A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping
The orange-spotted grouper, Epinephelus coioides , is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a geno...
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| Veröffentlicht in: | Science China. Life sciences 2018-08, Vol.61 (8), p.934-946 |
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| creator | Yu, Hui You, Xinxin Li, Jia Zhang, Xinhui Zhang, Shuai Jiang, Shoujia Lin, Xueqiang Lin, Hao-Ran Meng, Zining Shi, Qiong |
| description | The orange-spotted grouper,
Epinephelus coioides
, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms (SNPs) were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including
adgrb2
,
csnkza1
,
cers5
,
col22a1
,
creb5
,
dnd1
,
dzank1
,
dnai1
,
npy2r
,
fat3
,
lrrk2
,
lrp5
,
map3k9
, and so on. Among these candidate genes,
npy2r
(neuropeptide Y receptor Y2) was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers. |
| doi_str_mv | 10.1007/s11427-017-9161-4 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2014142577</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2014142577</sourcerecordid><originalsourceid>FETCH-LOGICAL-c344t-c3f9f3bce8d284457c41235cc67c31707925478892bec07504934a5ba93d02393</originalsourceid><addsrcrecordid>eNp9kE9rGzEQxUVpqUPqD5BL0dE9KNG_tVZH46ZNIFAoyVnI2rGtYK82Gi3G375y7PbYOWgG5r0n5kfIjeC3gnNzh0JoaRgXhlkxF0x_IFeinVsm2tZ-rPPcaGYUbyZkivjKaynFpTGfyUTaRgtr-RU5LugG-rQHdogdUI-YQvQlpp5iGbsjrcMmp0PZ0pJ9LEhjT1P2_QYYDqkU6E77cYBMZ_dD7GHYwm5EGlJMNRG_0UOs5t-L7wzh7f2zcqy6zRfyae13CNNLvyYvP-6flw_s6dfPx-XiiQWldanv2q7VKkDbyVbrxgQtpGpCmJughOHGykaberJcQeCm4doq7ZuVt6rjUll1TWbn3CGntxGwuH3EALud7yGN6CQXupJsjKlScZaGnBAzrN2Q497noxPcnaC7M3RXobsTdKer5-slflztofvn-Iu4CuRZgHVVsWX3msbc15P_k_oHlHqM1g</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2014142577</pqid></control><display><type>article</type><title>A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping</title><source>MEDLINE</source><source>SpringerLink Journals</source><source>Alma/SFX Local Collection</source><creator>Yu, Hui ; You, Xinxin ; Li, Jia ; Zhang, Xinhui ; Zhang, Shuai ; Jiang, Shoujia ; Lin, Xueqiang ; Lin, Hao-Ran ; Meng, Zining ; Shi, Qiong</creator><creatorcontrib>Yu, Hui ; You, Xinxin ; Li, Jia ; Zhang, Xinhui ; Zhang, Shuai ; Jiang, Shoujia ; Lin, Xueqiang ; Lin, Hao-Ran ; Meng, Zining ; Shi, Qiong</creatorcontrib><description>The orange-spotted grouper,
Epinephelus coioides
, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms (SNPs) were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including
adgrb2
,
csnkza1
,
cers5
,
col22a1
,
creb5
,
dnd1
,
dzank1
,
dnai1
,
npy2r
,
fat3
,
lrrk2
,
lrp5
,
map3k9
, and so on. Among these candidate genes,
npy2r
(neuropeptide Y receptor Y2) was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.</description><identifier>ISSN: 1674-7305</identifier><identifier>EISSN: 1869-1889</identifier><identifier>DOI: 10.1007/s11427-017-9161-4</identifier><identifier>PMID: 29541990</identifier><language>eng</language><publisher>Beijing: Science China Press</publisher><subject>Animals ; Bass - genetics ; Bass - growth & development ; Biomedical and Life Sciences ; Body Weight - genetics ; Chromosome Mapping ; Chromosomes - genetics ; Fish Proteins - genetics ; Genome - genetics ; Genome-Wide Association Study - methods ; Genotype ; Life Sciences ; Linkage Disequilibrium ; Phenotype ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; Research Paper ; Sequence Analysis, DNA - methods</subject><ispartof>Science China. Life sciences, 2018-08, Vol.61 (8), p.934-946</ispartof><rights>Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2018</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c344t-c3f9f3bce8d284457c41235cc67c31707925478892bec07504934a5ba93d02393</citedby><cites>FETCH-LOGICAL-c344t-c3f9f3bce8d284457c41235cc67c31707925478892bec07504934a5ba93d02393</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/s11427-017-9161-4$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11427-017-9161-4$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29541990$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yu, Hui</creatorcontrib><creatorcontrib>You, Xinxin</creatorcontrib><creatorcontrib>Li, Jia</creatorcontrib><creatorcontrib>Zhang, Xinhui</creatorcontrib><creatorcontrib>Zhang, Shuai</creatorcontrib><creatorcontrib>Jiang, Shoujia</creatorcontrib><creatorcontrib>Lin, Xueqiang</creatorcontrib><creatorcontrib>Lin, Hao-Ran</creatorcontrib><creatorcontrib>Meng, Zining</creatorcontrib><creatorcontrib>Shi, Qiong</creatorcontrib><title>A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping</title><title>Science China. Life sciences</title><addtitle>Sci. China Life Sci</addtitle><addtitle>Sci China Life Sci</addtitle><description>The orange-spotted grouper,
Epinephelus coioides
, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms (SNPs) were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including
adgrb2
,
csnkza1
,
cers5
,
col22a1
,
creb5
,
dnd1
,
dzank1
,
dnai1
,
npy2r
,
fat3
,
lrrk2
,
lrp5
,
map3k9
, and so on. Among these candidate genes,
npy2r
(neuropeptide Y receptor Y2) was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.</description><subject>Animals</subject><subject>Bass - genetics</subject><subject>Bass - growth & development</subject><subject>Biomedical and Life Sciences</subject><subject>Body Weight - genetics</subject><subject>Chromosome Mapping</subject><subject>Chromosomes - genetics</subject><subject>Fish Proteins - genetics</subject><subject>Genome - genetics</subject><subject>Genome-Wide Association Study - methods</subject><subject>Genotype</subject><subject>Life Sciences</subject><subject>Linkage Disequilibrium</subject><subject>Phenotype</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Reproducibility of Results</subject><subject>Research Paper</subject><subject>Sequence Analysis, DNA - methods</subject><issn>1674-7305</issn><issn>1869-1889</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kE9rGzEQxUVpqUPqD5BL0dE9KNG_tVZH46ZNIFAoyVnI2rGtYK82Gi3G375y7PbYOWgG5r0n5kfIjeC3gnNzh0JoaRgXhlkxF0x_IFeinVsm2tZ-rPPcaGYUbyZkivjKaynFpTGfyUTaRgtr-RU5LugG-rQHdogdUI-YQvQlpp5iGbsjrcMmp0PZ0pJ9LEhjT1P2_QYYDqkU6E77cYBMZ_dD7GHYwm5EGlJMNRG_0UOs5t-L7wzh7f2zcqy6zRfyae13CNNLvyYvP-6flw_s6dfPx-XiiQWldanv2q7VKkDbyVbrxgQtpGpCmJughOHGykaberJcQeCm4doq7ZuVt6rjUll1TWbn3CGntxGwuH3EALud7yGN6CQXupJsjKlScZaGnBAzrN2Q497noxPcnaC7M3RXobsTdKer5-slflztofvn-Iu4CuRZgHVVsWX3msbc15P_k_oHlHqM1g</recordid><startdate>20180801</startdate><enddate>20180801</enddate><creator>Yu, Hui</creator><creator>You, Xinxin</creator><creator>Li, Jia</creator><creator>Zhang, Xinhui</creator><creator>Zhang, Shuai</creator><creator>Jiang, Shoujia</creator><creator>Lin, Xueqiang</creator><creator>Lin, Hao-Ran</creator><creator>Meng, Zining</creator><creator>Shi, Qiong</creator><general>Science China Press</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><scope>7X8</scope></search><sort><creationdate>20180801</creationdate><title>A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping</title><author>Yu, Hui ; You, Xinxin ; Li, Jia ; Zhang, Xinhui ; Zhang, Shuai ; Jiang, Shoujia ; Lin, Xueqiang ; Lin, Hao-Ran ; Meng, Zining ; Shi, Qiong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c344t-c3f9f3bce8d284457c41235cc67c31707925478892bec07504934a5ba93d02393</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Animals</topic><topic>Bass - genetics</topic><topic>Bass - growth & development</topic><topic>Biomedical and Life Sciences</topic><topic>Body Weight - genetics</topic><topic>Chromosome Mapping</topic><topic>Chromosomes - genetics</topic><topic>Fish Proteins - genetics</topic><topic>Genome - genetics</topic><topic>Genome-Wide Association Study - methods</topic><topic>Genotype</topic><topic>Life Sciences</topic><topic>Linkage Disequilibrium</topic><topic>Phenotype</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Reproducibility of Results</topic><topic>Research Paper</topic><topic>Sequence Analysis, DNA - methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yu, Hui</creatorcontrib><creatorcontrib>You, Xinxin</creatorcontrib><creatorcontrib>Li, Jia</creatorcontrib><creatorcontrib>Zhang, Xinhui</creatorcontrib><creatorcontrib>Zhang, Shuai</creatorcontrib><creatorcontrib>Jiang, Shoujia</creatorcontrib><creatorcontrib>Lin, Xueqiang</creatorcontrib><creatorcontrib>Lin, Hao-Ran</creatorcontrib><creatorcontrib>Meng, Zining</creatorcontrib><creatorcontrib>Shi, Qiong</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Science China. Life sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yu, Hui</au><au>You, Xinxin</au><au>Li, Jia</au><au>Zhang, Xinhui</au><au>Zhang, Shuai</au><au>Jiang, Shoujia</au><au>Lin, Xueqiang</au><au>Lin, Hao-Ran</au><au>Meng, Zining</au><au>Shi, Qiong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping</atitle><jtitle>Science China. Life sciences</jtitle><stitle>Sci. China Life Sci</stitle><addtitle>Sci China Life Sci</addtitle><date>2018-08-01</date><risdate>2018</risdate><volume>61</volume><issue>8</issue><spage>934</spage><epage>946</epage><pages>934-946</pages><issn>1674-7305</issn><eissn>1869-1889</eissn><abstract>The orange-spotted grouper,
Epinephelus coioides
, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms (SNPs) were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including
adgrb2
,
csnkza1
,
cers5
,
col22a1
,
creb5
,
dnd1
,
dzank1
,
dnai1
,
npy2r
,
fat3
,
lrrk2
,
lrp5
,
map3k9
, and so on. Among these candidate genes,
npy2r
(neuropeptide Y receptor Y2) was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.</abstract><cop>Beijing</cop><pub>Science China Press</pub><pmid>29541990</pmid><doi>10.1007/s11427-017-9161-4</doi><tpages>13</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1674-7305 |
| ispartof | Science China. Life sciences, 2018-08, Vol.61 (8), p.934-946 |
| issn | 1674-7305 1869-1889 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_2014142577 |
| source | MEDLINE; SpringerLink Journals; Alma/SFX Local Collection |
| subjects | Animals Bass - genetics Bass - growth & development Biomedical and Life Sciences Body Weight - genetics Chromosome Mapping Chromosomes - genetics Fish Proteins - genetics Genome - genetics Genome-Wide Association Study - methods Genotype Life Sciences Linkage Disequilibrium Phenotype Polymorphism, Single Nucleotide Reproducibility of Results Research Paper Sequence Analysis, DNA - methods |
| title | A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping |
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