Molecular cloning and single nucleotide polymorphism analysis of IGF2a genes in the common carp (Cyprinus carpio)

Su, Schneider; Dong, Zaijie; Qu, Junjie; Liang, Zhiqing; Zhang, J.Q.; Ma, Limei; Liu, W.; Xu, Pao; Yuan, Xiang-Nan

doi:10.4238/2012.may.15.3

Cited by 5 publications

(3 citation statements)

References 29 publications

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“…The genome structure of igf2 of L. maculatus comprised four exons and three introns ( Figure 2 ). This structure is consistent with that of other fish types, including largemouth bass ( Micropterus salmoides ), common carp ( Cyprinus carpio ), salmon ( Oncorhynchus keta ), tilapia ( Oreochromis niloticus ), Asian sea bass ( Lates calcarifer ), and pike perch ( Sander lucioperca ) [ 25 , 26 , 27 , 28 , 29 , 30 , 31 ]. This result indicates that the structure of the igf2 genome of fish is relatively conserved.…”

Section: Discussionsupporting

confidence: 83%

Molecular Cloning, Screening of Single Nucleotide Polymorphisms, and Analysis of Growth-Associated Traits of igf2 in Spotted Sea Bass (Lateolabrax maculatus)

Fan

Wang

Zhao

et al. 2023

Animals

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The insulin-like growth factor 2 gene (igf2) is thought to be a key factor that could regulate animal growth. In fish, few researchers have reported on the single nucleotide polymorphisms (SNPs) located in igf2 and their association with growth traits. We screened the SNPs of igf2 from the spotted sea bass (Lateolabrax maculatus) by Sanger sequencing and made an association between these SNPs with growth traits. The full-length complementary (c) DNA of igf2 was 1045 bp, including an open reading frame of 648 bp. The amino acid sequence of Igf2 contained a signal peptide, an IGF domain, and an IGF2_C domain. Multiple sequence alignment showed that the IGF domain and IGF2_C domain were conserved in vertebrates. The genome sequence of igf2 had a length of 6227 bp. Fourteen SNPs (13 in the introns and one in one of the exons) were found in the genome sequence of igf2. Four SNPs located in the intron were significantly associated with growth traits (p < 0.05). These results demonstrated that these SNPs could be candidate molecular markers for breeding programs in L. maculatus.

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Section: Discussionsupporting

confidence: 83%

Molecular Cloning, Screening of Single Nucleotide Polymorphisms, and Analysis of Growth-Associated Traits of igf2 in Spotted Sea Bass (Lateolabrax maculatus)

Fan

Wang

Zhao

et al. 2023

Animals

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“…Two IGF2 sequences ( IGF2a and IGF2b ) were annotated in this region of the common carp genome (Xu et al, 2014b). As most mammals and teleost fishes possess only one IGF2 gene copy, in order to assess the (dis)similarity of these two sequences, Su et al cloned IGF2a and aligned it with IGF2b , and proposed homology between these paralogs in common carp and zebrafish (Su et al, 2012). We aligned the two genomic regions containing these two genes, including the upstream and downstream sequences, and found a high similarity of the two paralogs to their zebrafish orthologs (Figure 4C).…”

Section: Resultsmentioning

confidence: 99%

Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain

et al. 2018

Front. Genet.

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Common carp is one of the oldest and most popular cultured freshwater fish species both globally and in China. In a previous study, we used a carp strain with a long breeding tradition in China, named Huanghe, to create a new fast-growing strain by selection for fast growth for 6 years. The growth performance at 8 months of age has been improved by 20.84%. To achieve this, we combined the best linear unbiased prediction with marker-assisted selection techniques. Recent progress in genome-wide association studies and genomic selection in livestock breeding inspired common carp breeders to consider genome-based breeding approaches. In this study, we developed a 2b-RAD sequence assay as a means of investigating the quantitative trait loci in common carp. A total of 4,953,017,786 clean reads were generated for 250 specimens (average reads/specimen = 19,812,071) with BsaXI Restriction Enzyme. From these, 56,663 SNPs were identified, covering 50 chromosomes and 3,377 scaffolds. Principal component analysis indicated that selection and control groups are relatively clearly distinct. Top 1% of Fst values was selected as the threshold signature of artificial selection. Among the 244 identified loci, genes associated with sex-related factors and nutritional metabolism (especially fat metabolism) were annotated. Eighteen QTL were associated with growth parameters. Body length at 3 months of age and body weight (both at 3 and 8 months) were controlled by polygenic effects, but body size (length, depth, width) at 8 months of age was controlled mainly by several loci with major effects. Importantly, a single shared QTL (IGF2 gene) partially controlled the body length, depth, and width. By merging the above results, we concluded that mainly the genes related to neural pathways, sex and fatty acid metabolism contributed to the improved growth performance of the new Huanghe carp strain. These findings are one of the first investigations into the potential use of genomic selection in the breeding of common carp. Moreover, our results show that combining the Fst, QTL mapping and CRISPR–Cas9 methods can be an effective way to identify important novel candidate molecular markers in economic breeding programs.

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“…Most tetrapods harbor a single bmp2 gene, while two bmp2 genes are reportedly presented in teleosts [27]. Previous studies have shown that the bmp2b gene has the highest expression level in the muscles of common carp (Cyprinus carpio) [28]. Furthermore, the bmp2a gene is highly expressed in calcified bone tissue of the gilthead seabream (Sparus aurata) [29] and in the ovaries of African clawed frogs (Xenopus laevis) [30].…”

Section: Introductionmentioning

confidence: 99%

A Comparative Genomic and Transcriptional Survey Providing Novel Insights into Bone Morphogenetic Protein 2 (bmp2) in Fishes

Guang

Qin

Kou

et al. 2019

IJMS

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Intermuscular bones (IBs) are only found in the muscles of fish. Bone morphogenetic protein 2 (bmp2) is considered to be the most active single osteogenesis factor. It promotes cell proliferation and differentiation during bone repair, as well as inducing the formation of bones and cartilages in vivo. However, detailed investigations of this family in fish are incredibly limited. Here, we have used a variety of published and unpublished bmp2 sequences for teleosts and cartilage fish in order to explore and expand our understanding of bmp2 genes in fish. Our results confirmed that teleost genomes contain two or more bmp2 genes, and the diversity of bmp2 genes in vertebrates appears to be as a result of a combination of whole genome duplication (WGD) and gene loss. Differences were also observed in tissue distribution and relative transcription abundance of the bmp2s through a transcriptomic analysis. Our data also indicated that bmp2b may play an important role in the formation of IBs in teleosts. In addition, protein sequence alignments and 3D structural predictions of bmp2a and bmp2b supported their similar roles in fishes. To summarize, our existing work provided novel insights into the bmp2 family genes in fishes through a mixture of comparative genomic and transcriptomic analysis.

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Molecular cloning and single nucleotide polymorphism analysis of IGF2a genes in the common carp (Cyprinus carpio)

Cited by 5 publications

References 29 publications

Molecular Cloning, Screening of Single Nucleotide Polymorphisms, and Analysis of Growth-Associated Traits of igf2 in Spotted Sea Bass (Lateolabrax maculatus)

Molecular Cloning, Screening of Single Nucleotide Polymorphisms, and Analysis of Growth-Associated Traits of igf2 in Spotted Sea Bass (Lateolabrax maculatus)

Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain

A Comparative Genomic and Transcriptional Survey Providing Novel Insights into Bone Morphogenetic Protein 2 (bmp2) in Fishes

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