Genome-wide association study of feed conversion ratio in turbot (Scophthalmus maximus) based on genome resequencing
The feed conversion rate (FCR) is a crucial economic trait in aquaculture fish, as feed costs account for the vast majority of aquaculture costs. Given the importance of this trait, there have little efforts to unravel the genomic architecture of FCR and identify key genes or genomic regions useful...
Published in: | Aquaculture Reports |
---|---|
Main Authors: | , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Elsevier
2023
|
Subjects: | |
Online Access: | https://doi.org/10.1016/j.aqrep.2023.101804 https://doaj.org/article/583085e196a641e59a1b41f00a26537c |
id |
ftdoajarticles:oai:doaj.org/article:583085e196a641e59a1b41f00a26537c |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:583085e196a641e59a1b41f00a26537c 2024-01-21T10:10:17+01:00 Genome-wide association study of feed conversion ratio in turbot (Scophthalmus maximus) based on genome resequencing Zhifeng Liu Haowen Chang Fei Xu Haichi Zhao Liguang Zhu Zhibin Sun Mingchao Yang Xinan Wang Aijun Ma 2023-12-01T00:00:00Z https://doi.org/10.1016/j.aqrep.2023.101804 https://doaj.org/article/583085e196a641e59a1b41f00a26537c EN eng Elsevier http://www.sciencedirect.com/science/article/pii/S2352513423003435 https://doaj.org/toc/2352-5134 2352-5134 doi:10.1016/j.aqrep.2023.101804 https://doaj.org/article/583085e196a641e59a1b41f00a26537c Aquaculture Reports, Vol 33, Iss , Pp 101804- (2023) Turbot Feed conversion ratio (FCR) Genome-wide association study (GWAS) Genome resequencing Aquaculture. Fisheries. Angling SH1-691 article 2023 ftdoajarticles https://doi.org/10.1016/j.aqrep.2023.101804 2023-12-24T01:47:31Z The feed conversion rate (FCR) is a crucial economic trait in aquaculture fish, as feed costs account for the vast majority of aquaculture costs. Given the importance of this trait, there have little efforts to unravel the genomic architecture of FCR and identify key genes or genomic regions useful as selection makers. This situation may stem from the inherent swimming behavior of fish, which presents challenges in obtaining individual FCRs. In this work, we developed a specialized small cage culture system. Through this system, the Feed Conversion Ratio (FCR) of 300 individuals was successfully determined, marking the first successful determination of individual FCRs for turbot. The results revealed a range of FCR values from 35.3% to 192.6%, with an average of 126.5% ± 23.5%. On this basis, a genome-wide association study (GWAS) was conducted to identify single nucleotide polymorphisms (SNP) associated with FCR. A total of 2613,115 SNPs on 22 chromosomes were selected for GWAS analysis by Efficient Mixed-Model Association eXpedited (EMMAX) software. A linear mixed model was employed to test the association between each SNP and FCR, considering population structure and genetic relatedness among individuals. Two significant SNPs on Chr6 were identified to be correlated with FCR. According to their localization in genome, four candidate genes were identified on Chr6, including uncharacterized protein KIAA1755, Kinesin Family Member 21B (KIF21B), Discs large homolog-associated protein 4B (DLGAP4B), and Copine 5B (CPNE5B), all of which are closely located in the genome and exhibit significant functional similarities. Our results will facilitate the implementation of marker-assisted selection in breeding programs and serve as a foundation for future research in this area. Article in Journal/Newspaper Scophthalmus maximus Turbot Directory of Open Access Journals: DOAJ Articles Aquaculture Reports 33 101804 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Turbot Feed conversion ratio (FCR) Genome-wide association study (GWAS) Genome resequencing Aquaculture. Fisheries. Angling SH1-691 |
spellingShingle |
Turbot Feed conversion ratio (FCR) Genome-wide association study (GWAS) Genome resequencing Aquaculture. Fisheries. Angling SH1-691 Zhifeng Liu Haowen Chang Fei Xu Haichi Zhao Liguang Zhu Zhibin Sun Mingchao Yang Xinan Wang Aijun Ma Genome-wide association study of feed conversion ratio in turbot (Scophthalmus maximus) based on genome resequencing |
topic_facet |
Turbot Feed conversion ratio (FCR) Genome-wide association study (GWAS) Genome resequencing Aquaculture. Fisheries. Angling SH1-691 |
description |
The feed conversion rate (FCR) is a crucial economic trait in aquaculture fish, as feed costs account for the vast majority of aquaculture costs. Given the importance of this trait, there have little efforts to unravel the genomic architecture of FCR and identify key genes or genomic regions useful as selection makers. This situation may stem from the inherent swimming behavior of fish, which presents challenges in obtaining individual FCRs. In this work, we developed a specialized small cage culture system. Through this system, the Feed Conversion Ratio (FCR) of 300 individuals was successfully determined, marking the first successful determination of individual FCRs for turbot. The results revealed a range of FCR values from 35.3% to 192.6%, with an average of 126.5% ± 23.5%. On this basis, a genome-wide association study (GWAS) was conducted to identify single nucleotide polymorphisms (SNP) associated with FCR. A total of 2613,115 SNPs on 22 chromosomes were selected for GWAS analysis by Efficient Mixed-Model Association eXpedited (EMMAX) software. A linear mixed model was employed to test the association between each SNP and FCR, considering population structure and genetic relatedness among individuals. Two significant SNPs on Chr6 were identified to be correlated with FCR. According to their localization in genome, four candidate genes were identified on Chr6, including uncharacterized protein KIAA1755, Kinesin Family Member 21B (KIF21B), Discs large homolog-associated protein 4B (DLGAP4B), and Copine 5B (CPNE5B), all of which are closely located in the genome and exhibit significant functional similarities. Our results will facilitate the implementation of marker-assisted selection in breeding programs and serve as a foundation for future research in this area. |
format |
Article in Journal/Newspaper |
author |
Zhifeng Liu Haowen Chang Fei Xu Haichi Zhao Liguang Zhu Zhibin Sun Mingchao Yang Xinan Wang Aijun Ma |
author_facet |
Zhifeng Liu Haowen Chang Fei Xu Haichi Zhao Liguang Zhu Zhibin Sun Mingchao Yang Xinan Wang Aijun Ma |
author_sort |
Zhifeng Liu |
title |
Genome-wide association study of feed conversion ratio in turbot (Scophthalmus maximus) based on genome resequencing |
title_short |
Genome-wide association study of feed conversion ratio in turbot (Scophthalmus maximus) based on genome resequencing |
title_full |
Genome-wide association study of feed conversion ratio in turbot (Scophthalmus maximus) based on genome resequencing |
title_fullStr |
Genome-wide association study of feed conversion ratio in turbot (Scophthalmus maximus) based on genome resequencing |
title_full_unstemmed |
Genome-wide association study of feed conversion ratio in turbot (Scophthalmus maximus) based on genome resequencing |
title_sort |
genome-wide association study of feed conversion ratio in turbot (scophthalmus maximus) based on genome resequencing |
publisher |
Elsevier |
publishDate |
2023 |
url |
https://doi.org/10.1016/j.aqrep.2023.101804 https://doaj.org/article/583085e196a641e59a1b41f00a26537c |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_source |
Aquaculture Reports, Vol 33, Iss , Pp 101804- (2023) |
op_relation |
http://www.sciencedirect.com/science/article/pii/S2352513423003435 https://doaj.org/toc/2352-5134 2352-5134 doi:10.1016/j.aqrep.2023.101804 https://doaj.org/article/583085e196a641e59a1b41f00a26537c |
op_doi |
https://doi.org/10.1016/j.aqrep.2023.101804 |
container_title |
Aquaculture Reports |
container_volume |
33 |
container_start_page |
101804 |
_version_ |
1788701542725976064 |