基于全基因组重测序评估郏县红牛保种群遗传多样性与群体结构

doi:10.16431/j.cnki.1671-7236.2024.07.019

Abstract

Abstract: 【Objective】 This study was aimed to understand the genetic diversity and population structure of Jiaxian Red cattle conservation population,make a better protection and utilization of the genetic resources of Jiaxian Red cattle.【Method】 Based on whole genome sequencing technology,the single nucleotide polymorphism (SNP) of 30 Jiaxian Red cattle were detected,and a comprehensive assessment of the conservation effectiveness in Jiaxian Red cattle conservation population was conducted by analyzing population genetic diversity,population structure,distribution characteristics of runs of homozygosity (ROH),and kinship relationships.【Result】 A total of 41 215 797 high-quality SNPs were detected among 30 individuals of Jiaxian Red cattle.The genetic diversity within Jiaxian Red cattle population was extensive,with a minimum allele frequency of 0.13±0.13,polymorphic marker ratio of 0.58±0.33,expected heterozygosity of 0.192±0.152,observed heterozygosity of 0.191±0.158,and nucleotide diversity of 0.003±0.001.The effective population size of Jiaxian Red cattle population showed a decreasing trend over the generations,with an effective population size of 2 716 individuals before 1 000 generations ago, and 143 individuals before 20 generations ago.The genetic distance among individuals of Jiaxian Red cattle ranges from 0.80 to 0.89,with an average genetic distance of 0.83±0.02.Cluster analysis revealed that 30 individuals of Jiaxian Red cattle were divided into a total of 7 families,with 15 bulls being divided into 5 families.A total of 5 947 ROH were detected among 30 individuals of Jiaxian Red cattle,with a cumulative length of 2.8 Gb.The segments ranging from 0 to 0.5 Mb represented the highest proportion at 73.08%,while segments of 2 to 4 Mb represented the lowest proportion at 0.40%.The average inbreeding coefficient based on ROH was 0.19±0.07,and the average inbreeding coefficient of 15 bulls was 0.15±0.05.【Conclusion】 The conservation population of Jiaxian Red cattle exhibited rich genetic diversity and no obvious stratification,maintaining higher levels of inbreeding overall.For the emerging risk of inbreeding,it was necessary to strengthen breeding selection and matching efforts to ensure the sustainable development of genetic resource in Jiaxian Red cattle.

Key words: Jiaxian Red cattle; whole genome sequencing; genetic diversity; population structure

CLC Number:

S813.3

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.

References

[1] CHEN N,CAI Y,CHEN Q,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.
[2] 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.
[3] XIA X,YAO Y,LI C,et al.Genetic diversity of Chinese cattle revealed by Y-SNP and Y-STR markers[J].Animal Genetics,2019,50(1):64-69.
[4] 王秀娟,高翰,李海鹏,等.郏县红牛生长和肉用性能指标测定分析[J].中国牛业科学,2021,47(5):12-16. WANG X J,GAO H,LI H P,et al.Analysis of growth and meat performance in Jiaxian Red cattle[J].China Cattle Science,2021,47(5):12-16.(in Chinese)
[5] 魏成斌,吴姣,蔺萍,等.郏县红牛种质资源个性描述[J].中国牛业科学,2013,39(1):54-57. WEI C B,WU J,LIN P,et al.Genetic resource characteristics describing of Jiaxian Red cattle[J]. China Cattle Science,2013,39(1):54-57.(in Chinese)
[6] NICOLE AR W,SHANNON K M,SANDRA T P,et al.Single-nucleotide polymorphism masking[J].Alcohol Research&Health,2008,31(3):270-271.
[7] LIANG D,ZHAO P,SI J,et al.Genomic analysis revealed a convergent evolution of LINE-1 in coat color:A case study in water buffaloes (Bubalus bubalis)[J].Molecular Biology and Evolution,2021,38(3):1122-1136.
[8] YAN C L,LIN J,HUANG Y Y,et al.Population genomics reveals that natural variation in PRDM16 contributes to cold tolerance in domestic cattle[J].Zoological Research,2022,43(2):275-284.
[9] MA X H,CHENG H J,LIU Y K,et al.Assessing genomic diversity and selective pressures in Bohai Black cattle using whole-genome sequencing data[J].Animals,2022,12(5):665.
[10] 张任豹,周东辉,周李生,等.基于70K SNP芯片分析济宁青山羊保种群体的遗传结构[J].畜牧兽医学报2023,54(7):2836-2847. ZHANG R B,ZHOU D H,ZHOU L S,et al.Analysis of genetic structure of conservation population in Jining Gray goats based on 70K SNP chip[J].Acta Veterinaria et Zootechnica Sinica,2023,54(7):2836-2847.(in Chinese)
[11] 陶璇,杨雪梅,梁艳,等.基于SNP芯片的丫杈猪保种群体遗传结构研究[J].畜牧兽医学报,2023,54(6):2308-2319. TAO X,YANG X M,LIANG Y,et al.Analysis of genetic structure of conservation population in Yacha pig based on SNP chip[J]. Acta Veterinaria et Zootechnica Sinica,2023,54(6):2308-2319.(in Chinese)
[12] JAGANNATHAN V,GERBER V,RIEDER S,et al.Comprehensive characterization of horse genome variation by whole-genome sequencing of 88 horses[J].Animal Genetics,2019,50(1):74-77.
[13] FENG J,ZHU W,SHI H R,et al.Analysis of the selection signal of the Tibetan Black chicken genome based on whole-genome sequencing[J].Genes,2023,14(9):1672.
[14] BOLGER A M,LOHSE M,USADEL B,et al.Trimmomatic:A flexible trimmer for Illumina sequence data[J].Bioinformatics,2014,30(15):2114-2120.
[15] LI H.Aligning sequence reads,clone sequences and assembly contigs with BWA-MEM[J].arXiv:Genomics,2013,v2:1303.3997.
[16] 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.
[17] DANECEK P,AUTON A,ABECASIS G,et al.The variant call format and VCFtools[J].Bioinformatics,2011,27(15):2156-2158.
[18] CINGOLANI P.Variant annotation and functional prediction:SnpEff[J].Methods in Molecular Biology,2022,2493:289-314.
[19] PURCELL S,NEALE B,TODD-BROWN K,et al.PLINK:A tool set for whole-genome association and population-based linkage analyses[J].American Journal of Human Genetics,2007,81(3):559-575.
[20] BARBATO M,OROZCO-TERWENGEL P,TAPIO M,et al.SNeP:A tool to estimate trends in recent effective population size trajectories using genome-wide SNP data[J].Frontiers in Genetics,2015,6:109.
[21] BRADBURY PJ,ZHANG Z,KROON DE,et al.TASSEL:Software for association mapping of complex traits in diverse samples[J].Bioinformatics,2007,23(19):2633-2635.
[22] 王启贵,王海威,郭宗义,等.加强畜禽遗传资源保护推动我国畜牧种业发展[J].中国科学院院刊,2019,34(2):174-179. WANG Q G,WANG H W,GUO Z Y,et al.Strengthening protection of livestock and poultry genetic resources,promoting development of animal breed industry in China[J].Bulletin of Chinese Academy of Sciences,2019,34(2):174-179.(in Chinese)
[23] 张花菊,徐亚铂,王琳琳,等.郏县红牛与不同品种肉牛杂交后代肉用性能比较研究[J].中国畜牧兽医,2017,44(12):3482-3490. ZHANG H J,XU Y B,WANG L L,et al.Comparative study on the beef traits between Jiaxian Red cattle and crossbred beef cattle[J].China Animal Husbandry&Veterinary Medicine,2017,44(12):3482-3490.(in Chinese)
[24] 马桂变.郏县红牛的保种方法与选育方向[J].中国牛业科学,2011,37(2):69-70. MA G B.Conservation methods and breeding orientation of Jiaxian Red cattle[J].China Cattle Science,2011,37(2):69-70.(in Chinese)
[25] MARKERT J A,CHAMPLIN D M,GUTJAHR-GOBELL R,et al.Population genetic diversity and fitness in multiple environments[J].BMC Evolutionary Biology,2010,10:205.
[26] CHOUDHURY A,ARON S,SENGUPTA D,et al.African genetic diversity provides novel insights into evolutionary history and local adaptations[J].Human Molecular Genetics,2018,27(R2):R209-R218.
[27] JIN H,ZHAO S,JIA Y,et al.Estimation of linkage disequilibrium,effective population size,and genetic parameters of phenotypic traits in Dabieshan cattle[J].Genes (Basel),2022,14(1):107.
[28] GAO Y,GAUTIER M,DING X,et al.Species composition and environmental adaptation of indigenous Chinese cattle[J].Scientific Reports,2017,7(1):16196.
[29] ELLEGREN H,GALTIER N.Determinants of genetic diversity[J].Nature Reviews Genetics,2016,17(7):422-433.
[30] TABERLET P,VALENTINI A,REZAEI HR,et al.Are cattle,sheep,and goats endangered species?[J]. Molecular Ecology,2008,17(1):275-284.
[31] 路国彬,王夏晖,吕文魁,等.中国畜禽遗传资源保护问题分析[J].家畜生态学报,2014,35(4):1-6. LU G B,WANG X H,LYU W K,et al.Analysis of conservation status of Chinese livestock and poultry genetic resources[J].Journal of Domestic Animal Ecology,2014,35(4):1-6.(in Chinese)
[32] PURFIELD D C,BERRY D P,MCPARLAND S,et al.Runs of homozygosity and population history in cattle[J].BMC Genomic Data,2012,13:70.
[33] KELLER M C,VISSCHER P M,GODDARD M E,et al.Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data[J].Genetics,2011,189(1):237-249.
[34] FORUTAN M,MAHYARI SA,BAES C,et al.Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle[J].BMC Genomics,2018,19(1):98.
[35] 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)

Genetic Diversity and Population Structure Analysis of Jiaxian Red Cattle Based on Whole Genome Sequencing

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	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.
[2]	WANG Zi, SUN Miao, WANG Yongqiang, MENG Linghao, GENG Chao, SHI Jinchuan, CHEN Wei, QIU Jun, LIU Kai. Detection of Drug Resistance of Escherichia coli from Ducks in Some Areas of Tongliao and Whole Genome Sequencing Analysis of Multi-drug Resistant Strain YA-1 [J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(6): 2585-2596.
[3]	YU Fuxin, WU Siyu, YU Jieshi, ZHANG Xiaoai, YU Ting, DONG Bo, LI Jianbo, WANG Lei, WEI Wenkang. Isolation,Identification,Whole Genome Sequencing and Genetic Evolution Analysis of Goose Astrovirus in Some Areas of Guangdong Province [J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(6): 2633-2643.
[4]	DU Dongdong, QIAN Jing, CHANG Hengrui, LI Hongmin, WEI Xiangli, LIU Changyong, LUO Ruifeng, WANG Guohong, KANG Lichao. Whole Genome Sequencing Analysis of a ST515 Strain of Multidrug-resistant Listeria monocytogenes [J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(6): 2707-2716.
[5]	WANG Yingping, ZHAO Jingxian, SHANG Jiafu, HAO Chengsen, ZUO Yuqi, ZHU Huanyi, FENG Xudong, XU Tingting, NI Xingwei, LIU Xia, YANG Xiaowei, CAO Lanyun, ZHANG Liwu, TAN Changfan, CAO Lijing, ZHAO Guangwei. Isolation,Identification and Whole Genome Analysis of Aeromonas caviae from Micropterus salmoides [J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(4): 1706-1716.
[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]	SONG Xiangbin, ZHAO Xiaoyu, LI Chuanpu, MEN Xiaodong, LIANG Meng, WEI Xiuli, LI Youzhi, YANG Zhikun, ZHANG Dechen, GUO Yuqiu, TANG Wenli. Molecular Epidemiological Analysis of Avian Extended Spectrum β-lactamases Producing Escherichia coli in Shandong Province [J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(1): 407-416.
[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]	LI Cuihan, QU Zhina, GAO Yubin, LI Yan, WANG Juan, DUAN Xiaoxiao, WANG Lin, ZHANG Xiyue, ZHAO Ge, HUANG Xiumei, ZHAO Jianmei, ZHANG Qingqing, WANG Junwei, HUANG Baoxu, LIU Junhui. Epidemiology Investigation and Whole Genome Sequencing Analysis of Three Types of Poultry Originated Carbapenem-resistant Escherichia coli [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1653-1662.
[11]	LIU Kexin, WANG Chao, ZHANG Ao, LIU Jiali, TAN Bin, ZHANG Shuqin. Isolation,Identification and Genome Sequence Analysis of Bovine Viral Diarrhea Virus LN-1 Strain [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 1150-1159.
[12]	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.
[13]	GAO Duo, WANG Jinyu, LI Heyu, JIANG Qifeng, CHEN Zihan, XU Xiying, JIA Kun. Isolation,Identification and Biological Characterization Analysis of a Bacteriophage GD01 from Salmonella Enteritidis [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(12): 5160-5169.
[14]	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.
[15]	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.