柴达木牛和蒙古牛Y染色体基因组遗传多样性与父系起源研究

doi:10.11843/j.issn.0366-6964.2023.03.016

畜牧兽医学报 ›› 2023, Vol. 54 ›› Issue (3): 1026-1033.doi: 10.11843/j.issn.0366-6964.2023.03.016

柴达木牛和蒙古牛Y染色体基因组遗传多样性与父系起源研究

马志杰¹, 王世康², 张卫忠³, 郭卫兴¹, 赵海明⁴, 雷初朝^2*

1. 青海大学畜牧兽医科学院, 农业农村部青藏高原畜禽遗传育种重点实验室, 青海省高原家畜遗传资源保护与创新利用重点实验室, 西宁 810016;
2. 西北农林科技大学动物科技学院, 杨凌 712100;
3. 青海省格尔木市畜牧兽医站, 格尔木 816000;
4. 青海省格尔木市乌图美仁乡畜牧兽医站, 格尔木 816000

收稿日期:2022-09-13 出版日期:2023-03-23 发布日期:2023-03-21
通讯作者: 雷初朝,主要从事牛遗传资源研究,E-mail:leichuzhao1118@126.com
作者简介:马志杰(1978-)，男，甘肃张家川人，博士，主要从事高原动物遗传资源研究，E-mail:zhijiema@126.com
基金资助:
青海省自然科学基金项目(2021-ZJ-914)；国家肉牛牦牛产业技术体系(CARS-37)；青海省“昆仑英才·高端创新创业人才”计划项目

Y-chromosome Genomic Diversity and Paternal Origins of Qaidam Cattle and Mongolian Cattle

MA Zhijie¹, WANG Shikang², ZHANG Weizhong³, GUO Weixing¹, ZHAO Haiming⁴, LEI Chuzhao^2*

1. Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Key Laboratory of Livestock and Poultry Genetics and Breeding on the Qinghai-Tibet Plateau of Ministry of Agriculture and Rural Affairs, Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China;
2. College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling 712100, China;
3. Station of Animal Science and Veterinary Medicine of Golmud City of Qinghai Province, Golmud 816000, China;
4. Station of Animal Science and Veterinary Medicine of Wutumeiren Town in Golmud City of Qinghai Province, Golmud 816000, China

Received:2022-09-13 Online:2023-03-23 Published:2023-03-21

摘要/Abstract

摘要： 旨在从基因组水平探究柴达木牛和蒙古牛的父系遗传多样性和起源进化关系。本研究采用全基因组重测序技术对柴达木牛品种5个不同地理群体共计22个个体和蒙古牛23个个体的Y染色体单拷贝基因区进行SNP扫描，使用生物信息学方法分析其父系遗传多样性和系统发育关系。结果表明，22头柴达木牛共定义了4种单倍型，其单倍型多样度为0.610±0.093，核苷酸多样度为0.074±0.015，而23头蒙古牛共确定了10种单倍型，其单倍型多样度为0.925±0.025，核苷酸多样度为0.137±0.013，表明柴达木牛相比蒙古牛其父系遗传多样性较低。构建的系统发育树和单倍型网络图表明，22头柴达木牛明显地分为Y1(18.2%)和Y2(81.8%)两个单倍型组，其中Y2为优势单倍型组，Y2单倍型组又包括Y2a(18.2%)与Y2b(63.6%)两种亚单倍型组，其中Y2b亚单倍型组占优势，表明柴达木牛有Y1与Y2 两个父系起源；蒙古牛也拥有Y1(17.4%)和Y2(82.6%)两个父系起源，但Y2单倍型组以Y2a为主要亚单倍型组(47.8%)。上述结果表明，柴达木牛和蒙古牛具有相似的父系遗传组成，但考虑到柴达木牛的父系遗传多样性较低，故建议加大该品种内群体间种公牛的基因交流，提高其遗传多样性水平。本研究为明确柴达木牛和蒙古牛父系遗传差异，开展其种质资源的保护和开发利用提供了理论依据。

关键词: 柴达木牛, 蒙古牛, Y染色体基因组, SNP, 父系起源

Abstract: The study aimed to investigate the genetic diversity and evolutionary relationships of the sires from Qaidam cattle and Mongolian cattle at genomic level. In this study, the whole genome resequencing was used to scan the Y-chromosome single copy gene regions of a total of 22 individuals from 5 different geographical populations of the Qaidam cattle and 23 individuals from Mongolian cattle, and their paternal genetic diversity and phylogenetic relationship were analyzed using bioinformatics methods. The results showed that a total of 4 haplotypes were defined in 22 Qaidam cattle, with a haplotype diversity of 0.610±0.093 and a nucleotide diversity of 0.074±0.015, whereas a total of 10 haplotypes were identified in 23 Mongolian cattle, with a haplotype diversity of 0.925±0.025 and a nucleotide diversity of 0.137±0.013, indicating that Qaidam cattle had lower paternal genetic diversity compared to Mongolian cattle. The phylogenetic tree and haplotype network diagrams constructed showed that the 22 Qaidam cattle were clearly divided into two haplogroups, namely Y1 (18.2%) and Y2 (81.8%), of which Y2 was the dominant haplogroup, and the Y2 haplogroup included two sub-haplogroups, namely Y2a (18.2%) and Y2b (63.6%), of which the Y2b sub-haplogroup was dominant, indicating that the Qaidam cattle had both Y1 and Y2 paternal origins. Mongolian cattle also had both Y1 (17.4%) and Y2 (82.6%) paternal origins, but the Y2 haplogroup was dominated by the Y2a sub-haplogroup (47.8%). The above results suggest that Qaidam and Mongolian cattle have similar paternal genetic composition. However, considering the lower paternal genetic diversity of Qaidam cattle, it is suggested to increase the gene exchange of bulls from different populations within this breed for improving their genetic diversity. This study provides a theoretical basis for clarifying the paternal genetic differences between Qaidam cattle and Mongolian cattle, and for the conservation and exploitation of their germplasm resources.

Key words: Qaidam cattle, Mongolian cattle, Y chromosome genome, SNP, paternal origin

中图分类号:

S823.2

马志杰, 王世康, 张卫忠, 郭卫兴, 赵海明, 雷初朝. 柴达木牛和蒙古牛Y染色体基因组遗传多样性与父系起源研究[J]. 畜牧兽医学报, 2023, 54(3): 1026-1033.

MA Zhijie, WANG Shikang, ZHANG Weizhong, GUO Weixing, ZHAO Haiming, LEI Chuzhao. Y-chromosome Genomic Diversity and Paternal Origins of Qaidam Cattle and Mongolian Cattle[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 1026-1033.

参考文献 32

[1]	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.WANME C L.Investigation and analysis of the germplasm characteristics of Qinghai Qaidam Cattle[J].Chinese Journal of Animal Husbandry and Veterinary Medicin,2011(8):124-125.(in Chinese)
[2]	张才骏,张海峰,晃生玉.柴达木黄牛与我国其它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)
[3]	齐昱,邢燕平,潘静,等.基于转录组数据的蒙古牛皮肤组织抗寒相关信号通路及候选基因的筛选[J].畜牧兽医学报,2017,48(12):2301-2313.QI Y,XING Y P,PAN J,et al.Screening of cold Tolerance-related signaling pathways and candidate genes in Mongolia cattle skin tissues based on transcriptome data[J].Acta Veterinaria et Zootechnica Sinica,2017,48(12):2301-2313.(in Chinese)
[4]	马哈沙提·吐苏别克.关于蒙古牛改良沿革及肉牛饲养技术路线[J].畜禽业,2020,31(3):14.MA H S T.On the history of Mongolian cattle improvement and the technical route of beef cattle rearing[J].Livestock and Poultry Industry,2020,31(3):14.(in Chinese)
[5]	王小梅,查嘎巴拉.自然放牧条件下锡林郭勒盟地区蒙古牛胴体性状的研究[J].当代畜禽养殖业,2019(11):12-14.WANG X M,CHA G B L.Study on carcass traits of Mongolian cattle in Xilinguolemeng region under natural grazing conditions[J].Modern Animal husbandry,2019(11):12-14.(in Chinese)
[6]	CORTEZ D,MARIN R,TOLEDO-FLORES D,et al.Origins and functional evolution of Y chromosomes across mammals[J].Nature,2014,508(7497):488-493.
[7]	董依萌,王天骄,刘华淼,等.线粒体DNA和Y染色体主要基因的研究进展[J].安徽农业科学,2020,48(8):18-22.DONG Y M,WANG T J,LIU H M,et al.Research progress on the major genes of mitochondria and Y chromosome[J].Journal of Anhui Agricultural Sciences,2020,48(8):18-22.(in Chinese)
[8]	常振华,黄洁萍,徐苹,等.中国黄牛Y-STRs遗传多样性与起源研究[J].中国牛业科学,2012,38(3):9-13.CHANG Z H,HUANG J P,XU P,et al.Genetic diversity and ori n based on Y-STRs in Chinese cattle[J].China Cattle Science,2012,38(3):9-13.(in Chinese)
[9]	常振华,卫利选,张润锋,等.中国黄牛Y-SNPs遗传多样性与起源研究[J].畜牧兽医学报,2011,42(11):1537-1542.CHANG Z H,WEI L X,ZHANG R F,et al.Genetic diversity and origin based on Y-SNPs in Chinese cattle[J].Acta Veterinaria et Zootechnica Sinica,2011,42(11):1537-1542.(in Chinese)
[10]	GÖTHERSTRÖM A,ANDERUNG C,HELLBORG L,et al.Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe[J].Proc Biol Sci,2005,272(1579):2345-2350.
[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].Nat Commun,2018,9(1):2337.
[12]	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)
[13]	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)
[14]	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)
[15]	杨秋蕾,马志杰,李广祯,等.牛种间UTY基因内含子19(UTY19)序列遗传变异研究[J].青海畜牧兽医杂志,2020,50(6):7-10,14.YANG Q L,MA Z J,LI G Z,et al.Study on genetic variations of intron19 of UTY Gene (UTY19) among bovine interspecific[J].Chinese Qinghai Journal of Animal and Veterinary Sciences,2020,50(6):7-10,14.(in Chinese)
[16]	LI R,XIE W M,CHANG Z H,et al.Y chromosome diversity and paternal origin of Chinese cattle[J].Mol Biol Rep,2013,40(12):6633-6636.
[17]	LI R,ZHANG X M,CAMPANA M G,et al.Paternal origins of Chinese cattle[J].Anim Genet,2013,44(4):446-449.
[18]	YUE X P,LI R,LIU L,et al.When and how did Bos indicus introgress into Mongolian cattle?[J].Gene,2014,537(2):214-219.
[19]	BOLGER A M,LOHSE M,USADEL B.Trimmomatic:a flexible trimmer for Illumina sequence data[J].Bioinformatics, 2014,30(15):2114-2120.
[20]	HOUTGAST E J,SIMA V M,BERTELS K,et al.Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths[J].Comput Biol Chem,2018,75:54-64.
[21]	MCKENNA A,HANNA M,BANKS E,et al.The Genome Analysis Toolkit:a MapReduce framework for analyzing next-generation DNA sequencing data[J].Genome Res,2010,20(9):1297-1303.
[22]	DANECEK P,AUTON A,ABECASIS G,et al.The variant call format and VCFtools[J].Bioinformatics,2011,27(15):2156-2158.
[23]	CINGOLANI P,PLATTS A,WANG L L,et al.A program for annotating and predicting the effects of single nucleotide polymorphisms,SnpEff:SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3[J].Fly (Austin),2012, 6(2):80-92.
[24]	LIBRADO P,ROZAS J.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics, 2009,25(11):1451-1452.
[25]	EDGAR R C.MUSCLE:multiple sequence alignment with high accuracy and high throughput[J].Nucleic Acids Res,2004, 32(5):1792-1797.
[26]	STAMATAKIS A.RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies[J].Bioinformatics, 2014,30(9):1312-1313.
[27]	PARADIS E.pegas:an R package for population genetics with an integrated-modular approach[J].Bioinformatics, 2010,26(3):419-420.
[28]	XIA X T,ZHANG S J,ZHANG H J,et al.Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data[J].BMC Genomics,2021,22(1):43.
[29]	陈宁博,雷初朝.从DNA角度认识中国黄牛的起源和利用历史[J].第四纪研究,2022,42(1):92-100.CHEN N B,LEI C Z.The origins and utilization history of Chinese cattle as revealed by DNA analysis[J].Quaternary Sciences,2022,42(1):92-100.(in Chinese)
[30]	XIA X,YAO Y,LI C,et al.Genetic diversity of Chinese cattle revealed by Y-SNP and Y-STR markers[J].Anim Genet,2019,50(1):64-69.
[31]	尚有安,王照忠,杨坤.德令哈市柴达木黄牛品种资源调查[J].畜牧与兽医,2012,44(8):106-107.SHANG Y A,WANG Z Z,YANG K.A survey on the resources of the breed of Qaidam cattle in Delingha[J].Animal Husbandry & Veterinary Medicine,2012,44(8):106-107.(in Chinese)
[32]	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.National Livestock and Poultry Genetic Resources Committee.Animal genetic resources in China:Bovines[M].Beijing:China Agriculture Press,2011.(in Chinese)

柴达木牛和蒙古牛Y染色体基因组遗传多样性与父系起源研究

Y-chromosome Genomic Diversity and Paternal Origins of Qaidam Cattle and Mongolian Cattle

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