Bivariate genomic analysis identifies a hidden locus associated with bacteria hypersensitive response in Arabidopsis thaliana.
Multi-phenotype analysis has drawn increasing attention to high-throughput genomic studies, whereas only a few applications have justified the use of multivariate techniques. We applied a recently developed multi-trait analysis method on a small set of bacteria hypersensitive response phenotypes and identified a single novel locus missed by conventional single-trait genome-wide association studies. The detected locus harbors a minor allele that elevates the risk of leaf collapse response to the injection of avrRpm1-modified Pseudomonas syringae (P = 1.66e-08). Candidate gene AT3G32930 with in the detected region and its co-expressed genes showed significantly reduced expression after P. syringae interference. Our results again emphasize that multi-trait analysis should not be neglected in association studies, as the power of specific multi-trait genotype-phenotype maps might only be tractable when jointly considering multiple phenotypes.
Research Center of Precision Medicine, College of Life Sciences and Oceanography, Key laboratory of Optoelectronic Devices and System of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.|Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
Biao
B
Wang
Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China.
Zhuocheng
Z
Li
Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
Weilin
W
Xu
Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.|State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
Xiao
X
Feng
Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
Qianhui
Q
Wan
Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
Yanjun
Y
Zan
Research Center of Precision Medicine, College of Life Sciences and Oceanography, Key laboratory of Optoelectronic Devices and System of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.|HYK High-throughput Biotechnology Institute, Shenzhen, China.
Sitong
S
Sheng
Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.|Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom.
Xia
X
Shen
D000483:Alleles; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D056426:Genetic Loci; D055106:Genome-Wide Association Study; D005838:Genotype; D010641:Phenotype; D010935:Plant Diseases / Q000382:microbiology; D044224:Pseudomonas syringae / Q000472:pathogenicity*
D029681:Arabidopsis Proteins