基因组选择信号揭示西×荷杂交牛杂种优势相关基因

中国畜禽种业 ›› 2023, Vol. 19 ›› Issue (7): 9-18.

基因组选择信号揭示西×荷杂交牛杂种优势相关基因

范婷婷¹, 马毅², 王兢¹, 赵国耀¹, 徐凌洋¹, 陈燕¹, 张路培¹, 高会江¹, 李俊雅^1,*, 高雪^1,*

1.中国农业科学院北京畜牧兽医研究所,北京 100193;
2.天津市农业科学院畜牧兽医研究所,天津 300000

收稿日期:2023-03-13 出版日期:2023-07-26 发布日期:2023-07-24
通讯作者: ^*李俊雅（1968—）,男,内蒙古赤峰人,研究员,主要从事肉牛育种及全基因组选择技术研究,E-mail：lijunya@caas.cn;高雪（1976—）,女,陕西汉中人,研究员,主要从事肉牛分子育种及基因组学研究,E-mail：gaoxue76@126.com。
作者简介:范婷婷（1996—）,女,山东聊城人,硕士研究生,主要从事动物遗传育种与繁殖研究,E-mail：2964178431@qq.com。
基金资助:
国家重点研发计划（2018YFD0501802）; 国家自然基金（31572376）; 中国农业科学院创新工程（ASTIP-IAS03）

Detection of Related-Gene of Heterosis in Simmental×Holstein Cross

Fan Tingting¹, Ma Yi², Wang Jing¹, Zhao Guoyao¹, Xu Lingyang¹, Chen Yan¹, Zhang Lupei¹, Gao Huijiang¹, Li Junya^1,*, Gao Xue^1,*

1. Institute of Animal Science of Chinese Academy of Agricultural Sciences, Beijing 100193;
2. Animal Husbandry Institute of Tianjin Academy of Agricultural Sciences, Tianjin, 300000

Received:2023-03-13 Online:2023-07-26 Published:2023-07-24

摘要/Abstract

摘要： 为探究德系西门塔尔牛与荷斯坦牛的杂种优势,挖掘与杂种优势相关的候选基因,解析牛杂种优势的遗传机制。该研究选择系谱信息清晰的德系西门塔尔牛（父本）、荷斯坦牛（母本）及其杂交F₁代共91头个体,利用Illumina Bovine GGP100K高密度芯片进行基因分型,基于群体分化系数Fst对其开展研究,鉴定杂种优势相关基因。结果表明,F₁代与德系西门塔尔牛（父本）Fst分析发现,在全基因组水平Top 1%的阈值内,检测到859个SNPs位点区域Fst值>0.19,注释到候选基因249个;与荷斯坦牛（母本）的Fst分析,发现有860个SNPs位点区域Fst值>0.15,注释到261个候选基因。基因Pathway富集分析发现,F₁代与父本间受到选择的基因主要富集在轴突引导通路（P<0.01）;与母本间受到选择的基因主要富集在灶性粘连和催乳素信号通路（P<0.05）,这些通路上的基因可能对杂交后代杂种优势的产生具有较大的影响。对F₁代与父本、母本共同受到选择的SNPs位点进行定位与注释,鉴定发现共有38个与牛生长发育、产奶、肉质、胴体、繁殖等性状相关的基因,如OXTR、CHKA、PRKN等。结果表明这些基因可能为西×荷杂交牛杂种优势相关基因,并为西荷杂种优势利用提供了参考依据。

关键词: 全基因组, 选择信号, 杂种优势

Abstract: The aim of the study was to explore the heterosis of Simmental and Holstein, excavate its candidate genes associated with heterosis and analyze the genetic mechanisms of heterosis in cattle. 91 individuals including 9 Simmental bulls, 41 Holstein cows and 41 offspring of Simmental×Holstein were selected to conduct a genome-wide selection signal study using the illumina bovine GGP100k high-density chip. The top 1% of Fst value was used as the threshold. The results showed that 859 SNPs（Fst value >0.19) were selected by Fst within threshold of top 1%, and 249 candidate genes were annotated between F₁ offspring and Simmental (paternal). In addition, 860 SNPs（Fst value >0.15) were selected by Fst, and 261 candidate genes were annotated between F₁ offspring and Holstein (maternal). Gene pathway enrichment analysis found that the candidate genes were mainly enriched in the Axon guidance pathway (P<0.01), Focal adhesions and Prolactin signaling pathway (P<0.05) between F₁ and parents, respectively. It was found that 38 genes related to growth and development, milk production, carcass, reproduction and meat quality traits of cattle, such as OXTR, CHKA, PRKN, were positively selected in F₁. These findings will provide a reference for resolving genetic mechanisms of heterosis and guiding heterosis utilization.

Key words: Genome-wide, Selection signal, Heterosis

范婷婷, 马毅, 王兢, 赵国耀, 徐凌洋, 陈燕, 张路培, 高会江, 李俊雅, 高雪. 基因组选择信号揭示西×荷杂交牛杂种优势相关基因[J]. 中国畜禽种业, 2023, 19(7): 9-18.

Fan Tingting, Ma Yi, Wang Jing, Zhao Guoyao, Xu Lingyang, Chen Yan, Zhang Lupei, Gao Huijiang, Li Junya, Gao Xue. Detection of Related-Gene of Heterosis in Simmental×Holstein Cross[J]. The Chinese Livestock and Poultry Breeding, 2023, 19(7): 9-18.

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