基于D-loop区多态性分析新疆地区7个哈萨克牛群体遗传结构和母系起源

doi:10.16431/j.cnki.1671-7236.2025.03.019

Abstract

Abstract: 【Objective】 Mitochondrial DNA (mtNDA) D-loop sequence polymorphism was used as a marker to explore the genetic structure and maternal origin of 7 Kazakh cattle populations in Xinjiang,so as to provide basic data for the rational utilization and biodiversity protection of Xinjiang cattle breeds.【Method】 DNA was extracted from the blood of 179 Kazakh cattle,and the mtDNA D-loop sequence was determined,SnapGene software was used to compare and correct the sequencing sequence with the reference sequence to determine the length and position of the mtDNA D-loop region sequence,and the base content was counted.DnaSP 5.10 software was used to statistically analyze and calculate the parameters of single nucleotide polymorphism (SNP),number of haplotypes (H),nucleotide diversity (Pi) and haplotype diversity (Hd),respectively.The genetic structure of Kazakh cattle population was analyzed by Arlequin 3.0 software.The genetic distance of Kazakh cattle population in mtDNA D-loop region was calculated by Mega 11.0 software,and the Neighbor-Joining (NJ) phylogenetic tree was constructed.【Result】 The complete sequence of mtDNA D-loop region in Kazakh cattle population was 909-911 bp,the average contents of A,G,T and C were 32.8%,13.8%,28.8% and 24.6%,respectively.The content of AT was higher than that of GC.A total of 131 SNPs were detected in 179 individuals,of which the variation sites accounted for 14.40% of the total length of the measured nucleotides,and 89 haplotypes were defined,Hd and Pi were 0.974 and 0.01288,respectively,indicating that the genetic diversity of Kazakh cattle population was very rich.The results of molecular variation analysis showed that 97.13% of the variation was within the population,2.87% was from the variation between populations,and the genetic distance ranged from 0.0109 to 0.0186,the genetic differentiation index (Fst) ranged from ―0.0053 to 0.0782,and there was no significant differentiation (P＞0.05).Phylogenetic tree analysis showed that 7 Kazakh cattle populations in Xinjiang had two maternal origins:Common cattle and zebu cattle.【Conclusion】 Kazakh cattle in Xinjiang were derived from two maternal lines and had rich genetic diversity.Although there was genetic differentiation between populations,while there was no obvious geographical isolation,and the differences in genetic structure were narrowing.The results provided a theoretical reference for conservation and utilization of Kazakh cattle genetic resources.

Key words: Kazakh cattle; mtDNA D-loop; genetic diversity; systematic evolution

CLC Number:

S813.3

WANG Panpan, SHARAMATI·Bodai, BAKHET·Bodai, LI Zhenwei, ORALHAZI·Hazikhan. Analysis of Genetic Structure and Maternal Origin of Seven Kazakh Cattle Populations in Xinjiang Based on D-loop Polymorphism[J]. China Animal Husbandry and Veterinary Medicine, 2025, 52(3): 1166-1179.

References

[1] 汪琦，钟金城，柴志欣，等. 三江黄牛mtDNA Cytb基因序列多态性及其系统进化分析[J]. 中国畜牧杂志，2016，52(15)：20-27. WANG Q, ZHONG J C, CHAI Z X, et al. Genetic diversity and evolution relationship of Sanjiang cattle inferred from mtDNA Cytb[J]. Chinese Journal of Animal Science, 2016, 52(15) : 20-27.(in Chinese)
[2] 石自忠, 王明利, 胡向东, 等. 我国肉牛生产与农业机械化释放效应分析[J].华中农业大学学报(社会科学版), 2016, 126(6):32-40. SHI Z Z, WANG M L, HU X D, et al. Study on beef cattle production and its influence on agricultural mechanization in China[J]. Journal of Huazhong Agricultural University (Social Sciences Edition),2016,126(6):32-40. (in Chinese)
[3] 黄涛. 牛遗传资源评价与利用研究进展[J]. 贵州畜牧兽医, 2014, 38(1):16-18. HUANG T. Research progress on evaluation and utilization of bovine genetic resources[J]. Guizhou Animal Husbandry and Veterinary Science,2014, 38(1):16-18. (in Chinese)
[4] 周建同. 新疆牛品种介绍[J]. 新疆畜牧业，1987, 1：36-37. ZHOU J T. Introduction of cattle breeds in Xinjiang[J]. Xinjiang Animal Husbandry, 1987, 1: 36-37. (in Chinese)
[5] 国家畜禽遗传资源委员会组.中国畜禽遗传资源志—牛志[M]. 北京：中国农业出版社，2011. COMMITTEE ON DOMESTIC LIVESTOCK AND POULTRY GENETIC RESOURCES GROUP. Annals of Livestock and Poultry Genetic Resources in China—Cattle Annals[M]. Beijing: China Agriculture Press, 2011. (in Chinese)
[6] 刘守木, 阿德别克, 卡旦.新疆哈萨克牛[J]. 新疆农业科学, 1983, 2:40-42. LIU S M, ADBUIKE, KADAN. Xinjiang Kazak cattle[J]. Xinjiang Agricultural Sciences, 1983, 2:40-42. (in Chinese)
[7] 古丽娜尔, 阿米娜. 瑞杂牛F1与哈萨克牛育肥对比试验[J]. 甘肃畜牧兽医, 2007, 5:7-8. GUlINAR, AMINA. Comparative experiment on fatten of Riza cattle F1 and Kazak cattle[J]. Gansu Animal Science and Veterinary Medicine, 2007, 5:7-8. (in Chinese)
[8] 闫向民, 谢鹏贵, 李娜，等. 新疆伊犁地区新疆褐牛与哈萨克牛群体改良效果评价分析[J]. 草食家畜, 2019, 6:16-21. YAN X M, XIE P G, LI N, et al. Evaluation on the group improvement effects of Xinjiang Brown cattle and Kazakh cattle in Yili prefecture[J]. Grass-Feeding Livestock, 2019, 6:16-21. (in Chinese)
[9] 王琛琛,王建国,王洋.西门塔尔牛对哈萨克牛改良效果分析[J]. 现代畜牧兽医,2007，10:26-27. WANG C C, WANG J G, WANG Y. Analysis of improvement effect of Simmental cattle on Kazak cattle[J]. Modern Journal of Animal Husbandry and Veterinary Medicine,2007，10:26-27. (in Chinese)
[10] 安宁,余建国,赵青春.用荷斯坦牛改良土种黄牛效果分析[J]. 中国奶牛,2007，1:63. AN N, YU J G, ZHAO Q C. Growth performance of Holstein crossed with local Yellow cattle[J]. China Dairy Cattle,2007，1:63. (in Chinese)
[11] 韩大勇，周春宝，倪黎纲，等. 苏姜猪mtDNA D-loop区序列的遗传多样性分析[J]. 中国畜牧兽医，2023，50(4)：1472-1479. HAN D Y, ZHOU C B, NI L G,et al. Genetic diversity of mtDNA D-loop sequence in Sujiang pig[J]. China Animal Husbandry & Veterinary Medicine, 2023, 50(4): 1472-1479. (in Chinese)
[12] 曹渊婷，黄英飞，王自豪，等. 广西3个地方黄牛品种mtDNA D-loop区序列多态性及起源分析[J]. 中国牛业科学，2022，48(5)：33-38. CAO Y T, HUANG Y F, WANG Z H, et al. Origin and polymorphism of mitochondrial DNA D-loop sequences in three Guangxi cattle breeds[J]. China Cattle Science, 2012, 48(5): 33-38. (in Chinese)
[13] 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 C, CHEN H, YANG G S, et al. Study on mitochondrial DNA genetic diversity of some cattle breeds in China[J]. Journal of Genetics and Genomics, 2004,31(1):57-62. (in Chinese)
[14] 汪琦，钟金城，柴志欣，等.三江黄牛mtDNA D-Loop区遗传多样性及系统进化[J].西北农业学报,2016,25(9):1269-1278. WANG Q, ZHONG J C, CHAI Z X, et al. Analysis of genetic diversity of mtDNA D-Loop regions and phylogenetic evolution of Sanjiang cattle[J]. Acta Agriculturae Boreali-occidentalis Sinica, 2016,25(9):1269-1278. (in Chinese)
[15] 马云，于波，徐永杰，等. 中国部分地方牛种mtDNA D-loop区全序列的遗传多样性与系统进化分析[J].信阳师范学院学报(自然科学版)，2012，25(2):202-205. MA Y, YU B, XU Y J, et al. Analysis of genetic diversity of the mtDNA D-loop regions and phylogenetic evolution of Chinese local cattle[J]. Journal of Xinyang Normal University (Natural Science Edition),2012,25(2):202-205. (in Chinese)
[16] 雷初朝，陈宏，张志清，等. 南阳牛mtDNA D-loop序列多态性分析[J]. 黄牛杂志，2003，1：11-15. LEI C C, CHEN H, ZHANG Z Q, et al. Analysis on sequence polymorphism of mtDNA D-loop region in Nanyang cattle[J]. China Cattle Science, 2003, 1: 11-15. (in Chinese)
[17] LIBRADO P,ROZAS J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics，2009,25(11):1451-1452.
[18] TAMURA K, STECHER G, KUMAR S. Mega 11: Molecular evolutionary genetics analysis version 11[J]. Molecular Biology and Evolution, 2021，38(7):3022-3027.
[19] EXCOFFIER L, LISCHER H E. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows[J]. Molecular Ecology Resources, 2010, 10(3): 564-567.
[20] BANDELT H J, FORSTER P, RÖHL A. Median-Joining networks for inferring intraspecific phylogenies[J]. Molecular Biology and Evolution, 1999, 16(1):37-48.
[21] 李静，郭丽君，王莉，等. 喀喇昆仑-帕米尔地区牦牛mtDNA D-loop区遗传多样性及系统发育分析[J]. 中国畜牧兽医，2020，47(8)：2481-2492. LI J, GUO L J, WANG L, et al. Analyses of genetic diversity and phylogeny of mtDNA D-loop from yak in Karakoram-Pamir area[J]. China Animal Husbandry & Veterinary Medicine, 2020,47(8) : 2481-2492. (in Chinese)
[22] 彭彩淳, 李斌强, 王野影，等.基于线粒体Cytb基因的贵州野猪(Sus scrofa)群体遗传多样性分析[J]. 中国畜牧兽医, 2022, 49(7):2601-2612. PENG C C, LI B Q, WANG Y Y, et al. Genetic diversity analysis of Sus scrofa population in Guizhou based on mitochondrial Cytb gene[J]. China Animal Husbandry & Veterinary Medicine, 2012,49(7):2601-2612. (in Chinese)
[23] 程敏, 石高丽, 刘善斋, 等. 大别山牛mtDNA D-loop区遗传多样性和系统进化分析[J]. 安徽农业大学学报, 2018, 45(5):842-847. CHENG M, SHI G L, LIU S Z, et al. Analysis of genetic variation and phylogeny on mtDNA D-loop regions in Dabieshan cattle[J]. Journal of Anhui Agricultural University, 2018, 45(5):842-847. (in Chinese)
[24] 刘洪瑜，朱一笑，邱孝青，等. 皖南牛mtDNA D-loop区遗传多样性和系统进化分析[J]. 阜阳师范大学学报(自然科学版), 2023, 40(1):13-18. LIU H Y, ZHU Y X, QIU X Q, et al. Genetic diversity and evolution analysis of Wannan Cattle based on mtDNA D-loop region[J]. Journal of Fuyang Normal University (Natural Science Edition), 2023, 40(1):13-18. (in Chinese)
[25] 孙婷，夏小婷，党瑞华，等. 吉安牛mtDNA D-loop区遗传多样性研究[J].中国牛业科学,2018,44(2):1-3. SUN T, XIA X T, DANG R H, et al. Genetic diversity of mitochondrial DNA D-loop region in Ji’an cattle[J]. China Cattle Science, 2018, 44(2):1-3. (in Chinese)
[26] 张桂香，郑友民，王志刚, 等. 我国部分黄牛品种线粒体D-loop区遗传多样性与起源分化[J]. 遗传，2009，31(2)：160-168. ZHANG G X, ZHENG Y M, WANG Z G, et al. Genetic diversity and origin of mitochondria DNA D-loop region of some Chinese indigenous cattle breeds[J]. Hereditas(Beijing), 2009,31(2) : 160-168. (in Chinese)
[27] 邓娟, 张红平, 巴贵, 等.基于Cytb基因多态性研究西藏地区8个藏山羊群体遗传结构及母系起源[J]. 畜牧兽医学报,2018,49(1):65-74. DENG J, ZHANG H P, BA G, et al. Genetic structure and maternal origins of 8 Tibetan goat populations in Tibet inferred from Cytb gene diversity[J]. Acta Veterinaria et Zootechnica Sinica, 2018, 49(1):65-74. (in Chinese)
[28] 郭丹丹, 刘峰, 牛宝龙, 等. 基于线粒体Cytb基因和D-loop区的野生与养殖小黄鱼群体遗传多样性[J]. 浙江农业学报, 2022, 34(9):1856-1865. GUO D D, LIU F, NIU B L, et al. Genetic diversity of wild and cultured populations of little yellow croaker (Larimichthys polyactis) based on mitochondrial Cytb gene and D-loop region[J]. Acta Agriculturae Zhejiangensis, 2012, 34(9):1856-1865. (in Chinese)
[29] WRIGHT S. Evolution in Mendelian populations[J]. Genetics, 1931, 16:97-159.
[30] DENG J, FENG J, LI L, et al. Polymorphisms, differentiation, and phylogeny of 10 Tibetan goat populations inferred from mitochondrial D-loop sequences[J]. Mitochondrial DNA Part A, 2018, 29(3):439-445.
[31] 魏旭东, 徐东辉, 曹萍, 等. 柴达木牛父系遗传多样性、群体结构及与中国北方部分黄牛品种的遗传关系[J]. 浙江大学学报(农业与生命科学版), 2024，28(4)：1-12. WEI X D, XU D H, CAO P, et al. Paternal genetic diversity and population structure of Qaidam cattle and its genetic relationship with other Yellow cattle breeds in Northern China[J]. Journal of Zhejiang University(Agriculture and Life Sciences), 2019, 28(4): 1-12. (in Chinese)
[32] 陈宏，邱怀，詹铁生，等. 中国四品种黄牛性染色体多态性的研究[J]. 遗传, 1993, 15(4):14-17. CHEN H, QIU H, ZHAN T S, et al. Studies on sex chromosome polymorphism of four local cattle (Bos taurus) breeds in China[J]. Hereditas(Beijing), 1993, 15(4):14-17. (in Chinese)
[33] 刘若余, 夏先林, 雷初朝，等. 贵州黄牛mtDNA D-loop遗传多样性研究[J]. 遗传, 2006，3:279-284. LIU R Y, XIA X L, LEI C C, et al. Genetic diversity of mitochondrial DNA D-loop sequences in cattle breeds in Guizhou[J]. Hereditas(Beijing), 2006，3:279-284. (in Chinese)
[34] 赵晓诚，党瑞华，黄永震，等. 岭南牛mtDNA D-loop区遗传多样性研究[J]. 中国牛业科学,2017,43(2):1-3. ZHAO X C, DANG R H, HUANG Y Z, et al. Genetic diversity of mtDNA D-loop region in Lingnan cattle[J]. China Cattle Science, 2017, 43(2):1-3. (in Chinese)
[35] 姚一博，贾媛，夏小婷，等. 湘西黄牛mtDNA D-loop区遗传多样性研究[J]. 中国牛业科学, 2017, 43(5):11-27. YAO Y B, JIA Y, XIA X T, et al. Genetic diversity of mitochondrial DNA D-loop region in Xiangxi cattle[J]. China Cattle Science, 2017, 43(5):11-27. (in Chinese)
[36] 李娜. miRNA、mRNA调控新疆褐牛和哈萨克牛肉质成脂性状分子机制研究[D]. 兰州：甘肃农业大学，2019. LI N. Study on molecular mechanism of miRNA and mRNA regulating the meaty fat-forming traits of Xinjiang Brown cattle and Kazakh cattle[D]. Lanzhou: Gansu Agricultural University, 2019. (in Chinese)

Analysis of Genetic Structure and Maternal Origin of Seven Kazakh Cattle Populations in Xinjiang Based on D-loop Polymorphism

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	LI Chaojie, MENG Meng, LI Bo, JIN Guang, WANG Kun, CHE Leijie, QIAO Xiaochun, ZHANG Yuanqing, NIU Xiaoyan. Analysis of Genetic Diversity and Genetic Differentiations in 3 Local Cattle Populations of Shanxi Province Using Microsatellite Markers [J]. China Animal Husbandry and Veterinary Medicine, 2025, 52(1): 226-237.
[2]	WANG Xintong, ZHANG Yanli, GONG Ying, LIU Xuexue, JIANG Lin, MA Yuehui, LIU Shuqin, PU Yabin. Construction of Specific Genetic Markers for Tibetan Horses Through Population Structure Analysis of Global Domestic Horses [J]. China Animal Husbandry and Veterinary Medicine, 2025, 52(1): 238-248.
[3]	CAO Ping, LI Ruizhe, CHEN Shengmei, XUE Bin, HAN Shenglan, MEI Sa, DA Sang, CAI Jia, SUN Yonggang, MA Zhijie. Paternal Genetic Molecular Assessment of Four Yak Populations in Golog Tibetan Autonomous Prefecture, Qinghai [J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(9): 3948-3957.
[4]	ZHANG Yan, WEI Zhitong, HU Yehao, ZHANG Huaju, ZHANG Man, FU Tong, LIU Xian, LI Zhigang, QI Xinglei, WANG Eryao, ZHANG Zijing, LIANG Dong, GAO Tengyun. Genetic Diversity and Population Structure Analysis of Jiaxian Red Cattle Based on Whole Genome Sequencing [J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(7): 2933-2942.
[5]	HUANG Xianghui, ZHANG Tianneng, ARZUGUL·Musha, WANG Yutao. Genetic Diversity and Phylogenetic Analysis of Goat Population in Karakoram-Pamir Region [J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(6): 2533-2544.
[6]	SHI Haina, WANG Yongjie, LIANG Wanpeng, GENG Zhiguang, LI Shien, XU Zhenfei, LIU Gang, LIU Zhe. Genetic Diversity and Origin Evolution Analysis of Qingyang Donkey Based on mtDNA D-loop Region Sequence [J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(2): 601-613.
[7]	WAN Weican, ZHANG Xu, HUANG Xuan, YAN Haifeng, JIANG Guitao, LI Chuang. Assessment of Conservation Effects of Lingxian White Goose Based on Whole Genome Resequencing [J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(11): 4890-4898.
[8]	YUE Yunfeng, HUANG Weiping, LIU Min, JIN Suyu, HUANG Lin, ZHENG Yucai. Genetic Diversity Analysis of Liangshan Black Sheep Population Based on Mitochondrial Cytb Gene [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(9): 3671-3679.
[9]	LUO Shimin, LI Zhongbo. Genetic Diversity and Genetic Evolution of H and F genes of Canine Distemper Virus in Huaihua District [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(8): 3248-3257.
[10]	HAN Dayong, ZHOU Chunbao, NI Ligang, CHEN Zhangyan, ZHAO Jinming. Genetic Diversity of mtDNA D-loop Sequence in Sujiang Pig [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1472-1479.
[11]	ZHUANG Mingliang, LI Jianfei, GE Peng, WANG Qi, WANG Zhi, QI Jingwen, NIU Qingsheng, LI Zhiyong. Genetic Diversity Study of Changbaishan Chinese Bee [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(12): 4992-4999.
[12]	YE Wen, SUN Dongxiao, HAN Bo. Application Progress on Whole Genome Resequencing in Farm Animals [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(10): 4125-4132.
[13]	XIONG Chenyong, YIN Yanwen, SHI Kaichuang, LI Jun, ZHENG Min, WEI Xiankai, FENG Shuping, LONG Feng, QU Sujie, LU Wenjun, ZHOU Hongjin, HUANG Hailian, XIE Shouyu, LI Zongqiang. Genetic Diversity Analysis of Duck Tembusu Virus in Guangxi During 2019-2021 [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 3099-3111.
[14]	PENG Caichun, LI Binqiang, WANG Yeying, SU Haijun. Genetic Diversity Analysis of Sus scrofa Population in Guizhou Based on Mitochondrial CytbGene [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(7): 2601-2612.
[15]	ZHANG Qiang, LUOSANG Dunzhu, BASANG Wangdui, PENG Yangyang, E Guangxin, NIMA Ciren, SUOLANG Duoji, BA Duo, DAN Ba, XIAN Lili, DANBA Jiacan, ZHI Zhang, PINGCUO Zhandui. Estimation of Genetic Diversity and Population Structure of Five Tibet Yak Populations Using Microsatellites Markers [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(6): 2228-2238.