Characterization of rrp44 gene in channel catfish (Ictalurus punctatus): Molecular cloning, tissue distribution, and single nucleotide polymorphisms (SNPs) association analysis with growth traits

Understanding the genetic basis for variations in growth-associated traits in channel catfish (Ictalurus punctatus) has important implications for the catfish breeding industry. Rrp44/Dis3, an RNase II family protein, is the exosome catalytic subunit. Through GWAS significant marker-trait associatio...

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Published in:Aquaculture Reports
Main Authors: Hongyan Liu, Wenping Zhang, Minghua Wang, Siqi Xu, Liqiang Zhong, Wenji Bian, Shiyong Zhang, Xiaohui Chen
Format: Article in Journal/Newspaper
Language:English
Published: Elsevier 2023
Subjects:
Online Access:https://doi.org/10.1016/j.aqrep.2023.101613
https://doaj.org/article/1150afab540441bbb7f78a907691c538
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spelling ftdoajarticles:oai:doaj.org/article:1150afab540441bbb7f78a907691c538 2023-07-16T03:57:25+02:00 Characterization of rrp44 gene in channel catfish (Ictalurus punctatus): Molecular cloning, tissue distribution, and single nucleotide polymorphisms (SNPs) association analysis with growth traits Hongyan Liu Wenping Zhang Minghua Wang Siqi Xu Liqiang Zhong Wenji Bian Shiyong Zhang Xiaohui Chen 2023-06-01T00:00:00Z https://doi.org/10.1016/j.aqrep.2023.101613 https://doaj.org/article/1150afab540441bbb7f78a907691c538 EN eng Elsevier http://www.sciencedirect.com/science/article/pii/S2352513423001527 https://doaj.org/toc/2352-5134 2352-5134 doi:10.1016/j.aqrep.2023.101613 https://doaj.org/article/1150afab540441bbb7f78a907691c538 Aquaculture Reports, Vol 30, Iss , Pp 101613- (2023) Channel catfish Gene clone Growth traits Rrp44/Dis3 SNPs Aquaculture. Fisheries. Angling SH1-691 article 2023 ftdoajarticles https://doi.org/10.1016/j.aqrep.2023.101613 2023-06-25T00:37:42Z Understanding the genetic basis for variations in growth-associated traits in channel catfish (Ictalurus punctatus) has important implications for the catfish breeding industry. Rrp44/Dis3, an RNase II family protein, is the exosome catalytic subunit. Through GWAS significant marker-trait associations were found between the rrp44 gene and growth traits.In this study, we investigated the rrp44 gene in channel catfish through molecular cloning and genomics methods, to explore its potential role in growth. We obtained the full-length coding sequence (2853 bp) of the rrp44 gene, encoding 951 amino acids. Multiple sequence alignments and synteny comparisons confirmed that rrp44 paralogs were widespread in fish genomes (Atlantic cod, Japanese medaka, southern platyfish, channel catfish, Atlantic salmon and zebrafish. Phylogenetic analyses showed that the phylogenetic tree of fish can be divided into four clades (Siluriformes, Cypriniformes, Salmoniformes and Perciformes). In fish, Pangasianodon hypophthalmus, Silurus meridionalis and Ictalurus punctatus have close kinship, in agreement with their traditional taxonomic status. Quantitative real-time PCR demonstrated that rrp44 had the highest expression in the kidneys, and the lowest expression in the spleen. A target-seq strategy was used to screen and genotype single nucleotide polymorphisms (SNPs) of the rrp44 gene. SNP genotypes and diplotypes of the rrp44 gene and their associations with growth traits were also examined. The results revealed 78 SNPs in the rrp44 gene, of which seven (rs2, rs5, rs6, rs13, rs17, rs19 and rs20) were associated with body weight. The masses of fish with the rs2 CC and rs13 GC genotypes were 6.97 % and 5.49 % higher than the group average mass, respectively. Furthermore, rs20 caused a mutation in the RNB domain of Rrp44 (serine to glutamine substitution), and fish carrying one or two copies of the adenine mutant allele of rs20 had significantly higher body mass than GG individuals (P < 0.005). Furthermore, two haploid combinations ... Article in Journal/Newspaper atlantic cod Atlantic salmon Directory of Open Access Journals: DOAJ Articles Aquaculture Reports 30 101613
institution Open Polar
collection Directory of Open Access Journals: DOAJ Articles
op_collection_id ftdoajarticles
language English
topic Channel catfish
Gene clone
Growth traits
Rrp44/Dis3
SNPs
Aquaculture. Fisheries. Angling
SH1-691
spellingShingle Channel catfish
Gene clone
Growth traits
Rrp44/Dis3
SNPs
Aquaculture. Fisheries. Angling
SH1-691
Hongyan Liu
Wenping Zhang
Minghua Wang
Siqi Xu
Liqiang Zhong
Wenji Bian
Shiyong Zhang
Xiaohui Chen
Characterization of rrp44 gene in channel catfish (Ictalurus punctatus): Molecular cloning, tissue distribution, and single nucleotide polymorphisms (SNPs) association analysis with growth traits
topic_facet Channel catfish
Gene clone
Growth traits
Rrp44/Dis3
SNPs
Aquaculture. Fisheries. Angling
SH1-691
description Understanding the genetic basis for variations in growth-associated traits in channel catfish (Ictalurus punctatus) has important implications for the catfish breeding industry. Rrp44/Dis3, an RNase II family protein, is the exosome catalytic subunit. Through GWAS significant marker-trait associations were found between the rrp44 gene and growth traits.In this study, we investigated the rrp44 gene in channel catfish through molecular cloning and genomics methods, to explore its potential role in growth. We obtained the full-length coding sequence (2853 bp) of the rrp44 gene, encoding 951 amino acids. Multiple sequence alignments and synteny comparisons confirmed that rrp44 paralogs were widespread in fish genomes (Atlantic cod, Japanese medaka, southern platyfish, channel catfish, Atlantic salmon and zebrafish. Phylogenetic analyses showed that the phylogenetic tree of fish can be divided into four clades (Siluriformes, Cypriniformes, Salmoniformes and Perciformes). In fish, Pangasianodon hypophthalmus, Silurus meridionalis and Ictalurus punctatus have close kinship, in agreement with their traditional taxonomic status. Quantitative real-time PCR demonstrated that rrp44 had the highest expression in the kidneys, and the lowest expression in the spleen. A target-seq strategy was used to screen and genotype single nucleotide polymorphisms (SNPs) of the rrp44 gene. SNP genotypes and diplotypes of the rrp44 gene and their associations with growth traits were also examined. The results revealed 78 SNPs in the rrp44 gene, of which seven (rs2, rs5, rs6, rs13, rs17, rs19 and rs20) were associated with body weight. The masses of fish with the rs2 CC and rs13 GC genotypes were 6.97 % and 5.49 % higher than the group average mass, respectively. Furthermore, rs20 caused a mutation in the RNB domain of Rrp44 (serine to glutamine substitution), and fish carrying one or two copies of the adenine mutant allele of rs20 had significantly higher body mass than GG individuals (P < 0.005). Furthermore, two haploid combinations ...
format Article in Journal/Newspaper
author Hongyan Liu
Wenping Zhang
Minghua Wang
Siqi Xu
Liqiang Zhong
Wenji Bian
Shiyong Zhang
Xiaohui Chen
author_facet Hongyan Liu
Wenping Zhang
Minghua Wang
Siqi Xu
Liqiang Zhong
Wenji Bian
Shiyong Zhang
Xiaohui Chen
author_sort Hongyan Liu
title Characterization of rrp44 gene in channel catfish (Ictalurus punctatus): Molecular cloning, tissue distribution, and single nucleotide polymorphisms (SNPs) association analysis with growth traits
title_short Characterization of rrp44 gene in channel catfish (Ictalurus punctatus): Molecular cloning, tissue distribution, and single nucleotide polymorphisms (SNPs) association analysis with growth traits
title_full Characterization of rrp44 gene in channel catfish (Ictalurus punctatus): Molecular cloning, tissue distribution, and single nucleotide polymorphisms (SNPs) association analysis with growth traits
title_fullStr Characterization of rrp44 gene in channel catfish (Ictalurus punctatus): Molecular cloning, tissue distribution, and single nucleotide polymorphisms (SNPs) association analysis with growth traits
title_full_unstemmed Characterization of rrp44 gene in channel catfish (Ictalurus punctatus): Molecular cloning, tissue distribution, and single nucleotide polymorphisms (SNPs) association analysis with growth traits
title_sort characterization of rrp44 gene in channel catfish (ictalurus punctatus): molecular cloning, tissue distribution, and single nucleotide polymorphisms (snps) association analysis with growth traits
publisher Elsevier
publishDate 2023
url https://doi.org/10.1016/j.aqrep.2023.101613
https://doaj.org/article/1150afab540441bbb7f78a907691c538
genre atlantic cod
Atlantic salmon
genre_facet atlantic cod
Atlantic salmon
op_source Aquaculture Reports, Vol 30, Iss , Pp 101613- (2023)
op_relation http://www.sciencedirect.com/science/article/pii/S2352513423001527
https://doaj.org/toc/2352-5134
2352-5134
doi:10.1016/j.aqrep.2023.101613
https://doaj.org/article/1150afab540441bbb7f78a907691c538
op_doi https://doi.org/10.1016/j.aqrep.2023.101613
container_title Aquaculture Reports
container_volume 30
container_start_page 101613
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