利用紧缩线性模型和贝叶斯模型对猪总产仔数和产活仔数性状的全基因组关联研究

doi:10.3724/SP.J.1005.2012.01261

[an error occurred while processing this directive]

HEREDITAS ›› 2012, Vol. 34 ›› Issue (10): 1261-1270.doi: 10.3724/SP.J.1005.2012.01261

• en • Previous Articles Next Articles

Genome-wide association study of total number born and number born alive in pigsusing both compressed mixed linear model and Bayes model

LIU Xiao-Lei¹, YANG Song-Bai¹, Max F Roths-child², ZHANG Zhi-Wu³, FAN Bin¹

1. Key Laboratory of AgriculturalAnimal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan 430070, China 2. Department of Animal Science, Iowa State University, Ames IA 50011, USA 3. Institute for Genomic Diversity, Cornell University, Ithaca NY 14853, USA

Received:2012-06-18 Revised:2012-07-27 Online:2012-10-20 Published:2012-10-25
Contact: Bin Fan E-mail:fanbin@mail.hzau.edu.cn

Abstract

Abstract: GWAS(Genome-wide association study) strategy has been extensively used for identification of economical trait loci in livestock animals. Using Illumina’s PorcineSNP60 BeadChip, a GWA study of 820 commercial pigs with reproductive traits recorded was performed. The PCA analysis showed that there was no significant population stratification. Two different statistical models Compressed Mixed Linear Model(GAPIT program package)and Bayes CPi (GenSel software) were used to implement GWAS on total number born and number born alive of the first and second parity. To compare the most significant 50 SNPs from each method, a total of 31 and 20 coincided SNPs for total number born in the first parity were identified, and there were 20 coincided SNPs for number born alive in the first parityinthe results of bothmethods. The most significant SNPs were also significant in the results of the other method. The most significantly associated regions for total number born in the first parity were located on SSC1, 2, 3, 7, 13, 16, and 18. The most significantly associated regions for number born alive in the first parity were locatedon SSC1, 3, 4, 13, and 16. There were 5 common regions significantly associated with bothtraits on SSC1, 3, 13, and 16. The most significantly associated regions forbothtotal number born and number born alive for the second parity were mainly located on six common regions on SSC7, 10, 12, 13, 14, and 16.

Key words: GWAS, total number born, number born alive, SNP chip, pig

LIU Xiao-Lei, YANG Song-Bai, Max F Roths-child, ZHANG Zhi-Wu, FAN Bin. Genome-wide association study of total number born and number born alive in pigsusing both compressed mixed linear model and Bayes model[J]. HEREDITAS, 2012, 34(10): 1261-1270.

References

[1] Rothschild M, Jacobson C, Vaske D, Tuggle C, Wang LZ, Short T, Eckardt G, Sasaki S, Vincent A, McLaren D, Southwood O, van der Steen H, Mileham A, Plastow G. The estrogen receptor locus is associated with a major gene influencing litter size in pigs. Proc Natl Acad Sci USA, 1996, 93(1): 201-205.
[2] Li N, Zhao YF, Xiao L, Zhang FJ, Chen YZ. Candidate gene approach for identification of genetic loci controlling litter size in swine. In: Proceedings of the 6th World Con-gress Quatitative Genetics of Livestock. 1998, 26: 183-188.
[3] 赵要风, 李宁, 肖璐, 曹更生, 陈怡真, 张顺, 陈永福, 吴常信, 张建生, 孙士铨, 徐学清. 猪FSHβ亚基基因结构区逆转座子插入突变及其与猪产仔数关系的研究. 中国科学c辑, 1999, 29(1): 81-86.
[4] Fan B, Onteru SK, Du ZQ, Garrick DJ, Stalder KJ, Rothschild MF. Genome-wide association study identifies loci for body composition and structural soundness traits in pigs. PLoS One, 2011, 6(2): e14726.
[5] Gorbach DM, Cai W, Dekker JCM, Young JM. Whole-genome analyses for genes associated with residual feed intake and related traits utilizing the PorcineSNP60 BeadChip. In: Pig Genome III Conference. Hinxton, Cambridge, UK, 2009.
[6] Onteru SK, Fan B, Du ZQ, Garrick DJ, Stalder KJ, Rothschild MF. A whole-genome association study for pig reproductive traits. Anim Genet, 2012, 43(1): 18-26.
[7] Onteru SK, Fan B, Nikkilä MT, Garrick DJ, Stalder KJ, Rothschild MF. Whole-genome association analyses for lifetime reproductive traits in the pig. J Anim Sci, 2011, 89(4): 988-995.
[8] Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analysis. Am J Hum Genet, 2007, 81(3): 559-575.
[9] Zhang ZW, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu JM, Arnett DK, Ordovas JM, Buckler ES. Mixed linear model approach adapted for genome-wide association studies. Nat Genet, 2010, 42(4): 355-360.
[10] Fernando RL, Garrick DJ. GenSel-User manualfor a Portfolio of genomic selection related analyses. Anim Breed Genet, Iowa State University, Ames. http://bigs.ansci. iastate.edu/bigsgui/login.html, 2008.
[11] Meuwissen THE, Hayes BJ, Goddard ME. Prediction of total genetic value using genome-wide dense marker maps. Genetics, 2001, 157(4): 1819-1829.
[12] Kizilkaya K, Fernando RL, Garrick DJ. Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymor-phism genotypes. J Anim Sci, 2010, 88(2): 544-551.
[13] Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. Association mapping in structured populations. Am J Human Genet, 2000, 67(1): 170-181.
[14] Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet, 2006, 2(12): e190.
[15] Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis cor-rects for stratification in genome-wide association studies. Nat Genet, 2006, 38(8): 904-909.
[16] Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doe-bley J, McMullen M, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet, 2005, 38(2): 203-208.
[17] 许志峰. 选殖猪母源性胚胎拉链状白胺酸蛋白质激酶之调控区域及其特性分析[学位论文]. 台湾大学动物科学技术学研究所, 2010.
[18] Hickson JA, Fong B, Watson PH, Watson AJ. PP2Cδ (Ppm1d, WIP1), an endogenous inhibitor of p38 MAPK, is regulated along with Trp53 and Cdkn2a following p38 MAPK inhibition during mouse preimplantation development. Mol Reproduct Dev, 2007, 74(7): 821-834.
[19] Ewing RM, Chu P, Elisma F, Li HY, Taylor P, Climine S, McBroon-Cerajewski L, Robinson MD, O’Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang SD, Ornatsky O, B

Metrics

Comments

www.chinagene.cn
备案号：京ICP备09063187号

Genome-wide association study of total number born and number born alive in pigsusing both compressed mixed linear model and Bayes model

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Wenrui Shi, Hongzhu Qu, Xiangdong Fang. Overview of multi-omics research in gout [J]. Hereditas(Beijing), 2023, 45(8): 643-657.
[2]	Yanan Li, Xianjun Zhang, Ning Zhang, Yalin Liang, Yuxing Zhang, Huaxing Zhao, Zicong Li, Sixiu Huang. Effects of overexpression of histone H3K9me3 demethylase on development of porcine cloned embryos [J]. Hereditas(Beijing), 2023, 45(1): 67-77.
[3]	Fei Gao, Yu Wang, Jiaxiang Du, Xuguang Du, Jianguo Zhao, Dengke Pan, Sen Wu, Yaofeng Zhao. Advances and applications of genetically modified pig models in biomedical and agricultural field [J]. Hereditas(Beijing), 2023, 45(1): 6-28.
[4]	Mengxuan Xu, Ming Zhou. Advances of RNA polymerase IV in controlling DNA methylation and development in plants [J]. Hereditas(Beijing), 2022, 44(7): 567-580.
[5]	Yan Zhao, Chenxin Wang, Tianming Yang, Chunshuang Li, Lihong Zhang, Dongni Du, Ruoxi Wang, Jing Wang, Min Wei, Xueqing Ba. Linking oxidative DNA lesion 8-OxoG to tumor development and progression [J]. Hereditas(Beijing), 2022, 44(6): 466-477.
[6]	Hui Qu, Yi Liu, Yawen Chen, Hui Wang. Alteration of imprinted genes and offspring organ development caused by environmental factors [J]. Hereditas(Beijing), 2022, 44(2): 107-116.
[7]	Yangjinghui Zhang, Peiyao Chang, Zishu Yang, Yuhang Xue, Xueqi Li, Yang Zhang. Advances in epigenetic modification affecting anthocyanin synthesis [J]. Hereditas(Beijing), 2022, 44(12): 1117-1127.
[8]	Qingwen Zhao, Dongning Pan. Progress on the epigenetic regulation of adipose tissue thermogenesis [J]. Hereditas(Beijing), 2022, 44(10): 867-880.
[9]	Jiayu Yu, Ting Chen, Zhihua Wang, Juan Zheng, Tianshu Zeng. Diagnosis, treatment and genetic analysis of a case of skin hyperpigmentation as the only manifestation with X-linked adrenoleukodystrophy [J]. Hereditas(Beijing), 2022, 44(10): 983-989.
[10]	Wang Ya'nan, Tao Xu, Wanpeng Wang, Qingzhu Zhang, Xie Li'nan. Role of epigenetic modifications in the development of crops essential traits [J]. Hereditas(Beijing), 2021, 43(9): 858-879.
[11]	Jiangping He, Jiekai Chen. Epigenetic control of transposable elements and cell fate decision [J]. Hereditas(Beijing), 2021, 43(9): 822-834.
[12]	Jie Yuan, Shiqing Cai. The regulatory mechanisms of behavioral and cognitive aging [J]. Hereditas(Beijing), 2021, 43(6): 545-570.
[13]	Tianyi Wang, Yingxiang Wang, Chenjiang You. Structural and functional characteristics of plant PHD domain-containing proteins [J]. Hereditas(Beijing), 2021, 43(4): 323-339.
[14]	Yige Li, Dandan Zhang. Progress on functional mechanisms of colorectal cancer causal SNPs in post-GWAS [J]. Hereditas(Beijing), 2021, 43(3): 203-214.
[15]	Dingwei Peng, Ruiqiang Li, Wu Zeng, Min Wang, Xuan Shi, Jianhua Zeng, Xiaohong Liu, Yaoshen Chen, Zuyong He. Editing the cystine knot motif of MSTN enhances muscle development of Liang Guang Small Spotted pigs [J]. Hereditas(Beijing), 2021, 43(3): 261-270.