基于简化基因组测序的黄色波尔山羊公羊亲缘关系及近交系数分析

doi:10.16431/j.cnki.1671-7236.2021.08.020

Abstract

Abstract: Accurate measuring of the inbreeding degree and genetic relationship on yellow Boer goat was an effective way to improve breeding efficiency and genetic progress of Yunnan Yellow goat breeding.The genotyping-by-sequencing (GBS) was used to sequence 37 yellow Boer rams from Yunnan breeding promotion center.High quality and high density SNP variation information was obtained through quality control.Principal component analysis (PCA), calculation of identity by state (IBS), construction of G matrix, calculation of genetic coefficient, NJ cluster analysis and calculation of inbreeding coefficient were carried out by Gmatrix v2, Plink v1.90 and MegaX v10.0 software.The results showed that 88 393 high-quality SNPs were detected on 29 autosomes in 37 yellow Boer rams, and 1 537 long homozygous fragments (ROH) ranging in length from 1 000.582 to 18 400.12 kb with an average length of 2 576.34 kb and 93.15 SNPs were detected.37 yellow Boer rams were divided into 11 families and 3 families had only one ram each.The genetic relationship between family A and family K was the farthest.The average genomic inbreeding coefficient (F_ROH) based on ROH was 0.043 and the F_ROH of 3 yellow Boer rams was more than 0.125 which meant more inbreeding accumulation existing.This study provided a scientific basis for the rational use of yellow Boer goat in the breeding of Yunnan Yellow goat, and also provided a powerful technical means for evaluating the inbreeding level of goats, preventing inbreeding decline, and optimizing the breeding and matching scheme.

Key words: yellow Boer rams; GBS; ROH; F_ROH; kinship coefficient

CLC Number:

S813.3

LAN Rong, ZHU Lan, JIANG Yanting, OUYANG Yina, SHAO Qingyong. Analysis on Genetic Relationship and Inbreeding Coefficient of Yellow Boer Rams by Genotyping-by-Sequencing[J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(8): 2878-2888.

References

[1] 刘瑶.我国羊肉产业现状及未来发展趋势[J].中国饲料,2019,17:112-117. LIU Y.Present situation and future development trend of mutton industry in China[J].China Feed,2019,17:112-117.(in Chinese)
[2] BANOS G,WIGGANS G R,POWELL R L.Impact of paternity errors in cow identification on genetic evaluations and international comparisons[J].Journal of Dairy Science,2001,84(11):2523-2529.
[3] LEUTENEGGER A L,PRUM B,GENIN E,et al.Estimation of the inbreeding coefficient through use of genomic data[J].American Journal of Human Genetics,2003,73(3):516-523.
[4] WOODS C G,VALENTE E M,BOND J,et al.A new method for autozygosity mapping using single nucleotide polymorphisms(SNPs) and EXCLUDEAR[J].Journal of Medical Genetics,2004,41(8):e101.
[5] 张静静,高会江,吴洋,等.利用SNP标记估计西门塔尔牛亲缘关系系数的准确性[J].畜牧兽医学报,2016,47(2):268-275. ZHANG J J,GAO H J,WU Y,et al.Estimation of the kinship coefficient in Simmental cattle on SNP markers[J].Acta Veterinaria et Zootechnica Sinica,2016,47(2):268-275.(in Chinese)
[6] 杨湛澄,黄河天,闫青霞,等.利用高密度SNP标记分析中国荷斯坦牛基因组近交[J].遗传,2017,39(1):41-47. YANG Z C,HUANG H T,YAN Q X,et al.Estimation of genomic inbreeding coefficients based on high-density SNP markers in Chinese Holstein cattle[J].Hereditas,2017,39(1):41-47.(in Chinese)
[7] 曹愉夏,韩威,李国辉,等.基于RAD-seq简化基因组测序估算狼山鸡分子亲缘系数和近交系数[J].中国家禽,2019,41(10):14-19. CAO Y X,HAN W,LI G H,et al.Estimation of genomic kinship coefficients and inbreeding coefficients based on RAD-seq simplified genome sequencing data in Langshan chicken[J].China Poultry,2019,41(10):14-19.(in Chinese)
[8] 刘彬,沈林園,陈映,等.基于SNP芯片分析青峪猪保种群体的遗传结构[J].畜牧兽医学报,2020,51(2):260-269. LIU B,SHEN L Y,CHEN Y,et al.Analysis of genetic structure of conservation population in Qingyu pig based on SNP chip[J].Acta Veterinaria et Zootechnica Sinica,2020,51(2):260-269.(in Chinese)
[9] VANRADEN P M.Efficient methods to compute genomic predictions[J].Journal of Dairy Science,2008,91(11):4414-4423.
[10] HILL W G,SALISBURY B A,WEBB A J.Parentage identification using single nucleotide polymorphism genotypes:Application to product tracing[J].Journal of Animal Science,2008,86(10):2508-2517.
[11] SANTURE A W,STAPLEY J,BALL A D,et al.On the use of large marker panels to estimate inbreeding and relatedness:Empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs[J].Molecular Ecology,2010,19(7):1439-1451.
[12] PURFIELD D C,BERRY D P,MCPARLAND S,et al.Runs of homozygosity and population history in cattle[J].BMC Genetics,2012,13:70.
[13] 刘家鑫,魏霞,邓天宇,等.绵羊全基因组ROH检测及候选基因鉴定[J].畜牧兽医学报,2019,50(8):1554-1566. LIU J X,WEI X,DENG T Y,et al.Genome-wide scan for run of homozygosity and identification of corresponding candidate genes in sheep populations[J].Acta Veterinaria et Zootechnica Sinica,2019,50(8):1554-1566.(in Chinese)
[14] 张志恒,王玉琴,任国艳,等.舍饲条件下波尔山羊与河南淮山羊杂交羊生长发育、屠宰性能及肉品质特性研究[J].中国畜牧兽医,2020,47(8):2518-2527. ZHANG Z H,WANG Y Q,REN G Y,et al.Study on growth and development,slaughter performance and meat quality characteristic of crossbreed goat from Boer and Henan Huai goat under the condition of house feeding[J].China Animal Husbandry & Verinary Medicine,2020,47(8):2518-2527.(in Chinese)
[15] ZHANG Z,TODHUNTER R J,BUCKLER E S,et al.Technical note:Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood[J].Journal of Animal Science,2007,85(4):881-885.
[16] ZHU F,CUI Q Q,HOU Z C.SNP discovery and genotyping using genotyping-by-sequencing in Pekin ducks[J].Scientific Reports,2016,6:36223.
[17] 张彩云,王晓亮,涂盈盈,等.基于GBS技术的新杨绿壳纯系蛋鸡SNPs检测[J].中国家禽,2018,40(13):7-10. ZHANG C Y,WANG X L,TU Y Y,et al.SNPs detection of Xinyang Blue-shelled pureline layers by GBS[J].China Poultry,2018,40(13):7-10.(in Chinese)
[18] 阮鹏,陈究成,徐宁迎,等.基于简化基因组测序嘉兴黑猪的遗传多样性分析[J].浙江畜牧兽医,2017,42(4):1-2. RUAN P,CHENG J C,XU N Y,et al.Genetic diversity analysis of Jiaxing Black pig based on simplified genome sequencing[J].Zhejiang Journal Animal Science and Veterinary Medicine,2017,42(4):1-2.(in Chinese)
[19] 董世武,王天骄,刘华淼,等.基于GBS技术对梅花鹿,马鹿及其杂交后代基因组SNP特征的分析[J].畜牧兽医学报,2019,50(12):2422-2430. DONG S W,WANG T J,LIU H M,et al.Analysis of genomic SNP characteristics of sika deer,red deer and their hybrid progenies based on GBS technology[J].Acta Veterinaria et Zootechnica Sinica,2019,50(12):2422-2430.(in Chinese)
[20] ROSWITHA B,JOHANN S.Pedigree and marker information requirements to monitor genetic variability[J].Genetics Selection Evolution,2003,35(4):369-383.
[21] XU Z,SUN H,ZHANG Z,et al.Assessment of autozygosity derived from runs of homozygosity in Jinhua pigs disclosed by sequencing data[J].Frontiers in Genetics,2019,10:274.
[22] ISLAM R,LIU Z F,LI Y F,et al.Conservation assessment of the state goat farms by using SNP genotyping data[J].Genes,2020,11(6):652.
[23] FORUTAN M,MAHYARI S A,BAES C,et al.Inbreeding and runs of homozygosity before and after genomic selection in North Amercian Holstein cattle[J].BMC Genomics,2018,19:98.

Analysis on Genetic Relationship and Inbreeding Coefficient of Yellow Boer Rams by Genotyping-by-Sequencing

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 4

Recommended Articles

Metrics

Comments

[1]	BAO Qi, BAO Pengjia, MA Xiaoming, WU Xiaoyun, MENG Guangyao, CHU Min, CAO Hongmei, LANG Jianying, AN Yufeng, LIANG Chunnian, YAN Ping. Genetic Structure,Selection Signal Analysis and ROH Detection of Sunan Yak Population [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 2992-3005.
[2]	XUE Tao, LI Li, GAO Qing-qing, CHEN Xian-liang, LI Tian-tian, QU Xin-qin, GAO Song. Study on the Virulence Gene Distribution and Genetic Evolution of Cattle Shiga Toxin-producing Escherichia coli Isolates [J]. , 2017, 44(10): 2878-2885.
[3]	HUANG Cheng-cheng, SUN Lei, ZHANG Ze-hui, ZHANG Peng, ZHANG De-xian, LIU Ming-chun. Review on the Prohibitive Effect of Gradients in Chinese Traditional Herbs on Hemolysin in Bacteria [J]. , 2016, 43(12): 3363-3367.
[4]	WEI Bo, LIU Ming-qiang, HUHE Baterer. Development of Regulation Factor of Type Ⅲ Secretion Systems in Enterohaemorrhagic Escherichia coli [J]. , 2012, 39(6): 161-164.