Identification of a Potential SNP Related to the Expression of Immune Genes and Its Possible Application to Selection of WSSV-Resistant Pacific White Shrimp (<I>Litopenaeus vannamei</I>)
Highlight Research • A molecular marker for shrimp selection in disease resistance. • Single nucleotide polymorphisms (SNP) in the ALF gene strongly correlate with shrimp resistance to WSSV infection. • Higher ALF gene expression in survivor shrimp. • SNP as molecular marker inherited in the fi...
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Faculty of Fisheries and Marine Universitas Airlangga
2023-01-01
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| Series: | Jurnal Ilmiah Perikanan dan Kelautan |
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| Online Access: | https://e-journal.unair.ac.id/JIPK/article/view/39110 |
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| author | Bagus Rahmat Basuki Alimuddin Alimuddin Dinar Tri Soelistyowati Sri Nuryati |
| author_facet | Bagus Rahmat Basuki Alimuddin Alimuddin Dinar Tri Soelistyowati Sri Nuryati |
| author_sort | Bagus Rahmat Basuki |
| collection | DOAJ |
| description | Highlight Research
• A molecular marker for shrimp selection in disease resistance.
• Single nucleotide polymorphisms (SNP) in the ALF gene strongly correlate with shrimp resistance to WSSV infection.
• Higher ALF gene expression in survivor shrimp.
• SNP as molecular marker inherited in the first generation (G1) shrimp.
• ARMS-PCR method successfully detect SNP in the shrimp ALF gene.
Abstract
The Pacific white shrimp (Litopenaeus vannamei) is Indonesia's main export commodity, but its production is constrained by the white spot syndrome virus (WSSV). Selective breeding of disease-resistant broodstock based on single nucleotide polymorphism (SNP) in the anti-lipopolysaccharide factor (ALF) gene is an alternative strategy for solving the disease problem. This study aimed to detect the SNP g.455 A>G in the anti-lipopolysaccharide factor (ALF) shrimp gene, evaluate the correlation of SNP with WSSV-resistance trait, analyze the expression level of immunity genes and genotype frequencies of the WSSV-resistance population shrimp and analyze the SNP inheritance in the first generation of selected shrimp. A total of 120 individuals from 4 families were used to detect the SNP marker using tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). The correlation of the SNP marker with survival rate (SR) was analyzed using a general linear model (GLM) between genotype frequencies and SR. Genotypic similarities between broodstock and pedigree were analyzed using Chi-square. SNP g.455 A>G was successfully detected using the ARMS-PCR method and had a strong correlation between the marker and SR (p-value of AA = 0.012; AG = 0.359, and GG = 0.001). The resistant population has significantly higher ALF and SOD gene expression levels and AA genotype frequency. The SNP marker was inherited, so the broodstock and pedigree have the same genotype frequencies according to chi-square analysis (χ2 = 0.46 and p-value = 0.497). These results suggested that the g.455 genotype AA could be selected to produce WSSV-resistant Pacific white shrimp. |
| format | Article |
| id | doaj-art-9f6bbfc0445c46b08597fd80ff94ff5c |
| institution | DOAJ |
| issn | 2085-5842 2528-0759 |
| language | English |
| publishDate | 2023-01-01 |
| publisher | Faculty of Fisheries and Marine Universitas Airlangga |
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| series | Jurnal Ilmiah Perikanan dan Kelautan |
| spelling | doaj-art-9f6bbfc0445c46b08597fd80ff94ff5c2025-08-20T03:18:55ZengFaculty of Fisheries and Marine Universitas AirlanggaJurnal Ilmiah Perikanan dan Kelautan2085-58422528-07592023-01-0115223624710.20473/jipk.vi.3911037180Identification of a Potential SNP Related to the Expression of Immune Genes and Its Possible Application to Selection of WSSV-Resistant Pacific White Shrimp (<I>Litopenaeus vannamei</I>)Bagus Rahmat Basuki0Alimuddin Alimuddin1https://orcid.org/0000-0002-8252-9148Dinar Tri Soelistyowati2https://orcid.org/0000-0003-2467-9567Sri Nuryati3https://orcid.org/0000-0003-1149-1485National Broodstock Centre for Shrimp and Mollusk, Ministry of Marine Affairs and Fisheries, Karangasem, Bali, 80811. IndonesiaDepartment of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. IndonesiaDepartment of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. IndonesiaDepartment of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. IndonesiaHighlight Research • A molecular marker for shrimp selection in disease resistance. • Single nucleotide polymorphisms (SNP) in the ALF gene strongly correlate with shrimp resistance to WSSV infection. • Higher ALF gene expression in survivor shrimp. • SNP as molecular marker inherited in the first generation (G1) shrimp. • ARMS-PCR method successfully detect SNP in the shrimp ALF gene. Abstract The Pacific white shrimp (Litopenaeus vannamei) is Indonesia's main export commodity, but its production is constrained by the white spot syndrome virus (WSSV). Selective breeding of disease-resistant broodstock based on single nucleotide polymorphism (SNP) in the anti-lipopolysaccharide factor (ALF) gene is an alternative strategy for solving the disease problem. This study aimed to detect the SNP g.455 A>G in the anti-lipopolysaccharide factor (ALF) shrimp gene, evaluate the correlation of SNP with WSSV-resistance trait, analyze the expression level of immunity genes and genotype frequencies of the WSSV-resistance population shrimp and analyze the SNP inheritance in the first generation of selected shrimp. A total of 120 individuals from 4 families were used to detect the SNP marker using tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). The correlation of the SNP marker with survival rate (SR) was analyzed using a general linear model (GLM) between genotype frequencies and SR. Genotypic similarities between broodstock and pedigree were analyzed using Chi-square. SNP g.455 A>G was successfully detected using the ARMS-PCR method and had a strong correlation between the marker and SR (p-value of AA = 0.012; AG = 0.359, and GG = 0.001). The resistant population has significantly higher ALF and SOD gene expression levels and AA genotype frequency. The SNP marker was inherited, so the broodstock and pedigree have the same genotype frequencies according to chi-square analysis (χ2 = 0.46 and p-value = 0.497). These results suggested that the g.455 genotype AA could be selected to produce WSSV-resistant Pacific white shrimp.https://e-journal.unair.ac.id/JIPK/article/view/39110anti-lipopolysaccharide factor (alf) genearms-pcrlitopenaeus vannameisingle nucleotide polymorphism (snp) |
| spellingShingle | Bagus Rahmat Basuki Alimuddin Alimuddin Dinar Tri Soelistyowati Sri Nuryati Identification of a Potential SNP Related to the Expression of Immune Genes and Its Possible Application to Selection of WSSV-Resistant Pacific White Shrimp (<I>Litopenaeus vannamei</I>) Jurnal Ilmiah Perikanan dan Kelautan anti-lipopolysaccharide factor (alf) gene arms-pcr litopenaeus vannamei single nucleotide polymorphism (snp) |
| title | Identification of a Potential SNP Related to the Expression of Immune Genes and Its Possible Application to Selection of WSSV-Resistant Pacific White Shrimp (<I>Litopenaeus vannamei</I>) |
| title_full | Identification of a Potential SNP Related to the Expression of Immune Genes and Its Possible Application to Selection of WSSV-Resistant Pacific White Shrimp (<I>Litopenaeus vannamei</I>) |
| title_fullStr | Identification of a Potential SNP Related to the Expression of Immune Genes and Its Possible Application to Selection of WSSV-Resistant Pacific White Shrimp (<I>Litopenaeus vannamei</I>) |
| title_full_unstemmed | Identification of a Potential SNP Related to the Expression of Immune Genes and Its Possible Application to Selection of WSSV-Resistant Pacific White Shrimp (<I>Litopenaeus vannamei</I>) |
| title_short | Identification of a Potential SNP Related to the Expression of Immune Genes and Its Possible Application to Selection of WSSV-Resistant Pacific White Shrimp (<I>Litopenaeus vannamei</I>) |
| title_sort | identification of a potential snp related to the expression of immune genes and its possible application to selection of wssv resistant pacific white shrimp i litopenaeus vannamei i |
| topic | anti-lipopolysaccharide factor (alf) gene arms-pcr litopenaeus vannamei single nucleotide polymorphism (snp) |
| url | https://e-journal.unair.ac.id/JIPK/article/view/39110 |
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