Identification of Candidate Growth-Related SNPs and Genes Using GWAS in Brown-Marbled Grouper (Epinephelus fuscoguttatus)
Brown-marbled grouper, Epinephelus fuscoguttatus , is not only an important commercial fish species, but also an important crossbreeding parent in grouper industry. Improvement of growth traits of this species contributes to the development of grouper breeding. Currently, the development of molecula...
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| Veröffentlicht in: | Marine biotechnology (New York, N.Y.) N.Y.), 2020-04, Vol.22 (2), p.153-166 |
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| container_title | Marine biotechnology (New York, N.Y.) |
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| creator | Yang, Yang Wu, Lina Wu, Xi Li, Bijun Huang, Wenhua Weng, Zhuoying Lin, Zixuan Song, Leling Guo, Yin Meng, Zining Liu, Xiaochun Xia, Junhong |
| description | Brown-marbled grouper,
Epinephelus fuscoguttatus
, is not only an important commercial fish species, but also an important crossbreeding parent in grouper industry. Improvement of growth traits of this species contributes to the development of grouper breeding. Currently, the development of molecular marker associated with growth of brown-marbled grouper is rare. Thus, we performed the first genome-wide association study (GWAS) for five growth traits in 172 brown-marbled groupers with 43,688 SNPs detected by ddRAD-seq. We identified a total of 5 significant and 18 suggestive QTLs located in multiple chromosomes associated with growth traits. In the 20 kb window of the significant SNPs and suggestive SNPs, 5 and 14 potential candidate genes affecting growth were detected, respectively. Five potential candidate genes near the significantly associated SNPs were selected for expression analysis. Among of which,
bmp2k
,
wasf1
, and
acyp2
involved in bone development, maintenance of mitochondrion structure, and metabolism were differentially expressed. Interestingly, the SNP 23:29601315 located in the intron of
bmp2k
was significantly associated with body weight, body length, body height, and body thickness and suggestively associated with total length. We verified the locus using another new group including 123 individuals. The results showed that individuals with CC genotype have better growth traits comparing other individuals. Our findings not only contribute to understanding the molecular mechanism of growth regulation, but also promote the advance of marker-assisted selection in brown-marbled grouper. |
| doi_str_mv | 10.1007/s10126-019-09940-8 |
| format | Article |
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Epinephelus fuscoguttatus
, is not only an important commercial fish species, but also an important crossbreeding parent in grouper industry. Improvement of growth traits of this species contributes to the development of grouper breeding. Currently, the development of molecular marker associated with growth of brown-marbled grouper is rare. Thus, we performed the first genome-wide association study (GWAS) for five growth traits in 172 brown-marbled groupers with 43,688 SNPs detected by ddRAD-seq. We identified a total of 5 significant and 18 suggestive QTLs located in multiple chromosomes associated with growth traits. In the 20 kb window of the significant SNPs and suggestive SNPs, 5 and 14 potential candidate genes affecting growth were detected, respectively. Five potential candidate genes near the significantly associated SNPs were selected for expression analysis. Among of which,
bmp2k
,
wasf1
, and
acyp2
involved in bone development, maintenance of mitochondrion structure, and metabolism were differentially expressed. Interestingly, the SNP 23:29601315 located in the intron of
bmp2k
was significantly associated with body weight, body length, body height, and body thickness and suggestively associated with total length. We verified the locus using another new group including 123 individuals. The results showed that individuals with CC genotype have better growth traits comparing other individuals. Our findings not only contribute to understanding the molecular mechanism of growth regulation, but also promote the advance of marker-assisted selection in brown-marbled grouper.</description><identifier>ISSN: 1436-2228</identifier><identifier>EISSN: 1436-2236</identifier><identifier>DOI: 10.1007/s10126-019-09940-8</identifier><identifier>PMID: 31927644</identifier><language>eng</language><publisher>New York: Springer US</publisher><subject>Biomarkers ; Biomedical and Life Sciences ; Body height ; Body length ; Body weight ; Breeding ; Chromosomes ; Commercial fishing ; Commercial species ; Cross-breeding ; crossing ; Engineering ; Epinephelus fuscoguttatus ; Fish ; Fishing ; Freshwater & Marine Ecology ; Gene expression ; gene expression regulation ; Gene loci ; Genes ; genetic markers ; Genome-wide association studies ; genome-wide association study ; Genomes ; genotype ; Genotypes ; grouper ; Growth ; growth traits ; Hybridization ; industry ; introns ; Laboratories ; Length ; Life Sciences ; loci ; Marine fishes ; Marker-assisted selection ; Metabolism ; Microbiology ; mitochondria ; Quantitative trait loci ; Review Article ; Salinity ; Single-nucleotide polymorphism ; skeletal development ; Zoology</subject><ispartof>Marine biotechnology (New York, N.Y.), 2020-04, Vol.22 (2), p.153-166</ispartof><rights>Springer Science+Business Media, LLC, part of Springer Nature 2020</rights><rights>Marine Biotechnology is a copyright of Springer, (2020). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c408t-6e3433ab880e9e503fc411a3b883f682c26ecd2a6e3e75ca6a15592e792555713</citedby><cites>FETCH-LOGICAL-c408t-6e3433ab880e9e503fc411a3b883f682c26ecd2a6e3e75ca6a15592e792555713</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/s10126-019-09940-8$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10126-019-09940-8$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31927644$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yang, Yang</creatorcontrib><creatorcontrib>Wu, Lina</creatorcontrib><creatorcontrib>Wu, Xi</creatorcontrib><creatorcontrib>Li, Bijun</creatorcontrib><creatorcontrib>Huang, Wenhua</creatorcontrib><creatorcontrib>Weng, Zhuoying</creatorcontrib><creatorcontrib>Lin, Zixuan</creatorcontrib><creatorcontrib>Song, Leling</creatorcontrib><creatorcontrib>Guo, Yin</creatorcontrib><creatorcontrib>Meng, Zining</creatorcontrib><creatorcontrib>Liu, Xiaochun</creatorcontrib><creatorcontrib>Xia, Junhong</creatorcontrib><title>Identification of Candidate Growth-Related SNPs and Genes Using GWAS in Brown-Marbled Grouper (Epinephelus fuscoguttatus)</title><title>Marine biotechnology (New York, N.Y.)</title><addtitle>Mar Biotechnol</addtitle><addtitle>Mar Biotechnol (NY)</addtitle><description>Brown-marbled grouper,
Epinephelus fuscoguttatus
, is not only an important commercial fish species, but also an important crossbreeding parent in grouper industry. Improvement of growth traits of this species contributes to the development of grouper breeding. Currently, the development of molecular marker associated with growth of brown-marbled grouper is rare. Thus, we performed the first genome-wide association study (GWAS) for five growth traits in 172 brown-marbled groupers with 43,688 SNPs detected by ddRAD-seq. We identified a total of 5 significant and 18 suggestive QTLs located in multiple chromosomes associated with growth traits. In the 20 kb window of the significant SNPs and suggestive SNPs, 5 and 14 potential candidate genes affecting growth were detected, respectively. Five potential candidate genes near the significantly associated SNPs were selected for expression analysis. Among of which,
bmp2k
,
wasf1
, and
acyp2
involved in bone development, maintenance of mitochondrion structure, and metabolism were differentially expressed. Interestingly, the SNP 23:29601315 located in the intron of
bmp2k
was significantly associated with body weight, body length, body height, and body thickness and suggestively associated with total length. We verified the locus using another new group including 123 individuals. The results showed that individuals with CC genotype have better growth traits comparing other individuals. Our findings not only contribute to understanding the molecular mechanism of growth regulation, but also promote the advance of marker-assisted selection in brown-marbled grouper.</description><subject>Biomarkers</subject><subject>Biomedical and Life Sciences</subject><subject>Body height</subject><subject>Body length</subject><subject>Body weight</subject><subject>Breeding</subject><subject>Chromosomes</subject><subject>Commercial fishing</subject><subject>Commercial species</subject><subject>Cross-breeding</subject><subject>crossing</subject><subject>Engineering</subject><subject>Epinephelus fuscoguttatus</subject><subject>Fish</subject><subject>Fishing</subject><subject>Freshwater & Marine Ecology</subject><subject>Gene expression</subject><subject>gene expression regulation</subject><subject>Gene loci</subject><subject>Genes</subject><subject>genetic markers</subject><subject>Genome-wide association studies</subject><subject>genome-wide association study</subject><subject>Genomes</subject><subject>genotype</subject><subject>Genotypes</subject><subject>grouper</subject><subject>Growth</subject><subject>growth traits</subject><subject>Hybridization</subject><subject>industry</subject><subject>introns</subject><subject>Laboratories</subject><subject>Length</subject><subject>Life Sciences</subject><subject>loci</subject><subject>Marine fishes</subject><subject>Marker-assisted selection</subject><subject>Metabolism</subject><subject>Microbiology</subject><subject>mitochondria</subject><subject>Quantitative trait loci</subject><subject>Review Article</subject><subject>Salinity</subject><subject>Single-nucleotide polymorphism</subject><subject>skeletal 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Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Marine biotechnology (New York, N.Y.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yang, Yang</au><au>Wu, Lina</au><au>Wu, Xi</au><au>Li, Bijun</au><au>Huang, Wenhua</au><au>Weng, Zhuoying</au><au>Lin, Zixuan</au><au>Song, Leling</au><au>Guo, Yin</au><au>Meng, Zining</au><au>Liu, Xiaochun</au><au>Xia, Junhong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of Candidate Growth-Related SNPs and Genes Using GWAS in Brown-Marbled Grouper (Epinephelus fuscoguttatus)</atitle><jtitle>Marine biotechnology (New York, N.Y.)</jtitle><stitle>Mar Biotechnol</stitle><addtitle>Mar Biotechnol (NY)</addtitle><date>2020-04-01</date><risdate>2020</risdate><volume>22</volume><issue>2</issue><spage>153</spage><epage>166</epage><pages>153-166</pages><issn>1436-2228</issn><eissn>1436-2236</eissn><abstract>Brown-marbled grouper,
Epinephelus fuscoguttatus
, is not only an important commercial fish species, but also an important crossbreeding parent in grouper industry. Improvement of growth traits of this species contributes to the development of grouper breeding. Currently, the development of molecular marker associated with growth of brown-marbled grouper is rare. Thus, we performed the first genome-wide association study (GWAS) for five growth traits in 172 brown-marbled groupers with 43,688 SNPs detected by ddRAD-seq. We identified a total of 5 significant and 18 suggestive QTLs located in multiple chromosomes associated with growth traits. In the 20 kb window of the significant SNPs and suggestive SNPs, 5 and 14 potential candidate genes affecting growth were detected, respectively. Five potential candidate genes near the significantly associated SNPs were selected for expression analysis. Among of which,
bmp2k
,
wasf1
, and
acyp2
involved in bone development, maintenance of mitochondrion structure, and metabolism were differentially expressed. Interestingly, the SNP 23:29601315 located in the intron of
bmp2k
was significantly associated with body weight, body length, body height, and body thickness and suggestively associated with total length. We verified the locus using another new group including 123 individuals. The results showed that individuals with CC genotype have better growth traits comparing other individuals. Our findings not only contribute to understanding the molecular mechanism of growth regulation, but also promote the advance of marker-assisted selection in brown-marbled grouper.</abstract><cop>New York</cop><pub>Springer US</pub><pmid>31927644</pmid><doi>10.1007/s10126-019-09940-8</doi><tpages>14</tpages></addata></record> |
| fulltext | fulltext |
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| ispartof | Marine biotechnology (New York, N.Y.), 2020-04, Vol.22 (2), p.153-166 |
| issn | 1436-2228 1436-2236 |
| language | eng |
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| source | SpringerLink Journals - AutoHoldings |
| subjects | Biomarkers Biomedical and Life Sciences Body height Body length Body weight Breeding Chromosomes Commercial fishing Commercial species Cross-breeding crossing Engineering Epinephelus fuscoguttatus Fish Fishing Freshwater & Marine Ecology Gene expression gene expression regulation Gene loci Genes genetic markers Genome-wide association studies genome-wide association study Genomes genotype Genotypes grouper Growth growth traits Hybridization industry introns Laboratories Length Life Sciences loci Marine fishes Marker-assisted selection Metabolism Microbiology mitochondria Quantitative trait loci Review Article Salinity Single-nucleotide polymorphism skeletal development Zoology |
| title | Identification of Candidate Growth-Related SNPs and Genes Using GWAS in Brown-Marbled Grouper (Epinephelus fuscoguttatus) |
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