基于世界家马群体遗传结构构建藏马特异性遗传标签

doi:10.16431/j.cnki.1671-7236.2025.01.021

Abstract

Abstract: 【Objective】 This study was aimed to construct specific genetic markers for Tibetan horses based on the analysis of the population structure and genetic diversity of domestic horses,so as to provide a theoretical basis for identification of Tibetan horses. 【Method】 This study conducted population structure and genetic diversity analysis of global domestic horses and construct specific genetic markers for Tibetan horses utilizing genome sequences data of 404 horses from 47 breeds. 【Result】 The whole-genome resequencing yielded a total of 8 917 800 high-quality single nucleotide polymorphism (SNP).The results of the global domestic horse population structure analysis revealed significant ancestral genetic differences between Shetland ponies and other groups.The population genetic diversity analysis indicated that compared with Middle Eastern,European and American horses,as well as other Asian horse breeds,which had experienced strong selective breeding pressure and consequently a decrease in genetic diversity,Chinese domestic horses had maintained good genetic diversity.A set of 110 SNPs specific markers for Tibetan horses was constructed,which could effectively distinguish Tibetan horses from other domestic horses worldwide,with an identification accuracy rate of 100%. 【Conclusion】 In summary,the global domestic horse population structure was complex.Western horse populations had more similar genetic backgrounds and lower genetic diversity,whereas Chinese domestic horses possessed higher genetic diversity,offering greater breeding potential.The specific genetic markers for Tibetan horses developed in this study provided a theoretical basis for the identification of Tibetan horse breeds worldwide and offered new technical support for the conservation and development of local Chinese horse breeds.

Key words: domestic horses; Tibetan horse; population structure; genetic diversity; genetic markers

CLC Number:

S821.2

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.

References

[1] CURRY A.Horse nations[J].Science,2023,379(6639):1288-1293.
[2] ORLANDO L,LIBRADO P.Origin and evolution of deleterious mutations in horses[J].Genes,2019,10(9):649.
[3] LIBRADO P,FAGES A,GAUNITZ C,et al.The evolutionary origin and genetic makeup of domestic horses[J].Genetics,2016,204(2):423-434.
[4] 陶克涛.亚洲家马遗传多样性的研究——以中国和蒙古国种群为例[D].呼和浩特:内蒙古农业大学,2021. TAO K T.Study on genetic diversity of Asian domestic horse examples from Chinese and Mongolian populations[D].Hohhot:Inner Mongolia Agricultural University,2021.(in Chinese)
[5] 国家畜禽遗传资源委员会.中国畜禽遗传资源志·马驴驼志[M].北京:中国农业出版社,2010. CHINA NATIONAL COMMISSION OF ANIMAL GENETIC RESOURCES.Animal Genetic Resources in China:Horse,Donkeys and Camels[M].Beijing:China Agriculture Press,2010.(in Chinese)
[6] LIU X,ZHANG Y,LIU W,et al.A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses[J].Current Biology,2022,32(2):480-487.
[7] LIU X,ZHANG Y,LI Y,et al.EPAS1 gain-of-function mutation contributes to high-altitude adaptation in Tibetan horses[J].Molecular Biology and Evolution,2019,36(11):2591-2603.
[8] ZHAO J,LI T,ZHU C,et al.Selection and use of microsatellite markers for individual identification and meat traceability of six swine breeds in the Chinese market[J].Food Science and Technology International,2018,23(4):292-300.
[9] 章晓炜,许文武,曾涛,等.基于SSR标记的2个鹅群体品种鉴定[J].中国家禽,2022,44(10):14-18. ZHANG X W,XU W W,ZENG T,et al.Breed identification of two goose populations based on SSR markers[J].China Poultry,2022,44(10):14-18.(in Chinese)
[10] LV F H,AGHA S,KANTANEN J,et al.Adaptations to climate-mediated selective pressures in sheep[J].Molecular Biology and Evolution,2014,31(12):3324-3343.
[11] ROSTAMZADEH MAHDABI E,ESMAILIZADEH A,AYATOLLAHI MEHRGARDI A,et al.A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes[J].Genetics Selection Evolution,2021,53(1):72.
[12] 朱春红,刘宏祥,王志成,等.SNPs分子标记在地方品种鸭鉴定中的应用[J].中国家禽,2024,8:9-13. ZHU C H,LIU H X,WANG Z C,et al.Application of SNPs molecular markers in identification of indigenous duck breeds[J].China Poultry,2024,8:9-13.(in Chinese)
[13] NANAEI H A,ESMAILIZADEH A,MEHRGARDI A A,et al.Genomic footprints and genes associated with small body size in Chinese pony[J].BioMed Central Genomics,2020,21(1):496.
[14] CAPOMACCIO S,MILANESI M,NOCELLI C,et al.Splicing site disruption in the KIT gene as strong candidate for white dominant phenotype in an Italian trotter[J].Animal Genetics,2017,48(6):727-728.
[15] METZGER J,GAST A C,SCHRIMPF R,et al.Whole-genome sequencing reveals a potential causal mutation for dwarfism in the Miniature Shetland pony[J].Mammalian Genome,2017,28(3-4):143-151.
[16] WANG C,LI H,GUO Y,et al.Donkey genomes provide new insights into domestication and selection for coat color[J].Nature Communications,2020,11(1):6014.
[17] LI H,DURBIN R.Fast and accurate short read alignment with Burrows-Wheeler transform[J].Bioinformatics,2009,25(14):1754-1760.
[18] KALBFLEISCH T S,RICE E S,JR M S D,et al.Improved reference genome for the domestic horse increases assembly contiguity and composition[J].Communications Biology,2018,1:197.
[19] MCKENNA A,HANNA M,BANKS E,et al.The genome analysis toolkit:A MapReduce framework for analyzing next-generation DNA sequencing data[J].Genome Research,2010,20(9):1297-1303.
[20] YANG J,LEE S H,GODDARD M E,et al.GCTA:A tool for genome-wide complex trait analysis[J].American Journal of Human Genetics,2011,88(1):76-82.
[21] ALEXANDER D H,NOVEMBRE J,LANGE K.Fast model-based estimation of ancestry in unrelated individuals[J].Genome Research,2009,19(9):1655-1664.
[22] LETUNIC,I,BORK,P.Interactive tree of life (iTOL) v3:An online tool for the display and annotation of phylogenetic and other trees[J].Nucleic Acids Research,2016,44(W1):W242-W245.
[23] 胡紫平,王立刚,宗文成,等.基于基因组SNP和ROH的剑白香猪群体遗传结构解析[J].畜牧兽医学报,2023,54(10):4117-4125. HU Z P,WANG L G,XIAN W C,et al.Genetic structure analysis of Jianbai Xiang pig population based on genomic SNP and ROH[J].Acta Veterinaria et Zootechnica Sinica,2023,54(10):4117-4125.(in Chinese)
[24] 武艳平,魏岳,康昭风,等.基于全基因组SNP分析8个地方鸡品种的遗传多样性[J].畜牧兽医学报,2022,53(2):646-653. WU Y P,WEI Y,KANG S F,et al.Genetic diversity analysis of 8 local chicken breeds based on whole genome SNP[J].Acta Veterinaria et Zootechnica Sinica,2022,53(2):646-653.(in Chinese)
[25] 王志武,孙锐锋,赵鹏,等.SNP芯片评估欧拉藏羊群体遗传多样性和遗传结构[J].中国草食动物科学,2024,44(1):57-62. WANG Z W,SUN R F,ZHAO P,et al.Evaluated of genetic diversity and genetic structure in Euler Tibetan sheep population by SNP chip[J].China Herbivore Science,2024,44(1):57-62.(in Chinese)
[26] 马钧,樊安平,王武生,等.全基因组重测序解析秦川牛保种群遗传多样性和遗传结构[J].遗传,2023,45(7):602-616. MA J,FAN A P,WANG W S,et al.Analysis of genetic diversity and genetic structure of Qinchuan cattle conservation population using whole-genome resequencing[J].Hereditas,2023,45(7):602-616.(in Chinese)
[27] 王刚.基于全基因组测序分析中国家驴群体遗传结构及体型大小选择信号[D].杨凌:西北农林科技大学,2023. WANG G.Analysis on genetic structure and body size selection signature of Chinese domestic donkey population based on whole genome sequencing[D].Yangling:Northwest A&F University,2023.(in Chinese)
[28] GAUNITZ C,FAGES A,HANGHØJ K,et al.Ancient genomes revisit the ancestry of domestic and Przewalski’s horses[J].Science,2018,360(6384):111-114.
[29] BOWER M A,MCGIVNEY B A,CAMPANA M G,et al.The genetic origin and history of speed in the Thoroughbred racehorse[J].Nature Communications,2012,3:643.
[30] 付文强,姜迪,郭志恒,等.美国夸特马与赛马[J].黑龙江动物繁殖,2023,31(4):22-26. FU W Q,JIANG D,GUO Z H,et al.American Quarter horse and horse racing[J].Heilongjiang Journal of Animal Reproduction,2023,31(4):22-26.(in Chinese)
[31] 常铤晋.中国西南驴全基因组遗传多样性与选择信号分析[D].杨凌:西北农林科技大学,2023. CHANG T J.Whole-genome genetic diversity and selective signals analysis of Southwest donkeys in China[D].Yangling:Northwest A&F University,2023.(in Chinese)
[32] ORLANDO L.The evolutionary and historical foundation of the modern horse lessons from ancient genomics[J].Annual Review of Genetics,2020,54:563-581.
[33] KUMAR H,PANIGRAHI M,SARAVANAN K A,et al.SNPs with intermediate minor allele frequencies facilitate accurate breed assignment of Indian Tharparkar cattle[J].Gene,2021,777:145473.
[34] 王小鹏,唐建红,王成斌,等.中国地方猪种品种特异性遗传标签构建——以莱芜猪为例[J].猪业科学,2016,33(11):54-57. WANG X P,TANG J H,WANG C B,et al.Construction of breed-specific genetic markers for Chinese local pig breeds—A case study of Laiwu pig[J].Swine Industry Science,2016,33(11):54-57.(in Chinese)
[35] 胡亮.藏系绵羊种质资源鉴定技术的研究[D].扬州:扬州大学,2019. HU L.Study on identifcation techniques of Tibetan sheep germplasm resources[D].Yangzhou:Yangzhou University,2019.(in Chinese)

Construction of Specific Genetic Markers for Tibetan Horses Through Population Structure Analysis of Global Domestic Horses

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