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

doi:3969/j.issn.1004-1524.2023.02.05

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (2): 285-292.DOI: 3969/j.issn.1004-1524.2023.02.05

• Animal Science • Previous Articles Next Articles

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

Abstract

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

CLC Number:

S823.81

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.

Figures/Tables 5

References 23

[1]	BROWN W M. Mechanisms of evolution in animal mitochondrial DNA[J]. Annals of the New York Academy of Sciences, 1981, 361(1): 119-134.
[2]	KOCHER T D, THOMAS W K, MEYER A, et al. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers[J]. Proceedings of the National Academy of Sciences of the United States of America, 1989, 86(16): 6196-6200.
[3]	国家畜禽遗传资源委员会. 中国畜禽遗传资源志-牛志[M]. 北京: 中国农业出版社, 2011:198-200.
[4]	张才骏, 王勇, 卢福山, 等. 柴达木黄牛生化遗传标记的研究[J]. 青海畜牧兽医杂志, 2001, 31(6): 3-5.
	ZHANG C J, WANG Y, LU F S, et al. Investigation of biochemical genetic markers for Chaidamu yellow cattle[J]. Chinese Qhinghai Journal of Animal and Veterinary Sciences, 2001, 31(6): 3-5. (in Chinese with English abstract)
[5]	张才骏, 张海峰, 晃生玉. 柴达木黄牛与我国其他品种黄牛亲缘关系的探讨[J]. 中国畜牧杂志, 2001, 37(6): 9-11.
	ZHANG C J, ZHANG H F, HUANG S Y. Study on the blood relationship among Chaidamu and other breeds of yellow cattle in China[J]. Chinese Journal of Animal Science, 2001, 37(6): 9-11. (in Chinese with English abstract)
[6]	才仁山德布, 许乃军, 董卫民, 等. 柴达木黄牛及其杂种牛α-乳白蛋白和β-乳球蛋白的电泳分析[J]. 青海畜牧兽医杂志, 2001, 31(1): 6-7.
	CAIREN S D B, XU N J, DONG W M, et al. Analysis of α-lactalbumin and β-lactoglobulin for chaidamu yellow cattle and its crossbred cattle by electrophoresis[J]. Chinese Qhinghai Journal of Animal and Veterinary Sciences, 2001, 31(1): 6-7. (in Chinese with English abstract)
[7]	马志杰, 胡双龙, 李瑞哲, 等. 柴达木黄牛Y染色体单倍型组构成及父系起源: 基于USP9Y基因多态性的分析[J]. 中国畜牧杂志, 2017, 53(6): 36-39.
	MA Z J, HU S L, LI R Z, et al. Y chromosome haplogroups and paternal origin of Qaidam cattle: based on the polymor phism analysis of USP9Y gene[J]. Chinese Journal of Animal Science, 2017, 53(6): 36-39. (in Chinese with English abstract)
[8]	马志杰, 夏小婷, 陈生梅, 等. 基于Y染色体ZFY-10标记多态性探究柴达木黄牛父系支系组成和起源[J]. 中国农业大学学报, 2018, 23(6): 70-76.
	MA Z J, XIA X T, CHEN S M, et al. Explore the patrilineal branches and origin of Qaidam cattle based on the polymorphism of Y chromosome ZFY-10 marker[J]. Journal of China Agricultural University, 2018, 23(6): 70-76. (in Chinese with English abstract)
[9]	马志杰, 李瑞哲, 夏小婷, 等. 柴达木黄牛Y-SNPs遗传多样性、群体遗传结构及父系起源[J]. 基因组学与应用生物学, 2018, 37(5): 1920-1925.
	MA Z J, LI R Z, XIA X T, et al. Y-SNPs genetic diversity, population genetic structure and paternal origin of Qaidam cattle[J]. Genomics and Applied Biology, 2018, 37(5): 1920-1925. (in Chinese with English abstract)
[10]	闫碧瑶. 柴达木黄牛的群体基因组学研究[D]. 兰州: 兰州大学, 2019.
	YAN B Y. Population genomics of chaidamu cattle[D]. Lanzhou: Lanzhou University, 2019. (in Chinese with English abstract)
[11]	CHEN N B, CAI Y D, CHEN Q M, et al. Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia[J]. Nature Communications, 2018, 9(1): 2337.
[12]	雷初朝, 陈宏, 杨公社, 等. 中国部分黄牛品种mtDNA遗传多态性研究[J]. 遗传学报, 2004, 31(1): 57-62.
	LEI C Z, CHEN H, YANG G S, et al. Study on mitochondrial DNA genetic diversity of some cattle breeds in China[J]. Acta Genetica Sinica, 2004, 31(1): 57-62. (in Chinese with English abstract)
[13]	LAI S J, LIU Y P, LIU Y X, et al. Genetic diversity and origin of Chinese cattle revealed by mtDNA D-loop sequence variation[J]. Molecular Phylogenetics and Evolution, 2006, 38(1): 146-154.
[14]	CAI X, CHEN H, LEI C Z, et al. mtDNA Diversity and genetic lineages of eighteen cattle breeds from Bos taurus and Bos indicus in China[J]. Genetica, 2007, 131(2): 175-183.
[15]	XIA X, QU K, ZHANG G, et al. Comprehensive analysis of the mitochondrial DNA diversity in Chinese cattle[J]. Animal Genetics, 2019, 50(1): 70-73.
[16]	IRWIN D M, KOCHER T D, WILSON A C. Evolution of the cytochrome b gene of mammals[J]. Journal of Molecular Evolution, 1991, 32(2): 128-144.
[17]	HALL T A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT[J]. Nucleic Acids Symposium Series, 1999, 41(41), 95-98.
[18]	LIBRADO P, ROZAS J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics, 2009, 25(11): 1451-1452.
[19]	EXCOFFIER L, LAVAL G, SCHNEIDER S. Arlequin (version 3.0): an integrated software package for population genetics data analysis[J]. Evolutionary Bioinformatics Online, 2007, 1: 47-50.
[20]	TAMURA K, PETERSON D, PETERSON N, et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods[J]. Molecular Biology and Evolution, 2011, 28(10): 2731-2739.
[21]	BANDELT H J, FORSTER P, RÖHL A. Median-joining networks for inferring intraspecific phylogenies[J]. Molecular Biology and Evolution, 1999, 16(1): 37-48.
[22]	完么才郎. 青海柴达木黄牛种质特性的调查分析[J]. 畜牧兽医科技信息, 2011(8): 124-125.
	WANMO C L. Investigation and analysis of germplasm characteristics of Qinghai Qaidam cattle[J]. Chinese Journal of Animal Husbandry and Veterinary Medicine, 2011(8): 124-125. (in Chinese)
[23]	WRIGHT S. Evolution and genetics of populations. vol.IV: variability within and among natural populations[M]. Chicago: University of Chicago Press, 1978.

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

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

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	—

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	—

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

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 5

References 23

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	HONG Xia, LU Jilai, QI Huijuan, CHEN Xiaoshang. Genetic diversity analysis and core collection construction of ginger (Zingiber officinale Rosc.) germplasm accessions [J]. Acta Agriculturae Zhejiangensis, 2025, 37(6): 1233-1243.
[2]	QIN Douwen, LIU Weiqiang, TIAN Jiting, JU Xiuting. Establishment of cpDNA-PCR reaction system and genetic diversity analysis of Tulipa iliensis [J]. Acta Agriculturae Zhejiangensis, 2025, 37(1): 78-89.
[3]	ZHANG Yuanyuan, FENG Juling, XIAO Jingfeng, GUAN Yu, LONG Chuer, YAO Lirong, MENG Yaxiong, SI Erjing, LI Baochun, MA Xiaole, WANG Huajun, ZHOU Xirong, LIU Meijin, WANG Juncheng. Genetic diversity and association analysis between agronomic traits and SSR markers in hulless barley [J]. Acta Agriculturae Zhejiangensis, 2024, 36(9): 1977-1989.
[4]	DONG Lili, XU Zhihao, YAN Canlong, FAN Xiaoping, JIN Zelan, WANG Zhonghua. Molecular identification and genetic relationship of different breeding populations in Fritillaria thunbergii based on phenotype and molecular markers [J]. Acta Agriculturae Zhejiangensis, 2024, 36(8): 1719-1730.
[5]	HUANG Hui, CHU Tianjiang, XIE Nan, LIU Kai. Investigation on the genetic diversity of Sarcocheilichthys sinensis from diverse geographical populations and other species within the Sarcocheilichthys genus through the analysis of mitochondrial COI sequence segments [J]. Acta Agriculturae Zhejiangensis, 2024, 36(8): 1779-1788.
[6]	MA Li, LAN Yi, XIE Bingxin, ZHOU Chunlu, LUO Shuyuan, XU Wenkun, DONG Xinxing, YAN Dawei. Study of polymorphism in the VRTN gene and its association with production traits in (Duroc×Saba)♂×[Yorkshire×(Landrace×Saba)]♀ [J]. Acta Agriculturae Zhejiangensis, 2024, 36(7): 1502-1510.
[7]	WANG Baogen, CHEN Xiaoyang, WU Jian, LI Xiao, WANG Ying, WANG Jian, WU Xiaohua, LU Zhongfu, SUN Yuyan, DONG Wenqi, LI Guojing, WU Xinyi. Genetic diversity of cowpea landraces in Zhejiang Province, China [J]. Acta Agriculturae Zhejiangensis, 2024, 36(7): 1569-1582.
[8]	ZHU Yanyu, YU Wentao, GAO Shuilian, LYU Shuiyuan, WANG Pan, JIN Wanmin, GUI Wenjing, LIN Yi, YE Naixing. The diversity of tea germplasm resources and genetic relationship of ‘Tieguanyin’-derived varieties in Anxi, Fujian, China [J]. Acta Agriculturae Zhejiangensis, 2024, 36(7): 1591-1601.
[9]	ZHANG Ting, WANG Xueyan, GUO Qinwei, LI Chaosen, LIU Huiqin, XIANG Xiaomin, WEI Jing, ZHAO Dongfeng, WAN Hongjian. Genetic diversity of pepper germplasm resources based on agronomic traits [J]. Acta Agriculturae Zhejiangensis, 2024, 36(2): 325-333.
[10]	YANG Tianwen, WANG Jing, LI Jiong, XU Binqi, CHENG Jiaowen, HONG Yu, CAO Yi, CUI Junjie. Genetic diversity analysis and fingerprint construction of Dading bitter gourd germplasm resources [J]. Acta Agriculturae Zhejiangensis, 2024, 36(1): 103-114.
[11]	WU Qian, TANG Ziyi, TIAN Shengye, HE Haiye, PAN Weiwei, WANG Junfeng, BAO Honghua, ZHANG Huijuan, JIANG Ming. Genetic diversity of Rhododendron huadingense based on SARP molecular marker [J]. Acta Agriculturae Zhejiangensis, 2024, 36(1): 127-133.
[12]	ZHANG Xiaoli, ZHU Linglong, LI Fuzhen, TANG Xiumei, XIA Youlin, YOU Yu, ZHONG Ruichun. Evaluation and analysis of agronomic and quality traits of 115 peanut germplasm resources [J]. Acta Agriculturae Zhejiangensis, 2023, 35(9): 2033-2044.
[13]	YUAN Ye, LIU Rui, WANG Lingyun, SHEN Meng, YE Xuelian, QUAN Xinhua, WANG Ruisen, YAO Xiangtan. Genetic diversity analysis of Trapa L. cultivars in Jiangsu and Zhejiang Provinces using SLAF-seq [J]. Acta Agriculturae Zhejiangensis, 2023, 35(8): 1773-1781.
[14]	WANG Zhihao, XI Xinyan, WANG Li, YANG Shuna, GAO Zhiyuan, YIN Yiming, ZOU Hui, JIA Huijuan. Flower bud formation and physiological biochemistry characteristics of Hongmeiren citrus hybrid in northern Zhejiang, China [J]. Acta Agriculturae Zhejiangensis, 2023, 35(7): 1571-1581.
[15]	SONG Yaping, LEI Zhaoxiong, ZHAO Yi’ang, JIANG Chao, WANG Xingping, LUORENG Zhuoma, MA Yun, WEI Dawei. Cloning of CDS region of bovine FoxO1 gene and analysing expression pattern during adipocyte differentiation [J]. Acta Agriculturae Zhejiangensis, 2023, 35(5): 1016-1027.