基于RAD-seq测序的狼山鸡基因组选择信号分析

doi:10.16431/j.cnki.1671-7236.2020.09.002

中国畜牧兽医 ›› 2020, Vol. 47 ›› Issue (9): 2706-2714.doi: 10.16431/j.cnki.1671-7236.2020.09.002

基于RAD-seq测序的狼山鸡基因组选择信号分析

朱云芬¹, 殷建玫¹, 张吉发², 李国辉¹, 沈海玉¹, 薛倩¹, 张会永¹, 窦新红¹, 苏一军¹, 韩威¹

1. 江苏省家禽科学研究所, 扬州 225125;
2. 如东县狼山鸡种鸡场, 南通 226400

收稿日期:2020-03-12 出版日期:2020-09-20 发布日期:2020-09-16
通讯作者: 韩威 E-mail:hanwei830@163.com
作者简介:朱云芬(1981-),女,江苏扬州人,硕士,研究方向:家禽遗传资源保护、评价与利用,E-mail:zhuyufen@163.com;殷建玫(1979-),女,江苏扬州人,研究方向:家禽遗传资源保护、评价与利用,E-mail:857211371@qq.com
基金资助:
扬州市自然科学基金项目（YZ2018098）；国家自然科学基金面上项目（31572358）；江苏省"六大人才高峰"高层次人才项目（NY-024）；江苏省重点研发计划（现代农业）专项（BE2019353）；江苏省公益类科研院所自主科研经费项目（BM2018026）

Selective Signal Analysis of Langshan Chickens Based on RAD-seq

ZHU Yunfen¹, YIN Jianmei¹, ZHANG Jifa², LI Guohui¹, SHEN Haiyu¹, XUE Qian¹, ZHANG Huiyong¹, DOU Xinhong¹, SU Yijun¹, HAN Wei¹

1. Jiangsu Institute of Poultry Science, Yangzhou 225125, China;
2. Langshan Chicken Farm in Rudong County, Nantong 226400, China

Received:2020-03-12 Online:2020-09-20 Published:2020-09-16

摘要/Abstract

摘要： 试验旨在分析狼山鸡基因组选择信号，发掘狼山鸡重要种质特性基因。采用简化基因组RAD-seq测序鉴定狼山鸡及其他18个地方鸡种基因组SNP标记，构建系统进化树阐明狼山鸡的遗传结构，采用ZHp选择信号检测方法鉴定狼山鸡基因组受选择区域（基因）。结果显示，在狼山鸡中鉴定出320 874个SNPs。19个地方鸡种总体上聚为五大类，与品种形成历史和区域分布基本一致。狼山鸡16个常染色体上的46个区域受到选择作用（ZHp<-3.5），包含122个受选择基因，其中部分区域在遗传聚类同分支的安义瓦灰鸡（15个区域）、边鸡（14个区域）、大骨鸡（11个区域）和北京油鸡（13个区域）中也受到选择。GO分析结果显示，狼山鸡122个受选择基因显著富集在血细胞生成、转录调控、嗜酸性粒细胞趋化、骨化等生物学过程（P<0.05）。KEGG分析结果显示，狼山鸡122个受选择基因显著富集在心肌细胞肾上腺素能信号传导、Toll样受体信号通路、Ca²⁺信号通路、细胞质DNA传感通路、NOD样受体信号通路等（P<0.05）。选择作用主要体现在对狼山鸡刺激响应、先天免疫、代谢、神经系发育等方面的塑造。研究结果可为狼山鸡品种评价、保护及利用提供重要遗传信息。

关键词: 狼山鸡; 简化基因组测序; 选择信号; 受选择基因; 功能分析

Abstract: To identify characteristic genes of Langshan chickens through genome selection signal testing,RAD-seq simplified genome sequencing technology was employed to identify SNP markers in Langshan and other 18 indigenous chicken breeds.The genetic structure and selected genes were analyzed by constructing phylogenetic tree and testing genome selective signals.The results showed that 320 874 SNPs were identified in Langshan chickens.In general,19 indigenous chicken breeds were grouped into five clusters,which were consistent with the breeding history and geographical distribution.In total,46 selected areas and 122 genes in Langshan chickens were identified through ZHp signal testing (ZHp<-3.5).Among these areas,some were also selected in WH(15 areas),BJ(14 areas),DG(11 areas) and BY((13 areas)) chickens.GO and KEGG function analysis showed that the 122 selected genes in Langshan chickens were mainly enriched in hemopoiesis,regulation of transcription,eosinophil chemotaxis and ossification processes,and adrenergic signaling in cardiomyocytes,Toll-like receptor signaling pathway,calcium signaling pathway,cytosolic DNA-sensing pathway and NOD-like receptor signaling pathway,respectively (P<0.05).The selection mainly functioned on shaping characters of stimulus-response,innate immunity,metabolism as well as nervous system development in Langshan chickens.The results could provide important genetic information for evaluation,conservation and utilization of Langshan chickens.

Key words: Langshan chickens; simplified genome sequencing; selection signal; selection genes; function analysis

中图分类号:

S813.3

朱云芬, 殷建玫, 张吉发, 李国辉, 沈海玉, 薛倩, 张会永, 窦新红, 苏一军, 韩威. 基于RAD-seq测序的狼山鸡基因组选择信号分析[J]. 中国畜牧兽医, 2020, 47(9): 2706-2714.

ZHU Yunfen, YIN Jianmei, ZHANG Jifa, LI Guohui, SHEN Haiyu, XUE Qian, ZHANG Huiyong, DOU Xinhong, SU Yijun, HAN Wei. Selective Signal Analysis of Langshan Chickens Based on RAD-seq[J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(9): 2706-2714.

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基于RAD-seq测序的狼山鸡基因组选择信号分析

Selective Signal Analysis of Langshan Chickens Based on RAD-seq

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