新疆黑蜂基因组选择信号分析

【目的】 分析新疆黑蜂(Xinjiang Black bee)与4个引进西方蜜蜂品种间的遗传进化关系，并通过检测基因组选择信号，发掘新疆黑蜂重要种质特性相关的候选基因。【方法】 对新疆黑蜂、意大利蜜蜂(Apis mellifera ligustica)、高加索蜂(Apis mellifera caucasica)、卡尼鄂拉蜂(Apis mellifera carnica)、欧洲黑蜂(Apis mellifera mellifera)共5个蜂种50个蜂王个体和1个长白山中华蜜蜂蜂王(Apis cerana cerana)样本进行全基因组重测序数据分析，鉴定新疆黑蜂的单核苷酸多态性(single nucleotide polymorphism，SNP)标记，以长白山中华蜜蜂为外群利用邻接法构建系统进化树以阐明新疆黑蜂的进化关系，利用SNP信息进行新疆黑蜂的主成分分析、群体遗传结构分析及连锁不平衡分析;采用群体遗传分化指数(Fst)和核苷酸多样性比值(θπ)方法检测新疆黑蜂与其他西方蜜蜂群体间的选择信号，并对提取到的受选择区域候选基因进行GO功能和KEGG通路富集分析。【结果】 在新疆黑蜂中共鉴定出1 728 216个SNPs，其中18 526个非同义突变位点是后续研究新疆黑蜂遗传特性候选的SNPs位点;系统进化树和主成分分析结果表明，新疆黑蜂与其他蜂种间存在一定差异，其与卡尼鄂拉蜂、意大利蜂、欧洲黑蜂亲缘关系较近，与高加索蜂亲缘关系较远。群体遗传结构分析表明，在K>3时，新疆黑蜂来自一个与意大利蜂、高加索蜂、卡尼鄂拉蜂、欧洲黑蜂完全不同的独立祖先亚群。连锁不平衡分析表明，新疆黑蜂进化过程中受选择强度较大。GO功能富集分析结果表明，新疆黑蜂受选择基因主要富集于物质代谢、繁殖、信号转导等生物过程，细胞组分富集在细胞器、核小体、染色质和膜等，分子功能主要富集在有机环状化合物结合、离子结合等，并筛选到了Cyp314A1、Trichohyalin-like、CCDC112、Sorbitol dehydrogenase、SPI-3、Fer3HCH、TNS1、Pten、ADSL、Octβ2R、AFFG1、ARHGEF17共12个候选基因。KEGG通路富集分析结果表明，新疆黑蜂受选择基因主要富集于嘌呤代谢、胞吞作用、磷酸肌醇代谢等信号通路。【结论】 利用基因组SNP标记揭示了新疆黑蜂的遗传结构和独立遗传背景，选择作用主要体现在新疆黑蜂品种形成过程中的抗寒、繁殖、生长发育、抗病等方面，研究结果可为中国新疆黑蜂的遗传进化、资源评价及地方蜂种资源的保护利用提供重要遗传信息。

Genome-wide Selection Signal Analysis of Xinjiang Black Bee

【Objective】 This study was aimed to analyze the genetic evolutionary relationship between Xinjiang Black bee and 4 introduced Apis mellifera species,and explore candidate genes related to important germplasm characteristics of Xinjiang Black bee by detecting genome selection signal.【Method】 For Xinjiang Black bee,Apis mellifera ligustica,Apis mellifera caucasica,Apis mellifera carnica,Apis mellifera mellifera,a total of 50 Apis mellifera queen individuals from 5 species and 1 Apis cerana cerana queen were analyzed by whole genome resequencing to identify single nucleotide polymorphism (SNP) markers of Xinjiang Black bee.Apis cerana cerana was taken as reference group,the evolutionary relationship of different species was clarified by constructing Neighbor-Joining tree.SNP information was used to analyze principal component and population genetic structure and linkage disequilibrium of Xinjiang Black bee.Fst and θπ were used to detect the genome-wide selection signal between Xinjiang Black bee and other Apis mellifera populations,and the GO function and KEGG pathway enrichment of candidate genes were analyzed.【Result】 A total of 1 728 216 SNPs were identified in Xinjiang Black bee,18 526 non-synonymous mutation loci might be candidate SNPs for further study on genetic characteristics of Xinjiang Black bee;The result of phylogenetic tree and principal component analysis showed that there were some differences between Xinjiang Black bee and other species,which closely related to Apis mellifera ligustica,Apis mellifera carnica,Apis mellifera mellifera,but far related to Apis mellifera caucasica.Population genetic structure analysis showed that when K>3,Xinjiang Black bee came from an independent ancestral subpopulation,which was completely different from Apis mellifera ligustica,Apis mellifera caucasica,Apis mellifera carnica,Apis mellifera mellifera.Linkage disequilibrium analysis showed that Xinjiang Black bee groups were subjected to stronger selection intensity.The results of selection signal analysis showed that the selected genes of Xinjiang Black bee were mainly enriched in biological process related to substance metabolism,reproduction and endocytosis signaling,the cell component was enriched in the orbumin,nuclear body,chromatin and film,the molecular function was mainly enriched in organic cyclic compound binding,ion bonding and others.12 candidate genes Cyp314A1,Trichohyalin-like,CCDC112,Sorbitol dehydrogenase,SPI-3,Fer3HCH,TNS1,Pten,ADSL,Octβ2R,AFFG1 and ARHGEF17 were screened according to these molecular pathways.KEGG pathway enrichment analysis showed that the selected genes of Xinjiang black bee were mainly enriched in purine metabolism,entosis and phosphoinositol metabolism.【Conclusion】 The genomic SNP revealed the genetic structure and independent genetic background of Xinjiang Black bee,this study indicated that genes associated with cold resistance and reproduction and growth development and disease resistance in the genome of Xinjiang Black bee were subjected to strong selection pressure during variety formation.These selection signals could provide important genetics information for the genetic evolution,evaluation of Xinjiang Black bee,the protection and utilization of the creation of bee resources in China.