Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes.
Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes.
复制标题
使用宿主和病原体基因组进行联合关联分析的双向混合效应方法。
DOI：
10.1073/pnas.1710980115
复制
发表时间：
2018
影响因子：
11.1
通讯作者：
Bergelson,Joy
中科院分区：
文献类型：
--
作者：
Wang,Miaoyan;Roux,Fabrice;Bartoli,Claudia;Huard-Chauveau,Carine;Meyer,Christopher;Lee,Hana;Roby,Dominique;McPeek,MarySara;Bergelson,Joy
Infectious diseases are often affected by specific pairings of hosts and pathogens and therefore by both of their genomes. The integration of a pair of genomes into genome-wide association mapping can provide an exquisitely detailed view of the genetic landscape of complex traits. We present a statistical method, ATOMM (Analysis with a Two-Organism Mixed Model), that maps a trait of interest to a pair of genomes simultaneously; this method makes use of whole-genome sequence data for both host and pathogen organisms. ATOMM uses a two-way mixed-effect model to test for genetic associations and cross-species genetic interactions while accounting for sample structure including interactions between the genetic backgrounds of the two organisms. We demonstrate the applicability of ATOMM to a joint association study of quantitative disease resistance (QDR) in theArabidopsis thaliana–Xanthomonas arboricolapathosystem. Our method uncovers a clear host–strain specificity in QDR and provides a powerful approach to identify genetic variants on both genomes that contribute to phenotypic variation.
