Development of DNA Markers for Acute Hepatopancreatic Necrosis Disease Tolerance in <i>Litopenaeus vannamei</i> through a Genome-Wide Association Study
Shrimp aquaculture is facing a serious disease, acute hepatopancreatic necrosis disease (AHPND), caused by <i>Vibrio paraheamolyticus</i> (Vp<sub>APHND</sub>). For sustainable shrimp aquaculture, massive losses of shrimp infected with Vp<sub>APHND</sub> must be pr...
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2024-09-01
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| author | Sukhuman Whankaew Phassorn Suksri Ammara Sinprasertporn Jumroensri Thawonsuwan Ponsit Sathapondecha |
| author_facet | Sukhuman Whankaew Phassorn Suksri Ammara Sinprasertporn Jumroensri Thawonsuwan Ponsit Sathapondecha |
| author_sort | Sukhuman Whankaew |
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| description | Shrimp aquaculture is facing a serious disease, acute hepatopancreatic necrosis disease (AHPND), caused by <i>Vibrio paraheamolyticus</i> (Vp<sub>APHND</sub>). For sustainable shrimp aquaculture, massive losses of shrimp infected with Vp<sub>APHND</sub> must be prevented. Research and selection of shrimp tolerant to Vp<sub>APHND</sub> infection is a sustainable approach to reducing the risk of AHPND. This study focused on the identification and development of potential DNA markers associated with AHPND using DArT sequencing (DArTSeq) and a genome-wide association study. Three populations of post-larval <i>Litopenaeus vannamei</i> were immersed in Vp<sub>APHND</sub> to collect susceptible (D) and tolerant (S) samples. The 45 D and 48 S shrimp had their genotypes analyzed using DArTSeq. A total of 108,983 SNPs and 17,212 InDels were obtained from the DArTseq data, while the biallelic 516 SNPs and 2293 InDels were finally filtered with PIC < 0.1, MAF < 0.05, and a call rate ≥ 80%. The filtered variants were analyzed for their association with AHPND tolerance. Although there were no significantly associated SNPs and InDels above the Bonferroni correction threshold, candidate variants, four SNPs and 17 InDels corresponding to <i>p</i> < 0.01, were provided for further validation of the AHPND tolerance trait. The candidate SNPs are located on an exon of the zinc finger protein 239-like gene, an intron of an uncharacterized gene, and in intergenic regions. Most of the candidate InDels are in the intergenic regions, with fewer in the intronic and exonic regions. This study provides information on SNPs and InDels for white shrimp. These markers will support the variant database of shrimp and be useful in shrimp aquaculture for breeding selection. |
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| issn | 2079-7737 |
| language | English |
| publishDate | 2024-09-01 |
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| series | Biology |
| spelling | doaj-art-a0c3bde7c30c4f68a2fb8e993e50b7992025-08-20T01:56:00ZengMDPI AGBiology2079-77372024-09-0113973110.3390/biology13090731Development of DNA Markers for Acute Hepatopancreatic Necrosis Disease Tolerance in <i>Litopenaeus vannamei</i> through a Genome-Wide Association StudySukhuman Whankaew0Phassorn Suksri1Ammara Sinprasertporn2Jumroensri Thawonsuwan3Ponsit Sathapondecha4Faculty of Technology and Community Development, Thaksin University, Phatthalung Campus, Phatthalung 93210, ThailandCenter for Genomics and Bioinformatics Research, Division of Biological Sciences, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, ThailandSongkhla Aquatic Animal Health Research and Development Center, Department of Fisheries, Songkhla 90110, ThailandSongkhla Aquatic Animal Health Research and Development Center, Department of Fisheries, Songkhla 90110, ThailandCenter for Genomics and Bioinformatics Research, Division of Biological Sciences, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, ThailandShrimp aquaculture is facing a serious disease, acute hepatopancreatic necrosis disease (AHPND), caused by <i>Vibrio paraheamolyticus</i> (Vp<sub>APHND</sub>). For sustainable shrimp aquaculture, massive losses of shrimp infected with Vp<sub>APHND</sub> must be prevented. Research and selection of shrimp tolerant to Vp<sub>APHND</sub> infection is a sustainable approach to reducing the risk of AHPND. This study focused on the identification and development of potential DNA markers associated with AHPND using DArT sequencing (DArTSeq) and a genome-wide association study. Three populations of post-larval <i>Litopenaeus vannamei</i> were immersed in Vp<sub>APHND</sub> to collect susceptible (D) and tolerant (S) samples. The 45 D and 48 S shrimp had their genotypes analyzed using DArTSeq. A total of 108,983 SNPs and 17,212 InDels were obtained from the DArTseq data, while the biallelic 516 SNPs and 2293 InDels were finally filtered with PIC < 0.1, MAF < 0.05, and a call rate ≥ 80%. The filtered variants were analyzed for their association with AHPND tolerance. Although there were no significantly associated SNPs and InDels above the Bonferroni correction threshold, candidate variants, four SNPs and 17 InDels corresponding to <i>p</i> < 0.01, were provided for further validation of the AHPND tolerance trait. The candidate SNPs are located on an exon of the zinc finger protein 239-like gene, an intron of an uncharacterized gene, and in intergenic regions. Most of the candidate InDels are in the intergenic regions, with fewer in the intronic and exonic regions. This study provides information on SNPs and InDels for white shrimp. These markers will support the variant database of shrimp and be useful in shrimp aquaculture for breeding selection.https://www.mdpi.com/2079-7737/13/9/731<i>Vibrio parahaemolyticus</i>acute hepatopancreatic necrosis diseaseDArT sequencinggenome-wide association studyshrimp |
| spellingShingle | Sukhuman Whankaew Phassorn Suksri Ammara Sinprasertporn Jumroensri Thawonsuwan Ponsit Sathapondecha Development of DNA Markers for Acute Hepatopancreatic Necrosis Disease Tolerance in <i>Litopenaeus vannamei</i> through a Genome-Wide Association Study Biology <i>Vibrio parahaemolyticus</i> acute hepatopancreatic necrosis disease DArT sequencing genome-wide association study shrimp |
| title | Development of DNA Markers for Acute Hepatopancreatic Necrosis Disease Tolerance in <i>Litopenaeus vannamei</i> through a Genome-Wide Association Study |
| title_full | Development of DNA Markers for Acute Hepatopancreatic Necrosis Disease Tolerance in <i>Litopenaeus vannamei</i> through a Genome-Wide Association Study |
| title_fullStr | Development of DNA Markers for Acute Hepatopancreatic Necrosis Disease Tolerance in <i>Litopenaeus vannamei</i> through a Genome-Wide Association Study |
| title_full_unstemmed | Development of DNA Markers for Acute Hepatopancreatic Necrosis Disease Tolerance in <i>Litopenaeus vannamei</i> through a Genome-Wide Association Study |
| title_short | Development of DNA Markers for Acute Hepatopancreatic Necrosis Disease Tolerance in <i>Litopenaeus vannamei</i> through a Genome-Wide Association Study |
| title_sort | development of dna markers for acute hepatopancreatic necrosis disease tolerance in i litopenaeus vannamei i through a genome wide association study |
| topic | <i>Vibrio parahaemolyticus</i> acute hepatopancreatic necrosis disease DArT sequencing genome-wide association study shrimp |
| url | https://www.mdpi.com/2079-7737/13/9/731 |
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