利用混合线性模型和BayesCPi进行QTL-MAS2011公共数据集的全基因组关联分析

doi:10.11843/j.issn.0366-6964.2014.05.003

Abstract

Abstract:

In this study，the program MTDFREML was used to estimate the variance component of simulated traits in QTL-MAS2011 dataset.Heritability was figured out approximately to be 029.Principal component analysis showed that there wasn’t population stratification in population，and then the two kinds of models analysis of genome-wide association studies were used.Genome-wide association analyses of the 15th QTL-MAS workshop data using mixed linear model of GAPIT package was processed，by which ten significant single nucleotide polymorphisms were detected within the whole genome.Among them，four significant SNPs were on chromosome 1，four significant SNPs were on chromosome 3，and two SNPs were on chromosome 5.The linkage disequilibrium analysis of 88 SNPs on three chromosomes was performed by HAPLOVIEW program，two QTLs(QTL1 and QTL5) were identified on chromosome 1 and 3，respectively.No QTLs were detected on chromosome 2，4，5.Another genome-wide association study method(BayesCPi) was used.The genome-wide association study was performed using BayesCPi model through genomic window variance map，one QTL was detected on chromosome 1，and two QTLs were identified on chromosome 2，and one QTL was detected on chromosome 3.

CLC Number:

S813.3

ZHU Bo，WU Yang, QI Xin，NIU Hong，ZHANG Jing-jing，WANG Yan-hui，CHEN Yan, ZHANG Lu-pei, GAO Hui-jiang，GAO Xue, LI Jun-ya, SUN Shao-hua. Genome-wide Association Analyses of the 15th QTL-MAS Workshop Data Using Mixed Linear Model and BayesCPi Method[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2014, 45(5): 692-698.

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Genome-wide Association Analyses of the 15th QTL-MAS Workshop Data Using Mixed Linear Model and BayesCPi Method

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