</scope><scope>AAFTH</scope><scope>FBQ</scope><scope>IQODW</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>K9.</scope><scope>7X8</scope></search><sort><creationdate>20100701</creationdate><title>A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes</title><author>Pryce, J.E. ; Bolormaa, S. ; Chamberlain, A.J. ; Bowman, P.J. ; Savin, K. ; Goddard, M.E. ; Hayes, B.J.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c460t-a4b73e8699b76fde89c3243c4b988d78349cf7964617588b4976235dd0c01e533</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>animal fertility</topic><topic>Animal productions</topic><topic>Animals</topic><topic>Biological and medical sciences</topic><topic>Breeding - methods</topic><topic>Cattle</topic><topic>chromosome mapping</topic><topic>chromosomes</topic><topic>dairy cattle</topic><topic>Dairying - methods</topic><topic>Female</topic><topic>Fertility - genetics</topic><topic>fertility traits</topic><topic>Food industries</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>genes</topic><topic>genetic marker</topic><topic>genome-wide association study</topic><topic>Genome-Wide Association Study - methods</topic><topic>Genome-Wide Association Study - standards</topic><topic>Genome-Wide Association Study - veterinary</topic><topic>genomics</topic><topic>haplotype</topic><topic>haplotypes</topic><topic>Haplotypes - genetics</topic><topic>Holstein</topic><topic>Jersey</topic><topic>Lactation - genetics</topic><topic>Male</topic><topic>Milk - secretion</topic><topic>Milk and cheese industries. Ice creams</topic><topic>milk production</topic><topic>mutation</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>quantitative trait loci</topic><topic>single nucleotide polymorphism</topic><topic>sires</topic><topic>Terrestrial animal productions</topic><topic>traits</topic><topic>validity</topic><topic>variable length haplotypes</topic><topic>Vertebrates</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Pryce, J.E.</creatorcontrib><creatorcontrib>Bolormaa, S.</creatorcontrib><creatorcontrib>Chamberlain, A.J.</creatorcontrib><creatorcontrib>Bowman, P.J.</creatorcontrib><creatorcontrib>Savin, K.</creatorcontrib><creatorcontrib>Goddard, M.E.</creatorcontrib><creatorcontrib>Hayes, B.J.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of dairy science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Pryce, J.E.</au><au>Bolormaa, S.</au><au>Chamberlain, A.J.</au><au>Bowman, P.J.</au><au>Savin, K.</au><au>Goddard, M.E.</au><au>Hayes, B.J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes</atitle><jtitle>Journal of dairy science</jtitle><addtitle>J Dairy Sci</addtitle><date>2010-07-01</date><risdate>2010</risdate><volume>93</volume><issue>7</issue><spage>3331</spage><epage>3345</epage><pages>3331-3345</pages><issn>0022-0302</issn><eissn>1525-3198</eissn><coden>JDSCAE</coden><abstract>Genome-wide association studies (GWAS) were used to discover genomic regions explaining variation in dairy production and fertility traits. Associations were detected with either single nucleotide polymorphism (SNP) markers or haplotypes of SNP alleles. An across-breed validation strategy was used to narrow the genomic interval containing causative mutations. There were 39,048 SNP tested in a discovery population of 780 Holstein sires and validated in 386 Holsteins and 364 Jersey sires. Previously identified mutations affecting milk production traits were confirmed. In addition, several novel regions were identified, including a putative quantitative trait loci for fertility on chromosome 18 that was detected only using haplotypes greater than 3 SNP long. It was found that the precision of quantitative trait loci mapping increased with haplotype length as did the number of validated haplotypes discovered, especially across breed. Promising candidate genes have been identified in several of the validated regions.</abstract><cop>New York, NY</cop><pub>Elsevier Inc</pub><pmid>20630249</pmid><doi>10.3168/jds.2009-2893</doi><tpages>15</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Elsevier ScienceDirect Journals Complete; EZB-FREE-00999 freely available EZB journals |
| subjects | animal fertility Animal productions Animals Biological and medical sciences Breeding - methods Cattle chromosome mapping chromosomes dairy cattle Dairying - methods Female Fertility - genetics fertility traits Food industries Fundamental and applied biological sciences. Psychology genes genetic marker genome-wide association study Genome-Wide Association Study - methods Genome-Wide Association Study - standards Genome-Wide Association Study - veterinary genomics haplotype haplotypes Haplotypes - genetics Holstein Jersey Lactation - genetics Male Milk - secretion Milk and cheese industries. Ice creams milk production mutation Polymorphism, Single Nucleotide - genetics quantitative trait loci single nucleotide polymorphism sires Terrestrial animal productions traits validity variable length haplotypes Vertebrates |
| title | A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes |
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