Whankaew Sukhuman, Suksri Phassorn, Sinprasertporn Ammara, Thawonsuwan Jumroensri, Sathapondecha Ponsit
Faculty of Technology and Community Development, Thaksin University, Phatthalung Campus, Phatthalung 93210, Thailand.
Center for Genomics and Bioinformatics Research, Division of Biological Sciences, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.
Biology (Basel). 2024 Sep 18;13(9):731. doi: 10.3390/biology13090731.
Shrimp aquaculture is facing a serious disease, acute hepatopancreatic necrosis disease (AHPND), caused by (Vp). For sustainable shrimp aquaculture, massive losses of shrimp infected with Vp must be prevented. Research and selection of shrimp tolerant to Vp 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 were immersed in Vp 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 < 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.
对虾养殖正面临一种由副溶血弧菌（Vp）引起的严重疾病——急性肝胰腺坏死病（AHPND）。为实现对虾养殖的可持续发展，必须防止感染Vp的对虾大量死亡。研究和选育耐Vp感染的对虾是降低AHPND风险的可持续方法。本研究聚焦于利用多样性微阵列技术测序（DArTSeq）和全基因组关联研究来鉴定和开发与AHPND相关的潜在DNA标记。将三个幼体后期对虾群体浸泡在Vp中，以收集易感（D）和耐病（S）样本。使用DArTSeq对45只D组和48只S组对虾的基因型进行分析。从DArTseq数据中总共获得了108,983个单核苷酸多态性（SNP）和17,212个插入缺失（InDel），而最终筛选出等位基因双态性的516个SNP和2,293个InDel，其多态信息含量（PIC）<0.1、最小等位基因频率（MAF）<0.05且检出率≥80%。对筛选出的变异进行与AHPND耐受性的关联分析。尽管在Bonferroni校正阈值以上没有显著相关的SNP和InDel，但提供了对应P值<0.01的四个SNP和17个InDel等候选变异，用于进一步验证AHPND耐受性性状。候选SNP位于锌指蛋白239样基因的一个外显子、一个未表征基因的一个内含子以及基因间区域。大多数候选InDel位于基因间区域，在内含子和外显子区域较少。本研究提供了凡纳滨对虾SNP和InDel的信息。这些标记将支持对虾的变异数据库，并在对虾养殖的育种选择中发挥作用。
