利用多因子降维法研究CXCR1和IL-8基因交互作用与中国荷斯坦牛乳房炎的关系

doi:10.3864/j.issn.0578-1752.2011.09.018

Abstract

Abstract: 【Objective】 Multifactor Dimensionality Reduction (MDR) model was used to identify the interaction of CXCR1 and IL-8 and their impacts on the risk of mastitis susceptibility of Chinese Holstein, and to test it’s feasibility in analyzing genes-genes interactions. 【Method】 The polymorphisms of 7 SNP sites including the 5′ flanking region and coding region of CXCR1 and exon 4 and exon 5 of IL-8 were detected by PCR-SSCP and direct sequencing for 634 Chinese Holstein, including 228 individual mastitis cow, from Jinshan Breeding Dairy Farm of Bright Dairy Group of Shanghai, and to identify the interaction of CXCR1 and IL-8 and their impacts on the risk of mastitis susceptibility using MDR and Logistic regression. 【Result】Four SNPs were found for CXCR1 including three SNPs (-1 830(A/G), -1 768(T/A), -344(T/C)) in 5′ flanking region and 783(C/A) in coding region. A linked mutation in 2 789(A/G) and 2 862(T/C) sites was found for IL-8 gene, and this mutation results in the transaction of AA from Ser to Gly, and Cys to Arg. The main effects of polymorphism of 5 SNPs of CXCR1 and IL-8 gene showed no significant impacts on the mastitis susceptibility of cow based on the single factor Logistic regression. The interactions of CXCR1-(-1 768)-IL-8, CXCR1-(-1 768)-(783)-IL-8, and CXCR1-(-1 768)-(-344)-(783)-IL-8 showed significant impacts on the mastitis susceptibility of cow using MDR model, and the cross-validation consistency was maximum (10/10). The interactions of CXCR1-(-1 768)-IL-8 and CXCR1-(-1 768)-(783)-IL-8 showed high testing balance accuracy (0.5457 and 0.5485, respectively). The interaction of CXCR1- (-1 768)-IL-8 was high degree synergy for mastitis susceptibility from the interaction dendrogram of multi-genotypes of CXCR1 and IL-8. In the meanwhile, the interactions of CXCR1-(-1 768)-IL-8 showed significant impacts on the mastitis susceptibility of cow using Logistic regression model including the main effect of 5 SNPs and the interaction effect of CXCR1-(-1 768)-IL-8 and CXCR1-(-1 768)-(783)-IL-8 (P＜0.05). 【Conclusion】The interactions of CXCR1-(-1 768)-IL-8 was the best multi-genotype model to estimate the risk of mastitis susceptibility of Chinese Holstein. MDR and Logistic regression can also be used to estimate the risk of mastitis susceptibility of Chinese Holstein. MDR appeares better ability than Logistic regression for detection of high-order interactions, and MDR and Logistic regression have advantages and disadvantages when compared to each other. Combined use of MDR and Logistic regression may be preferable when dealing with interaction analysis.

Key words: multifactor dimensionality reduction(MDR) , Logistic regression , CXCR1 , IL-8 , mastitis susceptibility

MAO Yong-jiang, CHEN Ren-jin, CHEN Ying, CHANG Ling-ling, SHI Xue-kui,ZHANG Ya-qin, YANG Zhang-ping. Using the MDR Model to Analyze the Relationship of Gene-Gene Interaction Between CXCR1 and IL-8 and the Risk of Mastitis Susceptibility of Chinese Holstein[J].Scientia Agricultura Sinica, 2011, 44(9): 1908-1915.

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Using the MDR Model to Analyze the Relationship of Gene-Gene Interaction Between CXCR1 and IL-8 and the Risk of Mastitis Susceptibility of Chinese Holstein

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