基于mtDNA Cyt b序列变异探究柴达木黄牛的母系遗传多样性及遗传背景

doi:3969/j.issn.1004-1524.2023.02.05

浙江农业学报 ›› 2023, Vol. 35 ›› Issue (2): 285-292.DOI: 3969/j.issn.1004-1524.2023.02.05

基于mtDNA Cyt b序列变异探究柴达木黄牛的母系遗传多样性及遗传背景

杨秋蕾¹(), 魏旭东¹, 马志杰¹^,^*(), 陈生梅¹, 晁生玉², 乌兰巴特尔²

1.青海大学畜牧兽医科学院,青海西宁 810016
2.青海省海西州农业技术推广服务中心,青海德令哈 817099

收稿日期:2021-10-05 出版日期:2023-02-25 发布日期:2023-03-14
通讯作者: 马志杰
作者简介:*马志杰,E-mail:zhijiema@126.com
杨秋蕾(1992—),女,辽宁铁岭人,硕士研究生,研究方向为动物遗传资源。E-mail:769391962@qq.com
基金资助:
青海省自然科学基金(2021-ZJ-914);青海省自然科学基金(2017-ZJ-906);国家自然科学基金(31960656)

Maternal genetic diversity and genetic background of Qaidam cattle based on mtDNA Cyt b sequence variations

YANG Qiulei¹(), WEI Xudong¹, MA Zhijie¹^,^*(), CHEN Shengmei¹, CHAO Shengyu², WULAN Bateer²

1. Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China
2. Agro-Technical Extension and Service Center in Haixi Prefecture of Qinghai Province, Delingha 817099, Qinghai, China

Received:2021-10-05 Online:2023-02-25 Published:2023-03-14
Contact: MA Zhijie

摘要/Abstract

摘要：

为探究柴达木黄牛的母系遗传多样性及遗传背景,本研究随机选取柴达木黄牛5个主产区268个个体,通过PCR方法和直接测序技术得到其mtDNA Cyt b基因全序列,使用生物信息学软件分析其遗传多样性、分化及母系起源,进而在分子水平上揭示其母系遗传多样性水平、分化程度及母系遗传背景。结果表明:柴达木黄牛Cyt b基因核苷酸序列长度为1 140 bp,比对分析共检测到29个核苷酸多态位点,其中单一多态位点4个,简约信息位点25个;依据序列间核苷酸变异共确定了12种单倍型,其中优势单倍型为H2,品种单倍型多样度为0.588 2±0.030 0,核苷酸多样度为0.004 0±0.002 2,表明柴达木黄牛具有较丰富的母系遗传多样性。柴达木黄牛品种内5个群体间分化指数Fst值在-0.010 4~0.161 8,提示品种内群体间分化程度存在差异,其中格尔木群体与乌兰群体间分化程度最大(Fst=0.161 8),大柴旦群体和茫崖群体间的分化程度最小(Fst=-0.010 4)。基于UPGMA法的品种内群体间聚类关系表明,柴达木黄牛品种内5个群体可聚为2类,其中格尔木群体与都兰群体最先聚在一起,大柴旦群体与茫崖群体也最先聚为一起,随后它们再聚为1类,而乌兰群体单独为另一类,2类最后聚为一大类。系统发育分析表明,柴达木黄牛由普通牛和瘤牛2个母系遗传支系组成,表明柴达木黄牛有普通牛和瘤牛2个母系起源且以普通牛起源为主。此外,研究发现,茫崖、乌兰、都兰各群体均有1个个体为牦牛mtDNA Cyt b单倍型序列类型,占总头数的1.12%,提示柴达木黄牛品种中存在一定程度的牦牛基因渗入。

关键词: 柴达木黄牛, mtDNA, Cyt b, 遗传多样性, 分化, 母系起源

Abstract:

To investigate the maternal genetic diversity and genetic background of Qaidam cattle,a total of 268 individuals from five main living areas of Qaidam cattle were selected, and the sequences of mtDNA Cyt b gene were obtained by PCR and direct sequencing. Bioinformatics softwares were used to reveal the maternal genetic diversity, differentiation and genetic background of Qaidam cattle. The results showed that the length of nucleotide sequence of Cyt b gene in Qaidam cattle was 1 140 bp. A total of 29 nucleotide polymorphic sites were detected by sequence alignment analysis, including four single polymorphic sites and 25 parsimonious information sites. According to the nucleotide variation among sequences, 12 haplotypes were identified, in which the dominant haplotype was H2. The nucleotide diversity of the breed was 0.004 0±0.002 2 and the haplotype diversity was 0.588 2±0.030 0, which indicated that Qaidam cattle owned rich maternal genetic diversity. The Fst value among five populations in Qaidam cattle was from -0.010 4 to 0.161 8, indicating that the degree of differentiation among populations was different. Among them, the differentiation degree between Golmud population and Wulan population was the highest (Fst=0.161 8), and that between Dachaidan population and Mangya population was the lowest (Fst=-0.010 4). Based on the UPGMA method, the five populations in Qaidam cattle could be clustered into two groups, in which Golmud population and Dulan population were firstly gathered together, and Dachaidan population and Mangya population were also clustered together first, then they were clustered into one group, but Wulan population was an independent group. Lastly, two sub-groups were finally clustered into one big group. Phylogenetic analysis showed that Qaidam cattle was composed of two maternal genetic branches(i.e. Bos taurus and Bos indicus), indicating that it had two maternal origins with mainly originated from Bos taurus. In addition, three individuals in Qaidam cattle carried the Bos grunniens mtDNA Cyt b sequence type. There was each one in Mangya, Wulan and Dulan populations respectively, accounting for 1.12% of the breed, suggesting that there was a certain degree of Bos grunniens genetic introgression in Qaidam cattle.

Key words: Qaidam cattle, mtDNA, Cyt b, genetic diversity, differentiation, maternal origin

中图分类号:

S823.81

杨秋蕾, 魏旭东, 马志杰, 陈生梅, 晁生玉, 乌兰巴特尔. 基于mtDNA Cyt b序列变异探究柴达木黄牛的母系遗传多样性及遗传背景[J]. 浙江农业学报, 2023, 35(2): 285-292.

YANG Qiulei, WEI Xudong, MA Zhijie, CHEN Shengmei, CHAO Shengyu, WULAN Bateer. Maternal genetic diversity and genetic background of Qaidam cattle based on mtDNA Cyt b sequence variations[J]. Acta Agriculturae Zhejiangensis, 2023, 35(2): 285-292.

图/表 5

图1 柴达木黄牛Cyt b基因12种单倍型序列核苷酸变异及其分布 “.”代表与H1单倍型序列中的核苷酸相同。

Fig.1 Distribution and nucleotide variations of 12 haplotypes based on Cyt b of Qaidam cattle “.”represented the same nucleotides as in H1 haplotype sequences.

表1 基于Cyt b序列变异的柴达木黄牛核苷酸多样度和单倍型多样度大小

Table 1 Nucleotide diversity and haplotype diversity of Qaidam cattle based on Cyt b sequence variations

群体 Populations	采样地 Sampling locations	样本数 Sample No.	单倍型数目 Number of haplotypes	核苷酸多样度 Nucleotide diversity	单倍型多样度 Haplotype diversity
格尔木Golmud	格尔木市乌图美仁乡Wutu Meiren Town, Golmud City	88	4	0.103 9±0.062 4	0.599 5±0.040 4
乌兰Wulan	乌兰县柯柯镇Keke Town, Wulan County	58	3	0.011 2±0.013 2	0.329 7±0.073 3
都兰Dulan	都兰县宗加乡、香加乡	61	9	0.188 6±0.102 0	0.713 1±0.042 3
	Zongjia and Xiangjia Towns, Dulan County
大柴旦	大柴旦行政区Dachaidan Administrative District	26	4	0.103 9±0.062 4	0.452 3±0.108 8
Dachaidan
茫崖Mangya	茫崖市Mangya City	32	7	0.179 2±0.099 1	0.695 6±0.079 6
合计Total		265	12	0.004 0±0.002 2	0.588 2±0.030 0

表2 柴达木黄牛品种内群体间Fst值(下三角)和Rst值(上三角)

Table 2 Fst values (Below diagonal) and Rst values (Above diagonal) among five populations in Qaidam cattle

群体Populations	格尔木Golmud	乌兰Wulan	都兰Dulan	大柴旦Dachaidan	茫崖Mangya
格尔木Golmud	—	0.193 0	0	0.036 3	0.020 2
乌兰Wulan	0.161 8	—	0.142 7	0.067 8	0.147 6
都兰Dulan	-0.004 5	0.124 9	—	0.002 9	0.000 2
大柴旦Dachaidan	0.035 0	0.063 5	0.002 9	—	0
茫崖Mangya	0.019 8	0.128 6	0.000 2	-0.010 4	—

图2 基于UPGMA法构建的柴达木黄牛品种内群体间遗传关系聚类图

Fig.2 Clustering map of genetic relationship among populations of Qaidam cattle by UPGMA method

图3 基于NJ法(a)和MJ法(b)构建的柴达木黄牛12种单倍型间系统发育关系图中圆面积大小与各单倍型频率大小成正比。

Fig.3 Phylogenetic relationship among 12 haplotypes of Qaidam cattle based on NJ (a) and MJ (b) methods The size of the circle was proportional to the frequency of each haplotype.

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基于mtDNA Cyt b序列变异探究柴达木黄牛的母系遗传多样性及遗传背景

Maternal genetic diversity and genetic background of Qaidam cattle based on mtDNA Cyt b sequence variations

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