基于mtDNA和Y染色体基因片段的塔河马鹿种公鹿遗传多样性分析

doi:10.11843/j.issn.0366-6964.2023.06.019

畜牧兽医学报 ›› 2023, Vol. 54 ›› Issue (6): 2402-2413.doi: 10.11843/j.issn.0366-6964.2023.06.019

基于mtDNA和Y染色体基因片段的塔河马鹿种公鹿遗传多样性分析

杨苏坤¹, 董依萌¹, 王洪亮¹, 赵喜堂², 陈旭³, 邢秀梅^1*

1. 中国农业科学院特产研究所农业农村部特种经济动物遗传育种与繁殖重点实验室, 长春 130112;
2. 新疆兵团第二师三十四团农业发展服务中心, 库尔勒 841506;
3. 东北林业大学野生动物与自然保护地学院, 哈尔滨 150006

收稿日期:2022-08-30 出版日期:2023-06-23 发布日期:2023-06-16
通讯作者: 邢秀梅,主要从事特种经济动物种质资源保护与遗传育种研究,E-mail:xingxiumei2004@126.com
作者简介:杨苏坤(1995-),男,山东济宁人,硕士生,主要从事动物遗传资源研究,E-mail:15634530001@163.com
基金资助:
新疆生产建设兵团财政科技计划项目(2021BC005);中国农业科学院科技创新工程(CAAS-ASTIP-2021-ISAPS)

Genetic Diversity Analysis of Stud Tahe Red Deer Based on the Gene Fragments of mtDNA and Y Chromosome

YANG Sukun¹, DONG Yimeng¹, WANG Hongliang¹, ZHAO Xitang², CHEN Xu³, XING Xiumei^1*

1. Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals of Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun 130112, China;
2. Agriculture Development Service Center, Farm No. 34 of Agriculture Division No.2 of Xinjiang Corps, Korla 841506, China;
3. College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150006, China

Received:2022-08-30 Online:2023-06-23 Published:2023-06-16

摘要/Abstract

摘要： 旨在从分子层面探究塔河马鹿种公鹿的遗传多样性和塔河马鹿的祖先类型。本研究在锯茸期采集新鲜血液并提取DNA,通过PCR扩增和直接测序的方法对38头塔河马鹿种公鹿Y染色体的AMELY2、DBY、SRY基因和mtDNA的ND1、COX1、ATP6、ND5、Cytb基因进行分析,计算碱基组成、核苷酸多样性(Pi)、平均核苷酸差异数(K)、Tajima’D值、单倍型数量(H)以及单倍型多样性(Hd)来评估塔河马鹿种公鹿的遗传多样性;构建单倍型网络图并计算各单倍型之间的遗传距离,以白唇鹿为外群构建系统进化树,分析塔河马鹿种公鹿父母系的类型。结果显示,Y染色体的AMELY2、DBY、SRY基因比对后拼接长度为3 577 bp,共检测出17个SNPs多态位点,定义4个单倍型,优势单倍型为Hap-1,所占频率为65.79%。核苷酸多样性为0.001 95,单倍型多样性为0.495 0,遗传多样性水平较低,基于Y染色体基因构建的系统进化树显示存在A、B两大分支。mtDNA的ND1、COX1、ATP6、ND5、Cytb基因比对后拼接长度为6 160 bp,共检测出41个SNPs多态位点,定义8个单倍型,优势单倍型为Hap-1,所占频率为47.37%。核苷酸多样性为0.001 54,单倍型多样性为0.699 9,表现出高单倍型多样性低核苷酸多样性的不平衡状态,遗传多样性处于较低水平,基于mtDNA构建的系统进化树显示存在Ⅰ、Ⅱ两大分支。塔河马鹿种公鹿的遗传多样性处于较低的水平,塔河马鹿群体存在两个祖先类型。

关键词: mtDNA, Y染色体, 塔河马鹿种公鹿, 遗传多样性

Abstract: This study aimed to explore the genetic diversity and the ancestral types of Tahe red deer at the molecular level. DNA was extracted from fresh blood which was collected at the sawn antler stage, PCR amplification and direct sequencing were performed to analyze AMELY2, DBY, SRY genes on Y chromosome and ND1, COX1, ATP6, ND5, Cytb genes of mtDNA in 38 stud Tahe red deer species. Base composition, nucleotide diversity (Pi), mean nucleotide difference (K), Tajima’D value, haplotype number (H) and haplotype diversity (Hd) were calculated to evaluate the genetic diversity of stud Tahe red deer. The haplotype network diagram was constructed and the genetic distance between haplotypes was calculated. The phylogenetic tree was constructed and white-lipped deer was used as the outgroup to analyze the parental lines of stud Tahe red deer. The results showed that the length of the Y chromosome spliced by comparing the AMELY2, DBY and SRY genes was 3 577 bp, and a total of 17 SNPs polymorphic sites were detected, and 4 haplotypes were defined. The dominant haplotype was Hap-1, accounting for 65.79% of the frequency. The nucleotide diversity and haplotype diversity were 0.001 95 and 0.495 0, respectively, showing a low level of genetic diversity. The phylogenetic tree constructed based on the Y chromosome genes showed the existence of two branches, A and B. After comparison of ND1, COX1, ATP6, ND5 and Cytb genes of mtDNA, the splicing length was 6 160 bp, and a total of 41 SNPs polymorphic sites were detected, and 8 haplotypes were defined. The dominant haplotype was Hap-1, accounting for 47.37% of the frequency. The nucleotide diversity and haplotype diversity were 0.001 54 and 0.699 9, respectively, showing an imbalance of high haplotype diversity and low nucleotide diversity, and the genetic diversity was at a low level. The phylogenetic tree constructed based on mtDNA showed the existence of two branches, I and II. The genetic diversity of stud Tahe red deer is at a low level, and there are two ancestral types in the population of Tahe red deer.

Key words: mtDNA, Y chromosome, stud Tahe red deer, genetic diversity

中图分类号:

S813.3

杨苏坤, 董依萌, 王洪亮, 赵喜堂, 陈旭, 邢秀梅. 基于mtDNA和Y染色体基因片段的塔河马鹿种公鹿遗传多样性分析[J]. 畜牧兽医学报, 2023, 54(6): 2402-2413.

YANG Sukun, DONG Yimeng, WANG Hongliang, ZHAO Xitang, CHEN Xu, XING Xiumei. Genetic Diversity Analysis of Stud Tahe Red Deer Based on the Gene Fragments of mtDNA and Y Chromosome[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2402-2413.

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基于mtDNA和Y染色体基因片段的塔河马鹿种公鹿遗传多样性分析

Genetic Diversity Analysis of Stud Tahe Red Deer Based on the Gene Fragments of mtDNA and Y Chromosome

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