利用SNP标记估计西门塔尔牛亲缘关系系数的准确性

doi:10.11843/j.issn.0366-6964.2016.02.008

Abstract

Abstract:

The objective of the study was to determine the number of SNPs which could efficiently estimate the kinship coefficient in Simmental cattle.1 059 Simmental cattle born between 2008 and 2012 year were used as the reference population.Based on the interval of the minor allele frequency (MAF)，100，500，1 000，1 500，2 000，2 500 and 3 000 SNPs located in Illumina bovineHD（770 k）chip were selected to estimate individual kinship coefficient.The results showed that with the increase of the SNPs’ number，the estimation accuracy showed an increasing trend as well.Especially，when the SNPs’ number reached to 2 500，there was no significant difference between relationship coefficients estimated using 2 500 SNPs and all SNPs，and the relationship coefficients were above 0.89 between them.Furthermore，the SNPs in the same interval with different allele frequency had no significant impact on the results.It was concluded that when the number of selected SNPs reached more than 2 500，a relatively higher estimation accuracy could be obtained.Our work has built a theoretical basis for further study of the kinship coefficient with high density SNP and provides a new clue for analyzing individual kinship relationship in Simmental cattle.

CLC Number:

S823
S813.3

ZHANG Jing-jing，GAO Hui-jiang，WU Yang，ZHU Bo，QI Xin，GAO Xue，ZHANG Lu-pei，CHEN Yan. Estimation of the Kinship Coefficient in Simmental Cattle Based on SNP Markers[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2016, 47(2): 268-275.

0
/ / Recommend

Add to citation manager EndNote|Reference Manager|ProCite|BibTeX|RefWorks

URL: https://www.xmsyxb.com/EN/10.11843/j.issn.0366-6964.2016.02.008

https://www.xmsyxb.com/EN/Y2016/V47/I2/268

References

［1］BAUMUNG R，SÖLKNER J.Pedigree and marker information requirements to monitor genetic variability［J］.Genet Sel Evol，2003，35(4)：369-383.
［2］VISSCHER P M，MEDLAND S E，FERREIRA M A，et al.Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings［J］.PLoS Genet，2006，2(3)：e41.
［3］LI C C，HORVITZ D G.Some methods of estimating the inbreeding coefficient［J］.Am J Hum Genet，1953，5(2)：107-117.
［4］AULCHENKO Y S，RIPKE S，ISAACS A，et al.GenABEL：an R library for genome-wide association analysis［J］.Bioinformatics，2007，23(10)：1294-1296.
［5］QUELLER D C，GOODNIGHT K F.Estimating relatedness using genetic markers［J］.Evolution，1989，43(2)：258-275.
［6］周磊，初芹，刘林，等.利用微卫星和 SNP 标记信息进行奶牛亲子鉴定的模拟研究［J］.畜牧兽医学报，2011，42(2)：169-176.
ZHOU L，CHU Q，LIU L，et al.Simulation study on paternity identification in dairy cattle with microsatellite and SNP markers［J］.Acta Veterinaria et Zootechnica Sinica，2011，42(2)：169-176.(in Chinese)
［7］张哲，罗元宇，李晴晴，等.一种基于高密度遗传标记的亲子鉴定方法及其应用［J］.遗传，2014，36(8)：835-841.
ZHANG Z，LUO Y Y，LI Q Q，et al.Developing and applying of a parentage identification approach based on high density genetic markers［J］.Hereditas (Beijing)，2014，36(8)：835-841.(in Chinese)
［8］郭刚，周磊，刘林，等.利用 SNP 标记进行北京地区中国荷斯坦牛亲子推断的研究［J］.畜牧兽医学报，2012，43(1)：44-49.
GUO G，ZHOU L，LIU L，et al.Parentage inference with single nucleotide polymorphism markers in the Chinese holstein in Beijing［J］.Acta Veterinaria et Zootechnica Sinica，2012，43(1)：44-49.(in Chinese)
［9］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］.J Anim Sci，2007，85(4)：881-885.
［10］VANRADEN P M.Efficient methods to compute genomic predictions［J］.J Dairy Sci，2008，91(11)：4414-4423.
［11］HILL W G，SALISBURY B A，WEBB A J.Parentage identification using single nucleotide polymorphism genotypes：application to product tracing［J］.J Anim Sci，2008，86(10)：2508-2517.
［12］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］.Mol Ecol，2010，19(7)：1439-1451.
［13］LOPES M S，SILVA F F，HARLIZIUS B，et al.Improved estimation of inbreeding and kinship in pigs using optimized SNP panels［J］.BMC Genet，2013，14：92.
［14］ROLF M M，TAYLOR J F，SCHNABEL R D，et al.Impact of reduced marker set estimation of genomic relationship matrices on genomic selection for feed efficiency in Angus cattle［J］.BMC Genet，2010，11：24.
［15］PURCELL S，NEALE B，TODD-BROWN K，et al.PLINK：a tool set for whole-genome association and population-based linkage analyses［J］.Am J Hum Genet，2007，81(3)：559-575.
［16］LEWONTIN R C.The interaction of selection and linkage.I.General considerations；heterotic models［J］.Genetics，1964，49(1)：49-67.
［17］HILL W G.Estimation of linkage disequilibrium in randomly mating populations［J］.Heredity(Edinb)，1974，33(2)：229-239.
［18］ZHAO H，NETTLETON D，DEKKERS J C.Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms［J］.Genet Res，2007，89(1)：1-6.
［19］TERWILLIGER J D，HAGHIGHI F，HIEKKALINNA T S，et al.A bias-ed assessment of the use of SNPs in human complex traits［J］.Curr Opin Genet Dev，2002，12(6)：726-734.
［20］YANG J，BENYAMIN B，MCEVOY B P，et al.Common SNPs explain a large proportion of the heritability for human height［J］.Nat Genet，2010，42(7)：565-569.
［21］GUO S W.Variation in genetic identity among relatives［J］.Hum Hered，1996，46(2)：61-70.
［22］GARANT D，KRUUK L E.How to use molecular marker data to measure evolutionary parameters in wild populations［J］.Mol Ecol，2005，14(7)：1843-1859.
［23］PINTO N，GUSMÃO L，AMORIM A.X-chromosome markers in kinship testing：a generalisation of the IBD approach identifying situations where their contribution is crucial［J］.Forensic Sci Int Genet，2011，5(1)：27-32.
［24］CHEN C Y，MISZTAL I，AGUILAR I，et al.Effect of different genomic relationship matrices on accuracy and scale［J］.J Anim Sci，2011，89(9)：2673-2679.
［25］OGAWA S，MATSUDA H，TANIGUCHI Y，et al.Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle［J］.BMC Genet，2014，15：15.
［26］WEIR B S，ANDERSON A D，HEPLER A B.Genetic relatedness analysis：modern data and new challenges［J］.Nat Rev Genet，2006，7(10)：771-780.
［27］ARIAS J A，KEEHAN M，FISHER P，et al.A high density linkage map of the bovine genome［J］.BMC Genet，2009，10：18.
［28］TORTEREAU F，SERVIN B，FRANTZ L，et al.A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content［J］.BMC Genomics，2012，13：586.
［29］VERONEZE R，LOPES P S，GUIMARÃES S E，et al.Linkage disequilibrium and haplotype block structure in six commercial pig lines［J］. J Anim Sci，2013，91(8)：3493-3501.
［30］QANBARI S，PIMENTEL E C，TETENS J，et al.The pattern of linkage disequilibrium in German Holstein cattle［J］.Anim Genet，2010，41(4)：346-356.

[1]	LIU Xiaoqian, JIN Lanjie, DONG Yanqiu, LI Dongjie, ZHANG Cui, GU Shukai, LI Shijie. DNA Methylation Regulate the Genomic Imprinting of AQP1 Gene Specific in Bovine Placenta [J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(8): 2181-2189.
[2]	ZHANG Cui, CHEN Weina, LI Junliang, GU Shukai, XU Da, LI Dongjie, LI Shijie. Abnormal Expression of LINC24065 in Somatic Cell Nuclear Transfer Cattle [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(1): 44-51.
[3]	WANG Guan-nan, ZHAO Yu-peng, CHEN Wei-na, ZHANG Cui, XU Da, LI Dong-jie, LI Shi-jie. Genomic Imprinting Status of Gab1 and Sfmbt2 in Different Tissues of Adult Cattle [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2017, 48(6): 1000-1006.
[4]	XU Huai-chao,ZAN Lin-sen,WANG Hong-bao,NING Yue. Association of CRTC3 Gene Polymorphisms and Genotype Combination with Growth Traits of Qinchuan Cattle [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2016, 47(11): 2184-2190.
[5]	SONG Min-yan，WEI Yi-yuan，Muhammad Zahoor Khan，WANG Xin，YU Ying. Molecular Marker Study of Inflammatory Reaction in Bovine Mammary Epithelium Cell Line Induced by Methicillin-Resistant Staphylococcus aureus [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2016, 47(10): 1995-2002.
[6]	NIU Hong，BAO Jin-shan，WU Yang，ZHU Bo，ZHANG Wen-gang，XIA Jiang-wei，SONG Yu-xin，GUO Peng，XU Ling-yang，CHEN Yan，GAO Xue，ZHANG Lu-pei，GAO Hui-jiang，LI Jun-ya. Estimation of Genetic Parameters for Economic Important Traits in Chinese Simmental Beef Cattle [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2016, 47(9): 1817-1823.
[7]	MEI Chu-gang，ZHANG Qiong，FU Chang-zhen，LIU Yang，JIANG Bi-jie，CHENG Gong，ZAN Lin-sen. ADIG Inducing the Trans-differentiation of Bovine Myoblasts and Its Related Gene Expression [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2016, 47(4): 661-670.
[8]	FENG Wen，DONG Yi-chun，WANG Xiao，LIU Chao，WANG Xin，WANG Ya-chun，YU Ying. The Genetic Effect of TRAPPC9 on Mastitis Resistance to S.aureus in Dairy Cows [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2016, 47(2): 276-283.
[9]	GUO Yun-tao，ZHANG Xiu-xiu，MIAO Xiang-yang. Target Gene Prediction and Bioinformatics Analysis of bta-miR-320a [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2015, 46(11): 1952-1960.
[10]	LI Juan，DU Xin-hua，CHEN Yan，GAO Xue，LI Jun-ya，XU Shang-zhong. Study on Genetic Characteristic and Expression of Bovine FABP3 Gene in Transgenic Mice [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2015, 46(10): 1750-1758.
[11]	GUI Lin-sheng，ZAN Lin-sen，WANG Hong-bao，WANG Hong-cheng. Effects of Single and Combined Genotypes of SIRT1 and SIRT2 Genes on Meat Quality Traits in Qinchuan Cattle [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2015, 46(10): 1741-1749.
[12]	WU Xi-hong，ZHANG Ming-yue，YANG Wen-zhi，WU Guo-jiang，LI Shi-jie. Genomic Imprinting and Methylation in Regulating Imprinting of Wif1 Gene in Cattle [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2015, 46(8): 1325-1332.
[13]	HUAN Cong-cong，XU Hou-qiang，CHEN Wei，CHEN Xiang，ZHAO Jia-fu，ZHANG Wen，ZHOU Di，XIA Dan. Construction of MyoD I Promoter Eukaryotic Expression Vector in Guanling Cattle and Its Expression in Mouse C2C12 Cells [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2015, 46(5): 719-727.
[14]	SUN Xiao-li，LI Shu-feng，TONG Hui-li，ZHANG Wei-wei，YIN Hong-yan，YAN Yun-qin. The Construction of Different Muscle-specific Promoter IGF2 Expression Vector and Its Impact on Bovine Skeletal Muscle Satellite Cell Proliferation [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2015, 46(4): 555-560.
[15]	XIONG Ben-hai，YANG Liang，YANG Qin，PAN Xiao-hua，HAN Ying-dong，PANG Zhi-hong. Study on General Lactation Curve Models and Milk Composition Change Models of Chinese Holstein Cows in the North of China [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2014, 45(12): 1939-1948.

Estimation of the Kinship Coefficient in Simmental Cattle Based on SNP Markers

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments