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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)

Jurnal Ilmiah Perikanan dan Kelautan · Vol. 15 No. 2 (2023) · hlm. 236–247

DOI
10.20473/jipk.vi.39110
ISSN
2528-0759, 2085-5842
Terbit
2023-01-20
Penerbit
Faculty of Fisheries and Marine Universitas Airlangga
Bahasa
eng
Lisensi
creativecommons.org/licenses/by-nc-sa/4.0

Abstrak

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.

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  • IPB University
  • Hasanuddin University
  • National Research and Innovation Agency
  • Ministry of Marine Affairs and Fisheries
  • Universitas Gadjah Mada
  • Indonesia Open University
  • Indonesian Institute of Sciences
  • Organisasi lain
  • Afiliasi tidak diketahui
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Rekan penulisOrganisasiArtikel bersama
Nurly FaridahMinistry of Marine Affairs and Fisheries3
Utut WidyastutiIPB University2
Nur Bambang Priyo UtomoIPB University2
Widya AsmaraUniversitas Gadjah Mada2
Jaka WidadaUniversitas Gadjah Mada2
Agus Oman SudrajatIPB University2
Fadhila Maharani PutriAfiliasi tidak diketahui2
Dinamella WahjuningrumIPB University2
Dian HardianthoAfiliasi tidak diketahui2
Ade SunarmaAfiliasi tidak diketahui2
Mia SetiawatiIPB University2
Irzal EffendiIPB University2
AlimuddinAfiliasi tidak diketahui2
Sri MurtiniIPB University2
Andi Aliah HidayaniHasanuddin University1
Dody Dh. TrijunoHasanuddin University1
Yushinta FujayaHasanuddin University1
Basse Siang ParawansaHasanuddin University1
Moh. Tauhid UmarHasanuddin University1
Irmawati IrmawatiHasanuddin University1
Aidah Ambo Ala HusainHasanuddin University1
Asmi Citra Malina A.R. TassakkaHasanuddin University1
Nadiarti NadiartiIndonesia Open University1
Andi ParenrengiNational Research and Innovation Agency1
Tri HandayaniIndonesian Institute of Sciences1
Emma SuryatiNational Research and Innovation Agency1
Reni Agustina LubisIPB University1
Dewi YuniatiIPB University1
Shella MarlindaIPB University1
Anna OctaveraIPB University1
Harits Atika AriyatnaNational Research and Innovation Agency1
Sulasy RohmyIPB University1
Shavika MirantiUniversitas Maritim Raja Ali Haji1
AlimuddinIPB University1
. KurdiantoIPB University1
Goro YoshizakiTokyo University of Marine Science and Technology1

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Sumber metadata: OAI-PMH (metadata jurnal) https://e-journal.unair.ac.id/index.php/JIPK/oai, pertama di-harvest 9 Nov 2026, terakhir terlihat 9 Nov 2026.
Metadata asli (oai_dc) 
<oai_dc:dc xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/  http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
	<dc:title xml:lang="en-US">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)  </dc:title>
	<dc:creator>Basuki, Bagus Rahmat</dc:creator>
	<dc:creator>Alimuddin, Alimuddin</dc:creator>
	<dc:creator>Soelistyowati, Dinar Tri</dc:creator>
	<dc:creator>Nuryati, Sri</dc:creator>
	<dc:subject xml:lang="en-US">anti-lipopolysaccharide factor (ALF) gene</dc:subject>
	<dc:subject xml:lang="en-US">ARMS-PCR</dc:subject>
	<dc:subject xml:lang="en-US">Litopenaeus vannamei</dc:subject>
	<dc:subject xml:lang="en-US">Single Nucleotide Polymorphism (SNP) </dc:subject>
	<dc:description xml:lang="en-US">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&amp;gt;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&amp;gt;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.</dc:description>
	<dc:publisher xml:lang="en-US">Faculty of Fisheries and Marine Universitas Airlangga</dc:publisher>
	<dc:date>2023-01-20</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:format>text/xml</dc:format>
	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://e-journal.unair.ac.id/JIPK/article/view/39110</dc:identifier>
	<dc:identifier>10.20473/jipk.vi.39110</dc:identifier>
	<dc:source xml:lang="en-US">Jurnal Ilmiah Perikanan dan Kelautan; Vol. 15 No. 2 (2023): JURNAL ILMIAH PERIKANAN DAN KELAUTAN; 236-247</dc:source>
	<dc:source>2528-0759</dc:source>
	<dc:source>2085-5842</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://e-journal.unair.ac.id/JIPK/article/view/39110/41128</dc:relation>
	<dc:relation>https://e-journal.unair.ac.id/JIPK/article/view/39110/25788</dc:relation>
	<dc:rights xml:lang="en-US">Copyright (c) 2023 Jurnal Ilmiah Perikanan dan Kelautan</dc:rights>
	<dc:rights xml:lang="en-US">http://creativecommons.org/licenses/by-nc-sa/4.0</dc:rights>
</oai_dc:dc>