Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology
Chicken body weight (BW) is an economically important trait, and many studies have been conducted on genetic selection for BW. However, previous studies have detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing...
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| Veröffentlicht in: | Journal of applied genetics 2018-08, Vol.59 (3), p.305-312 |
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| creator | Li, Fuwei Han, Haixia Lei, Qiuxia Gao, Jinbo Liu, Jie Liu, Wei Zhou, Yan Li, Huimin Cao, Dingguo |
| description | Chicken body weight (BW) is an economically important trait, and many studies have been conducted on genetic selection for BW. However, previous studies have detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) on purebred Wengshang Barred chicken. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, and 175,211 SNPs were selected as candidate SNPs for genome-wide association analysis using TASSEL general linear models. Six SNP markers reached genome-wide significance. Of these, rs732048524, rs735522839, rs738991545, and rs15837818 were significantly associated with body weight at 28 days (BW28), while rs314086457 and rs315694878 were significantly associated with BW120. These SNPs are close to seven genes (
PRSS23
,
ME3
,
FAM181B
,
NABP1
,
SDPR
,
TSSK6L2
, and
RBBP8
). Moreover, 24 BW-associated SNPs reached “suggestive” genome-wide significance. Of these, 6, 13, 1, and 4 SNPs were associated with BW28, BW56, BW80, and BW120, respectively. These results would enrich the studies on BW and promote the use of Chinese chicken, especially the Wenshang Barred chicken. |
| doi_str_mv | 10.1007/s13353-018-0452-7 |
| format | Article |
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PRSS23
,
ME3
,
FAM181B
,
NABP1
,
SDPR
,
TSSK6L2
, and
RBBP8
). Moreover, 24 BW-associated SNPs reached “suggestive” genome-wide significance. Of these, 6, 13, 1, and 4 SNPs were associated with BW28, BW56, BW80, and BW120, respectively. These results would enrich the studies on BW and promote the use of Chinese chicken, especially the Wenshang Barred chicken.</description><identifier>ISSN: 1234-1983</identifier><identifier>EISSN: 2190-3883</identifier><identifier>DOI: 10.1007/s13353-018-0452-7</identifier><identifier>PMID: 29946990</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Analysis ; Animal Genetics and Genomics ; Animal Genetics • Review ; Animals ; Association analysis ; Biomedical and Life Sciences ; Body weight ; Body Weight - genetics ; Chickens ; Chickens - genetics ; Chromosome Mapping ; Cluster Analysis ; DNA microarrays ; Gene mutations ; Gene sequencing ; Genes ; Genome-wide association studies ; Genome-Wide Association Study ; Genomes ; Genomics ; Human Genetics ; Life Sciences ; Male ; Microbial Genetics and Genomics ; Mutation ; Phenotype ; Plant Genetics and Genomics ; Polymorphism ; Polymorphism, Single Nucleotide ; Poultry ; Quantitative Trait Loci ; Quantitative Trait, Heritable ; Sequence Analysis, DNA ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Studies ; Technology ; Technology application</subject><ispartof>Journal of applied genetics, 2018-08, Vol.59 (3), p.305-312</ispartof><rights>Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2018</rights><rights>COPYRIGHT 2018 Springer</rights><rights>Copyright Springer Science & Business Media 2018</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c505t-c992c774cbbd34eb07d1c1e0ede9a7294650b203af42b5919e9fb3d65a80cc143</citedby><cites>FETCH-LOGICAL-c505t-c992c774cbbd34eb07d1c1e0ede9a7294650b203af42b5919e9fb3d65a80cc143</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s13353-018-0452-7$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s13353-018-0452-7$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29946990$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Fuwei</creatorcontrib><creatorcontrib>Han, Haixia</creatorcontrib><creatorcontrib>Lei, Qiuxia</creatorcontrib><creatorcontrib>Gao, Jinbo</creatorcontrib><creatorcontrib>Liu, Jie</creatorcontrib><creatorcontrib>Liu, Wei</creatorcontrib><creatorcontrib>Zhou, Yan</creatorcontrib><creatorcontrib>Li, Huimin</creatorcontrib><creatorcontrib>Cao, Dingguo</creatorcontrib><title>Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology</title><title>Journal of applied genetics</title><addtitle>J Appl Genetics</addtitle><addtitle>J Appl Genet</addtitle><description>Chicken body weight (BW) is an economically important trait, and many studies have been conducted on genetic selection for BW. However, previous studies have detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) on purebred Wengshang Barred chicken. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, and 175,211 SNPs were selected as candidate SNPs for genome-wide association analysis using TASSEL general linear models. Six SNP markers reached genome-wide significance. Of these, rs732048524, rs735522839, rs738991545, and rs15837818 were significantly associated with body weight at 28 days (BW28), while rs314086457 and rs315694878 were significantly associated with BW120. These SNPs are close to seven genes (
PRSS23
,
ME3
,
FAM181B
,
NABP1
,
SDPR
,
TSSK6L2
, and
RBBP8
). Moreover, 24 BW-associated SNPs reached “suggestive” genome-wide significance. Of these, 6, 13, 1, and 4 SNPs were associated with BW28, BW56, BW80, and BW120, respectively. These results would enrich the studies on BW and promote the use of Chinese chicken, especially the Wenshang Barred chicken.</description><subject>Analysis</subject><subject>Animal Genetics and Genomics</subject><subject>Animal Genetics • Review</subject><subject>Animals</subject><subject>Association analysis</subject><subject>Biomedical and Life Sciences</subject><subject>Body weight</subject><subject>Body Weight - genetics</subject><subject>Chickens</subject><subject>Chickens - genetics</subject><subject>Chromosome Mapping</subject><subject>Cluster Analysis</subject><subject>DNA microarrays</subject><subject>Gene mutations</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genome-wide association studies</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Human Genetics</subject><subject>Life Sciences</subject><subject>Male</subject><subject>Microbial Genetics and Genomics</subject><subject>Mutation</subject><subject>Phenotype</subject><subject>Plant Genetics and Genomics</subject><subject>Polymorphism</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Poultry</subject><subject>Quantitative Trait Loci</subject><subject>Quantitative Trait, Heritable</subject><subject>Sequence Analysis, DNA</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Studies</subject><subject>Technology</subject><subject>Technology application</subject><issn>1234-1983</issn><issn>2190-3883</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kV1rFDEUhoMo7Vr9Ad5IwOvUfMxMJpdraauw0AsVL0M-zsyk7iRtMkvZf2-WrS2CJXAOOXmfk5O8CH1g9JxRKj8XJkQrCGU9oU3LiXyFVpwpSkTfi9doxbhoCFO9OEVvS7mlVPSN5CfolCvVdErRFZquIaYZyEPwgE0pyQWzhBRxWXZ-j9OAbar5AcI4LThE_AtimUwc8ReTM3jspuB-Q8TWlLqr4DIB_r5ZX5EC93gBN8W0TeP-HXozmG2B94_5DP28uvxx8ZVsbq6_Xaw3xLW0XYhTijspG2etFw1YKj1zDCh4UEbyOnZLLafCDA23rWIK1GCF71rTU-dYI87Qp2Pfu5zud1AWfZt2OdYrNaedZErV8KwazRZ0iENasnFzKE6vJaNdp-r_VtX5f1R1eZiDSxGGUOv_AOwIuJxKyTDouxxmk_eaUX2wTB8t09UyfbBMH5iPjwPv7Az-ifjrURXwo6DUozhCfn7Ry13_ACRsn6A</recordid><startdate>20180801</startdate><enddate>20180801</enddate><creator>Li, Fuwei</creator><creator>Han, Haixia</creator><creator>Lei, Qiuxia</creator><creator>Gao, Jinbo</creator><creator>Liu, Jie</creator><creator>Liu, Wei</creator><creator>Zhou, Yan</creator><creator>Li, Huimin</creator><creator>Cao, Dingguo</creator><general>Springer Berlin Heidelberg</general><general>Springer</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope></search><sort><creationdate>20180801</creationdate><title>Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology</title><author>Li, Fuwei ; Han, Haixia ; Lei, Qiuxia ; Gao, Jinbo ; Liu, Jie ; Liu, Wei ; Zhou, Yan ; Li, Huimin ; Cao, Dingguo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c505t-c992c774cbbd34eb07d1c1e0ede9a7294650b203af42b5919e9fb3d65a80cc143</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Analysis</topic><topic>Animal Genetics and Genomics</topic><topic>Animal Genetics • Review</topic><topic>Animals</topic><topic>Association analysis</topic><topic>Biomedical and Life Sciences</topic><topic>Body weight</topic><topic>Body Weight - genetics</topic><topic>Chickens</topic><topic>Chickens - genetics</topic><topic>Chromosome Mapping</topic><topic>Cluster Analysis</topic><topic>DNA microarrays</topic><topic>Gene mutations</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genome-wide association studies</topic><topic>Genome-Wide Association Study</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Human Genetics</topic><topic>Life Sciences</topic><topic>Male</topic><topic>Microbial Genetics and Genomics</topic><topic>Mutation</topic><topic>Phenotype</topic><topic>Plant Genetics and Genomics</topic><topic>Polymorphism</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Poultry</topic><topic>Quantitative Trait Loci</topic><topic>Quantitative Trait, Heritable</topic><topic>Sequence Analysis, DNA</topic><topic>Single nucleotide polymorphisms</topic><topic>Single-nucleotide polymorphism</topic><topic>Studies</topic><topic>Technology</topic><topic>Technology application</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Fuwei</creatorcontrib><creatorcontrib>Han, Haixia</creatorcontrib><creatorcontrib>Lei, Qiuxia</creatorcontrib><creatorcontrib>Gao, Jinbo</creatorcontrib><creatorcontrib>Liu, Jie</creatorcontrib><creatorcontrib>Liu, Wei</creatorcontrib><creatorcontrib>Zhou, Yan</creatorcontrib><creatorcontrib>Li, Huimin</creatorcontrib><creatorcontrib>Cao, Dingguo</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><jtitle>Journal of applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Fuwei</au><au>Han, Haixia</au><au>Lei, Qiuxia</au><au>Gao, Jinbo</au><au>Liu, Jie</au><au>Liu, Wei</au><au>Zhou, Yan</au><au>Li, Huimin</au><au>Cao, Dingguo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology</atitle><jtitle>Journal of applied genetics</jtitle><stitle>J Appl Genetics</stitle><addtitle>J Appl Genet</addtitle><date>2018-08-01</date><risdate>2018</risdate><volume>59</volume><issue>3</issue><spage>305</spage><epage>312</epage><pages>305-312</pages><issn>1234-1983</issn><eissn>2190-3883</eissn><abstract>Chicken body weight (BW) is an economically important trait, and many studies have been conducted on genetic selection for BW. However, previous studies have detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) on purebred Wengshang Barred chicken. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, and 175,211 SNPs were selected as candidate SNPs for genome-wide association analysis using TASSEL general linear models. Six SNP markers reached genome-wide significance. Of these, rs732048524, rs735522839, rs738991545, and rs15837818 were significantly associated with body weight at 28 days (BW28), while rs314086457 and rs315694878 were significantly associated with BW120. These SNPs are close to seven genes (
PRSS23
,
ME3
,
FAM181B
,
NABP1
,
SDPR
,
TSSK6L2
, and
RBBP8
). Moreover, 24 BW-associated SNPs reached “suggestive” genome-wide significance. Of these, 6, 13, 1, and 4 SNPs were associated with BW28, BW56, BW80, and BW120, respectively. These results would enrich the studies on BW and promote the use of Chinese chicken, especially the Wenshang Barred chicken.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>29946990</pmid><doi>10.1007/s13353-018-0452-7</doi><tpages>8</tpages></addata></record> |
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| identifier | ISSN: 1234-1983 |
| ispartof | Journal of applied genetics, 2018-08, Vol.59 (3), p.305-312 |
| issn | 1234-1983 2190-3883 |
| language | eng |
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| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Analysis Animal Genetics and Genomics Animal Genetics • Review Animals Association analysis Biomedical and Life Sciences Body weight Body Weight - genetics Chickens Chickens - genetics Chromosome Mapping Cluster Analysis DNA microarrays Gene mutations Gene sequencing Genes Genome-wide association studies Genome-Wide Association Study Genomes Genomics Human Genetics Life Sciences Male Microbial Genetics and Genomics Mutation Phenotype Plant Genetics and Genomics Polymorphism Polymorphism, Single Nucleotide Poultry Quantitative Trait Loci Quantitative Trait, Heritable Sequence Analysis, DNA Single nucleotide polymorphisms Single-nucleotide polymorphism Studies Technology Technology application |
| title | Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology |
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