基于RAD-Seq技术的大围山微型鸡遗传进化分析

Study on Genetic Evolution Mechanism of Daweishan Mini Chicken Based on RAD-Seq Technology

【目的】在分子水平上探讨大围山微型鸡的遗传进化。【方法】以大围山微型鸡与其他18个地方鸡品种及2个国外引进品种为研究对象,每个品种选取公鸡10只,母鸡20只,采血,提取全基因组DNA,进行简化基因组测序(RAD-Seq),鉴定21个品种基因组SNP,计算大围山微型鸡遗传统计量,分析遗传多样性和遗传结构、筛选受选择基因并进行功能富集分析。【结果】在大围山微型鸡群体中鉴定出331892个SNPs。大围山微型鸡的平均杂合度(Ho)为0.219、核苷酸多样度(Pi)为0.245,近交系数(Fis)为0.107,与其他18个地方鸡种相比遗传多样性呈中度多态。聚类分析发现,大围山微型鸡与瓢鸡、茶花鸡和藏鸡聚为一类,亲缘关系较近,且与瓢鸡的群体分化指数(Fst)最低(0.0929),亲缘关系最近,与河南斗鸡的Fst最高(0.2179),亲缘关系最远。共筛选出200个受选择基因。GO分析结果显示,这些受选择基因主要富集在运动、刺激应答、信号传导等生物学过程;KEGG分析结果表明,这些受选择基因主要富集在代谢、肌动蛋白细胞骨架的调节、MAPK等信号通路。【结论】大围山微型鸡遗传多样性呈中度多态,与瓢鸡亲缘关系最近,本研究筛选出了200个受到选择的基因,这些基因在代谢、信号传导、颅骨发育等多个方面发挥作用。

【Objective】This study was aimed to explore the genetic evolution of Daweishan Mini chicken at molecular level.【Method】Daweishan Mini chicken and other 18 indigenous chicken breeds,as well as two introduced breeds were used as research objects.10 roosters and 20 hens were selected from each breed.The whole genome DNA was extracted from blood samples,and simplified genome sequencing(RAD-Seq)was carried out to identify genome SNP of 21 breeds.Analysis of genetic structure and diversity of Daweishan Mini chicken,Calculate the genetic statistics,analyze genetic diversity and structure,screen selected genes and perform functional enrichment analysis.【Result】The results showed that 331892 SNPs markers were identified in Daweishan Mini chicken.The population genetic analysis indicated that Daweishan Mini chicken possessed moderate genetic diversity,with the average heterozygosity(Ho,0.219)and nucleotide diversity(Pi,0.245),inbreeding coefficient(Fis,0.107).The results of cluster analysis showed that Daweishan Mini chicken had closer genetical affinity with Piao chicken,Chahua chicken and Tibetan chicken.Daweishan Mini chicken had the lowest Fst(0.0929)with Piao chicken and the highest Fst(0.2179)with Henan Game chicken,which indicated that Daweishan Mini chicken had the closest relationship with Piao chicken and farthest genetic relationship with Game chicken.A total of 200 selected genes were screened out,GO analysis showed that these selected genes were mainly enriched in the biological processes of locomotion,stimulus response and signal transduction.KEGG analysis showed that these genes were mainly enriched in signaling pathways including metabolism,regulation of actin cytoskeleton and MAPK.【Conclusion】The genetic diversity of Daweishan Mini chicken was moderately polymorphic,and it was closely related to Piao chicken.200 selected genes were screened,which would play roles in metabolism,signal transduction and skull development.