尾分析法在不同规模群体中开展全基因组关联研究

doi:10.11843/j.issn.0366-6964.2017.07.002

Abstract

Abstract:

Tail analysis and genome-wide association studies(GWAS) were combined in this study to determine preliminary two tails selection criterions. A total of 2 000, 1 500, 1 000 and 500 samples and 20%, 15%, 12%, 10%, 8%, 5% of two tails were used to run GWAS to estimate the effects of the population size on GWAS and the effect of the proportion of two tails on GWAS, respectively. The results showed that the number of significant SNPs decreased with the reducing population size and the proportion of two tails. The preliminary selection criterions were:traits with heritability of about 0.38, the proportion of two tails of 8%, 10%, 10% and 20% from 2 000, 1 500, 1 000 and 500 samples, which were appropriate for two tails population for running GWAS, respectively. Further, the traits with heritability of about 0.50, the proportion of two tails of 5%, 5%, 10% and 15% from 2 000, 1 500, 1 000 and 500 samples were appropriate for two tails population for running GWAS, respectively. The present preliminary two tails selection criterions from populations with various sizes to run GWAS could detect significant SNPs effectively and also provide a strategy of reducing the cost of GWAS.

CLC Number:

S828
S813.1

WU Qun-qing, ZHANG Long-chao, HUANG Sheng-qiang, WANG Li-xian. A Genome-wide Association Study of Different Size Populations Based on Tail Analysis[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2017, 48(7): 1181-1190.

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References

[1] HIRSCHHORN J N, DALY M J. Genome-wide association studies for common diseases and complex traits[J]. Nat Rev Genet, 2005, 6(2):95-108.
[2] RISCH N, MERIKANGAS K. The future of genetic studies of complex human diseases[J]. Science, 1996, 273(5281):1516-1517.
[3] 段忠取, 朱军. 全基因组关联分析研究进展[J]. 浙江大学学报:农业与生命科学版, 2015, 41(4):385-393.
DUAN Z Q, ZHU J. Research progress of genome-wide association study[J]. Journal of Zhejiang University:Agriculture & Life Sciences, 2015, 41(4):385-393.(in Chinese)
[4] KLEIN R J, ZEISS C, CHEW E Y, et al. Complement factor H polymorphism in age-related macular degeneration[J]. Science, 2005, 308(5720):385-389.
[5] 陈广凤, 陈建省, 田纪春. 小麦株高相关性状与SNP标记全基因组关联分析[J]. 作物学报, 2015, 41(10):1500-1509.
CHEN G F, CHEN J S, TIAN J C. Genome-wide association analysis between SNP markers and plant height related traits in wheat[J]. Acta Agronomica Sinica, 2015, 41(10):1500-1509. (in Chinese)
[6] ZHAO K Y, TUNG C W, EIZENGA G C, et al. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa[J]. Nat Commun, 2011, 2:467.
[7] WANG M, YAN J B, ZHAO J R, et al. Genome-wide association study (GWAS) of resistance to head smut in maize[J]. Plant Sci, 2012, 196:125-131.
[8] 兰蓉, 朱兰, 姚新荣, 等. 山羊产羔数全基因组关联分析[J]. 畜牧兽医学报, 2015, 46(4):549-554.
LAN R, ZHU L, YAO X R, et al. Genome-wide association study of lambing number in goat[J]. Acta Veterinaria et Zootechnica Sinica, 2015, 46(4):549-554. (in Chinese)
[9] 孙艳发, 刘冉冉, 郑麦青, 等. 鸡胫长和胫围的全基因组关联分析[J]. 畜牧兽医学报, 2013, 44(3):358-365.
SUN Y F, LIU R R, ZHENG M Q, et al. Genome-wide association study on shank length and shank girth in chicken[J]. Acta Veterinaria et Zootechnica Sinica, 2013, 44(3):358-365. (in Chinese)
[10] 刘澳星, 郭刚, 王雅春, 等. 中国荷斯坦牛初产日龄遗传评估及全基因组关联分析[J]. 畜牧兽医学报, 2015, 46(3):373-381.
LIU A X, GUO G, WANG Y C, et al. Genetic analysis and genome wide association studies for age at first calving in chinese holsteins[J]. Acta Veterinaria et Zootechnica Sinica, 2015, 46(3):373-381. (in Chinese)
[11] 赵谦, 浦亚斌, 关伟军, 等. 猪重要性状全基因组关联分析的研究进展[J]. 畜牧兽医学报, 2015, 44(6):873-881.
ZHAO Q, PU Y B, GUAN W J, et al. Research progress of genome-wide association studies for important traits in pig[J]. Acta Veterinaria et Zootechnica Sinica, 2015, 44(6):873-881. (in Chinese)
[12] 王慰慰, 杜智恒, 白秀娟. 尾分析法检测北极狐自咬症关联的RAPD标记[J]. 动物学杂志, 2010, 45(3):154-158.
WANG W W, DU Z H, BAI X J. Detection of the linkage between RAPD markers and the self-biting syndrome in arctic fox by tail analysis method[J]. Chinese Journal of Zoology, 2010, 45(3):154-158. (in Chinese)
[13] LEBOWITZ R J, SOLLER M, BECKMANN J S. Trait-based analyses for the detection of linkage between marker loci and quantitative trait loci in crosses between inbred lines[J]. Theor Applied Genet, 1987, 73(4):556-562.
[14] LANDER E S, BOTSTEIN D. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps[J]. Genetics, 1989, 121(1):185-199.
[15] DARVASI A, SOLLER M. Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus[J]. Genetics, 1994, 138(4):1365-1373.
[16] MINOZZI G, PEDRETTI A, BIFFANI S, et al. Genome wide association analysis of the 16th QTL-MAS workshop dataset using the random forest machine learning approach[J]. BMC Proc, 2014, 8(S5):S4.
[17] BRADBURY P J, ZHANG Z W, KROON D E, et al. TASSEL:software for association mapping of complex traits in diverse samples[J]. Bioinformatics, 2007, 23(19):2633-2635.
[18] NICODEMUS K K, LIU W L, CHASE G A, et al. Comparison of type I error for multiple test corrections in large single-nucleotide polymorphism studies using principal components versus haplotype blocking algorithms[J]. BMC Genet, 2005, 6(S1):S78.
[19] 陈伟. 应用全基因组关联分析定位高度近视易感基因和应用外显子组测序分析大动脉转位致病基因[D]. 北京:中国科学院, 2011.
CHEN W. Application of genome-wide association study in mapping of susceptibility genes in high myopia and exome sequencing in identifying genes responsible for transposition of great arteries[D]. Beijing:Chinese Academy of Sciences, 2011. (in Chinese)
[20] 徐颜美. 中国汉族人群原发免疫性血小板减少症的全基因组关联研究[D]. 南昌:南昌大学, 2014.
XU Y M. A genome-wide association study for primary immune thrombocytopenia in China Han population[D]. Nanchang:Nanchang University, 2014. (in Chinese)
[21] ABRAHAM R, MOSKVINA V, SIMS R, et al. A genome-wide association study for late-onset Alzheimer's disease using DNA pooling[J]. BMC Med Genomic s, 2008, 1:44.
[22] FOWDAR J Y, GREALY R, LU Y, et al. A genome-wide association study of essential hypertension in an Australian population using a DNA pooling approach[J]. Mol Genet Genomics, 2017, 292(2):307-324.
[23] VALES M I, SCHÖN C C, CAPETTINI F, et al. Effect of population size on the estimation of QTL:a test using resistance to barley stripe rust[J]. Theor Appl Genet, 2005, 111(7):1260-1270.
[24] 郭家中. 奶牛重要经济性状的全基因组关联分析[D]. 杨凌:西北农林科技大学, 2013.
GUO J Z. Genome-wide association studies for economically important traits in dairy cattle[D]. Yangling:Northwest A&F University, 2013. (in Chinese)
[25] NEWTON-CHEH C, HIRSCHHORN J N. Genetic association studies of complex traits:design and analysis issues[J]. Mutat Res, 2005, 573(1-2):54-69.
[26] 严卫丽. 复杂疾病全基因组关联研究进展-研究设计和遗传标记[J]. 遗传, 2008, 30(4):400-406.
YAN W L. Genome-wide association study on complex diseases:study design and genetic markers[J]. Hereditas (Beijing), 2008, 30(4):400-406. (in Chinese)
[27] 李娜. 基于GWAS的猪肉品质性状候选基因研究[D]. 北京:中国农业大学, 2016.
LI N. Genome-wide association studies for pig meat traits and exploration of major genes[D]. Beijing:China Agricultural University, 2016. (in Chinese)
[28] HEFFNER E L, SORRELLS M E, JANNINK J L. Genomic selection for crop improvement[J]. Crop Sci, 2009, 49(1):1-12.

A Genome-wide Association Study of Different Size Populations Based on Tail Analysis

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