Tool for genomic selection and breeding to evolutionary adaptation: Development of a 100K single nucleotide polymorphism array for the honey bee

High-throughput high density genotyping arrays continue to be a fast,
accurate, and cost-effective method for genotyping thousands of
polymorphisms in high numbers of individuals. Here we have developed a new
high-density SNP genotyping array (103 270 SNPs) for honey bees, one of
the most ecologically and economically important pollinators worldwide.
SNPs were detected by conducting whole genome resequencing of 61 honey bee
drones (haploid males) from throughout Europe. Selection of SNPs for the
chip was done in multiple steps using several criteria. The majority of
SNPs were selected based on their location within known candidate regions
or genes underlying a range of honey bee traits, including hygienic
behaviour against pathogens, foraging and subspecies. Additionally,
markers from a GWAS of hygienic behaviour against the major honey bee
parasite Varroa destructor, were brought over. The chip also includes SNPs
associated with each of three major breeding objectives - honey yield,
gentleness and Varroa resistance. We validated the chip and make
recommendations for its use by determining error rates in repeat
genotypings, examining the genotyping performance of different tissues,
and by testing how well different sample types represent the queen’s
genotype. The latter is a key test because it is highly beneficial to be
able to determine the queen’s genotype by non-lethal means. The array is
now publicly available and we suggest it will be a useful tool in genomic
selection and honey bee breeding, as well as for GWAS of different traits,
and for population genomic, adaptation and conservation questions.

高通量高密度基因分型芯片仍是一种快速、精准且经济高效的技术，可对大量个体中的数千个多态性位点进行基因分型。本研究针对蜜蜂——全球生态与经济价值最为突出的传粉昆虫之一，开发了一款全新的高密度单核苷酸多态性（Single Nucleotide Polymorphism，SNP）基因分型芯片，共包含103270个SNP位点。本研究通过对全欧洲范围内的61只雄蜂（单倍体雄性）开展全基因组重测序，筛选得到了上述SNP位点。该芯片的SNP位点筛选历经多轮步骤，并依据多项标准完成：绝大多数SNP位点的筛选依据为其所在位置是否处于已知的候选区域或功能基因内，这些区域与基因关联蜜蜂的多种性状，包括针对病原体的卫生行为、觅食特性与亚种分化。此外，本研究还纳入了针对蜜蜂主要寄生生物瓦螨（Varroa destructor）的卫生行为开展的全基因组关联分析（Genome-Wide Association Study，GWAS）中筛选得到的标记位点。该芯片同时包含与三大核心育种目标相关的SNP位点，分别为蜂蜜产量、温顺性以及瓦螨抗性。本研究通过以下方式对该芯片进行性能验证并给出应用建议：测定重复基因分型的错误率、检测不同组织的基因分型效能，以及验证不同样本类型对蜂王基因型的代表性。后者是一项关键验证，因为通过非致死手段获取蜂王基因型具有极高的应用价值。目前该芯片已对外开放，我们认为其将成为蜜蜂基因组选择、育种工作，以及不同性状的全基因组关联分析、种群基因组学、适应性研究与保护生物学研究的实用工具。