College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Int J Mol Sci. 2023 Mar 25;24(7):6238. doi: 10.3390/ijms24076238.
Sacbrood virus (SBV) is a significant problem that impedes brood development in both eastern and western honeybees. Whole-genome sequencing has become an important tool in researching population genetic variations. Numerous studies have been conducted using multiple techniques to suppress SBV infection in honeybees, but the genetic markers and molecular mechanisms underlying SBV resistance have not been identified. To explore single nucleotide polymorphisms (SNPs), insertions, deletions (Indels), and genes at the DNA level related to SBV resistance, we conducted whole-genome resequencing on 90 larvae raised in vitro and challenged with SBV. After filtering, a total of 337.47 gigabytes of clean data and 31,000,613 high-quality SNP loci were detected in three populations. We used ten databases to annotate 9359 predicted genes. By combining population differentiation index (F) and nucleotide polymorphisms (π), we examined genome variants between resistant (R) and susceptible (S) larvae, focusing on site integrity (INT < 0.5) and minor allele frequency (MAF < 0.05). A selective sweep analysis with the top 1% and top 5% was used to identify significant regions. Two SNPs on the 15th chromosome with GenBank KZ288474.1_322717 (Guanine > Cytosine) and KZ288479.1_95621 (Cytosine > Thiamine) were found to be significantly associated with SBV resistance based on their associated allele frequencies after SNP validation. Each SNP was authenticated in 926 and 1022 samples, respectively. The enrichment and functional annotation pathways from significantly predicted genes to SBV resistance revealed immune response processes, signal transduction mechanisms, endocytosis, peroxisomes, phagosomes, and regulation of autophagy, which may be significant in SBV resistance. This study presents novel and useful SNP molecular markers that can be utilized as assisted molecular markers to select honeybees resistant to SBV for breeding and that can be used as a biocontrol technique to protect honeybees from SBV.
Sacbrood 病毒（SBV）是阻碍东方和西方蜜蜂幼虫发育的重大问题。全基因组测序已成为研究种群遗传变异的重要工具。已经使用多种技术对蜜蜂的 SBV 感染进行了大量研究，但尚未确定 SBV 抗性的遗传标记和分子机制。为了探索与 SBV 抗性相关的 DNA 水平的单核苷酸多态性（SNP）、插入、缺失（Indel）和基因，我们对用 SBV 体外感染的 90 头幼虫进行了全基因组重测序。过滤后，在三个群体中检测到 337.47 千兆字节的清洁数据和 31000613 个高质量 SNP 位点。我们使用十个数据库注释了 9359 个预测基因。通过结合种群分化指数（F）和核苷酸多态性（π），我们研究了抗性（R）和易感（S）幼虫之间的基因组变异，重点关注位点完整性（INT < 0.5）和次要等位基因频率（MAF < 0.05）。使用前 1%和前 5%的选择清洗分析来识别显著区域。在 SNP 验证后，发现第 15 号染色体上的两个 SNP，GenBank KZ288474.1_322717（鸟嘌呤>胞嘧啶）和 KZ288479.1_95621（胞嘧啶>硫胺素）与 SBV 抗性显著相关，其相关等位基因频率较高。每个 SNP 分别在 926 和 1022 个样本中进行了验证。对显著预测基因到 SBV 抗性的富集和功能注释途径的研究表明，免疫反应过程、信号转导机制、内吞作用、过氧化物酶体、吞噬体和自噬的调节可能在 SBV 抗性中具有重要意义。本研究提供了新的有用的 SNP 分子标记，可以作为辅助分子标记用于选择对 SBV 具有抗性的蜜蜂进行繁殖，也可以作为一种生物防治技术来保护蜜蜂免受 SBV 的侵害。
