Non-synonymous polymorphisms in candidate gene associated with growth traits in Channel catfish (Ictalurus punctatus, Rafinesque, 1818)

Suarez-Salgado, Diana; Parra‐Bracamonte, Gaspar Manuel; Benavides-González, Flaviano; Rincón, Ana María; Moreno-Medina, Víctor Ricardo; Rosa-Reyna, Xochitl Fabiola De la

doi:10.1007/s11033-019-05110-0

Cited by 4 publications

(6 citation statements)

References 29 publications

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“…A total of 10 putative SNPs were discovered in IGFBP-3 gene, including a non-synonymous SNP and 9 SNPs located in non-coding sequence (Table 3). Nonsynonymous SNP was rarely occurred in the examined fragments of IGFBP3 gene, which was consistent with previous SNP discoveries in teleost fish, such as salmon (Ferchaud et al, 2018), channel catfish (Suárez-Salgado et al, 2020), sole (Diopere et al, 2013), and turbot (Vera et al, 2013;Robledo et al, 2017). The explanation for this phenomenon is that SNPs in intron regions may accumulate more easily than in exon regions because of the differences in selective pressures (Mu et al, 2011;Zhang et al, 2019).…”

Section: Snps Discoverysupporting

confidence: 89%

“…The putative SNPs were filtered to the next step of SNP validation if they met at least one of two criteria. The first criterion was non-synonymous SNPs because the substitution of amino acid sequence may lead to the changing of structure or function of protein (Diopere et al, 2013), (Suárez-Salgado et al, 2020). The second criterion was that the ratio between alternative nucleotide and reference nucleotide (Alt/Ref) in at least one group was higher than 0.3 and the corresponding genotypic and/or allelic composition between fast-and slow-growing group significantly differed.…”

Section: Snps Discoverymentioning

confidence: 99%

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Non-synonymous polymorphism in IGFBP-3 gene associated with growth traits in striped catfish (Pangasianodon hypophthalmus, Sauvage, 1878)

Tran,

Le,

Nguyen

et al. 2023

Vietnam J. Biotechnol.

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Insulin-like growth factor binding protein-3 (IGFBP-3) has an important role on the growth of teleost fish. The association between genetic variations of IGFBP-3 gene and the growth of striped catfish, Pangasianodon hypophthalmus, was investigated in this study. To discover SNPs, fragments of IGFBP-3 gene from 10 fast-growing fish and 10 slow-growing fish were directly sequenced. Among 10 putative SNPs, a non-synonymous SNP 704 C>G (p.Leu8Val) located at coding region of exon 1 was filtered and subjected to validate in 70 fast-growing fish and 70 slow–growing fish by individual genotyping. Our statistical analysis showed the significant association between SNP 704 C>G (p.Leu8Val) and growth traits of striped catfish (p < 0.01). The genetic diversity of the SNP was evaluated by polymorphism content (PIC) and minor allele frequency (MAF). These values indicated that this SNP was common variant with moderate genetic diversity. The non-synonymous SNP 704 C>G (p.Leu8Val) in IGFBP-3 gene is a potential candidate for subsequent development of molecular marker for growth traits in breeding of the striped catfish.

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Section: Snps Discoverysupporting

confidence: 89%

Section: Snps Discoverymentioning

confidence: 99%

Non-synonymous polymorphism in IGFBP-3 gene associated with growth traits in striped catfish (Pangasianodon hypophthalmus, Sauvage, 1878)

Tran,

Le,

Nguyen

et al. 2023

Vietnam J. Biotechnol.

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“…These discovered SNP, which were determined in both of 20 individuals, were then filtered by criteria illustrated in the Figure 2. Top priority is nonsynonymous SNP because the change of amino acid in protein sequence may has biological significance (Suárez-Salgado et al, 2020), (Diopere et al, 2013). On the other hand, if SNPs are synonymous SNPs or located in non-coding regions, they were continuously evaluated when the ratio of alternative/ reference allele (Alt/Ref) at least in one group ≥0.3.…”

Section: Snp Discoverymentioning

confidence: 99%

Significant association between a non-synonymous snp in IGFBP5 gene and the growth of striped catfish (Pangasianodon hypophthalmus, Sauvage, 1878)

Tran

et al. 2023

Vietnam J. Biotechnol.

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Insulin-like growth factor binding protein 5 (IGFBP5) is the highest conserved member of IGFBP family, and has the broad range of biological activities effecting on the cell growth. This study aims to investigate the association between genetic variation in IGFBP5 gene and the growth of striped catfish (Pangasianodon hypophthalmus). Single nucleotide polymorphisms (SNPs) were discovered and validated in IGFBP5 gene from two growth-selected populations (fast- and slow- growing fish). For SNP discovery, the fragments of IGFBP5 from sample sets of 10 fast- growing fish and 10 slow- growing fish were directly sequenced by Sanger sequencing. In this stage, 4 exonic SNPs were discovered, including a non-synonymous SNP 525 T>A (p. Val16Glu) in exon 1, and three synonymous SNPs (8859 G>A, 11713 C>A, 11992 T>C) in exon 4. The non-synonymous SNP 525 T>A (p.Val16Glu) was filtered to the next step of SNP validation. For validation, the SNP was individually genotyped in the test populations of 70 fast- growing fish and 70 slow- growing fish by single base extension method. Data analysis from the total SNPs which were collected from 80 fast- growing fish and 80 slow- growing fish indicated that non-synonymous SNP 525 T>A (p.Val16Glu) was significantly associated to the growth of striped catfish (p-value <0.001). Analysis of genetic diversity parameters (PIC, MAF) suggested that this SNP is a common variant, contributes significantly to the genetic variance. The non-synonymous SNP 525 T>A (p.Val16Glu) in IGFBP5 gene would become a SNP marker candidate for marker assisted selection (MAS) that can be used in pangasius breeding.

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“…Theoretically, with the current available sequenced genes in different aquaculture species (Dunham & Perera, 2014), resequencing studies may be helpful in the discovering of novel variations, which potentially can be responsible (causal mutation) or associated (linkage disequilibrium) to economical important traits. Recently Suarez‐Salgado et al (2020) explored candidate gene approach and reported novel variations in growth trait related genes in Mexico, but not assessment on meat quality traits are available to date. Two fundamental genes involved in the fatty acid metabolic processes of long chain fatty‐acid biosynthesis are Stearoyl Co‐Desaturase and Fatty Acid Desaturase 2 that have key participation at first stages of the biosynthesis for polyunsaturated fatty acids (Bláhová et al., 2020; Evans et al., 2008) designating them as candidate genes for unrevealing genomic variations and eventually quantitative trait nucleotides.…”

Section: Introductionmentioning

confidence: 99%

“…The Channel catfish ( Ictalurus punctatus, Rafinesque, 1818 ) is one of the most important aquaculture species in the world. After Tilapia, this species represents the most important farmed aquaculture freshwater species of Mexico (Suarez‐Salgado et al, 2020). Based on a traditional management, farms use appearance and size selection and diverse broodstock on their breeding plans.…”

Section: Introductionmentioning

confidence: 99%

Novel polymorphisms in Stearoyl‐CoA Desaturase (SCD) and Fatty Acid Desaturase 2 (FADS2) in channel catfish ( Ictalurus punctatus, Rafinesque, 1818 )

et al. 2021

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The Channel catfish is one of the most important freshwater fish species in North America. Conventionally their selection for genetic improvement is focused in growth related traits but not on quality traits as flavor and fatty acid deposition. The aim of this study was the sequencing of Stearoyl‐CoA Desaturase (SCD) and Fatty Acid Desaturase 2 (FADS2) genes, two of main genes in the biosynthesis of long chain polyunsaturated fatty acids, for novel variation discovering as a preliminary of marker assisted broader assessment. In SCD gene, two novel synonym polymorphisms (Exon 1 and 3) and a non‐synonymous Serine coding polymorphism in exon 3, were found. In FADS2, two synonymous polymorphisms (Exon 1 and 3) and multiple polymorphisms in non‐coding regions were discovered . Further association analysis of these novel variations could reveal punctual effect on fatty acid deposition traits and their utility for marker assisted selection purposes.

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Non-synonymous polymorphisms in candidate gene associated with growth traits in Channel catfish (Ictalurus punctatus, Rafinesque, 1818)

Cited by 4 publications

References 29 publications

Non-synonymous polymorphism in IGFBP-3 gene associated with growth traits in striped catfish (Pangasianodon hypophthalmus, Sauvage, 1878)

Non-synonymous polymorphism in IGFBP-3 gene associated with growth traits in striped catfish (Pangasianodon hypophthalmus, Sauvage, 1878)

Significant association between a non-synonymous snp in IGFBP5 gene and the growth of striped catfish (Pangasianodon hypophthalmus, Sauvage, 1878)

Novel polymorphisms in Stearoyl‐CoA Desaturase (SCD) and Fatty Acid Desaturase 2 (FADS2) in channel catfish ( Ictalurus punctatus, Rafinesque, 1818 )

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