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Vol. 15 No. 2 (2023): JURNAL ILMIAH PERIKANAN DAN KELAUTAN

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Fisheries Biotechnology Molecular Genetics

Identification of a Potential SNP Related to the Expression of Immune Genes and Its Possible Application to Selection of WSSV-Resistant Pacific White Shrimp (Litopenaeus vannamei)

https://doi.org/10.20473/jipk.vi.39110
Bagus Rahmat Basuki
National Broodstock Centre for Shrimp and Mollusk, Ministry of Marine Affairs and Fisheries, Karangasem, Bali, 80811. Indonesia
Alimuddin Alimuddin
Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. Indonesia
https://orcid.org/0000-0002-8252-9148
Dinar Tri Soelistyowati
Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. Indonesia
https://orcid.org/0000-0003-2467-9567
Sri Nuryati
Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. Indonesia
https://orcid.org/0000-0003-1149-1485

Corresponding Author(s) : Alimuddin Alimuddin

alimuddin@apps.ipb.ac.id

Jurnal Ilmiah Perikanan dan Kelautan, Vol. 15 No. 2 (2023): JURNAL ILMIAH PERIKANAN DAN KELAUTAN

Abstract

Highlight Research



  1. A molecular marker for shrimp selection in disease resistance.

  2. Single nucleotide polymorphisms (SNP) in the ALF gene strongly correlate with shrimp resistance to WSSV infection.

  3. Higher ALF gene expression in survivor shrimp.

  4. SNP as molecular marker inherited in the first generation (G1) shrimp.

  5. 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.

Keywords

anti-lipopolysaccharide factor (ALF) gene ARMS-PCR Litopenaeus vannamei Single Nucleotide Polymorphism (SNP)
Basuki, B. R., Alimuddin, A., Soelistyowati, D. T., & Nuryati, S. (2023). 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, 15(2), 236–247. https://doi.org/10.20473/jipk.vi.39110
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Author Biographies

Bagus Rahmat Basuki, National Broodstock Centre for Shrimp and Mollusk, Ministry of Marine Affairs and Fisheries, Karangasem, Bali, 80811. Indonesia

Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. Indonesia

National Broodstock Centre for Shrimp and Mollusk, Ministry of Marine Affairs and Fisheries, Karangasem, Bali, 80811. Indonesia

Alimuddin Alimuddin, Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. Indonesia

Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. Indonesia

Dinar Tri Soelistyowati, Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. Indonesia

Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. Indonesia

Sri Nuryati, Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. Indonesia

Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University Bogor, West Java, 16680. Indonesia

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