1001 GENOMES
Scientists at the Vienna BioCenter were major contributors to the 1001 Genomes Project, a formidable international effort to provide the genomes, transcriptomes, and epigenomes of more than 1,000 strains of the most studied model plant, Arabidopsis thaliana, from across the globe. The data provide an enormous boost for plant and agricultural research, including fundamental insights into adaptation.
Arabidopsis thaliana is a widely used model organism for the study of fundamental physiological, cellular, and molecular processes, and was the first plant to have its genome sequenced. Decreasing genotyping costs in recent years have fueled interest in exploring the impact of natural genetic variation using genome-wide association studies (GWAS), which attempt to identify genes responsible for variation simply by correlating genotype with phenotype. Natural A. thaliana strains are found in strikingly different environments and accordingly show enormous phenotypic variation in physiological, morphological, and life history traits. This makes it ideally suited for studying genotype-environment interactions. Variable traits include plant stature, metabolite content, flowering, germination behavior, and responses to stress or disease. To understand the relationships between genetic variation and such traits, genome-wide data for a large number of phenotypically diverse individuals are required. Magnus Nordborg’s group at the GMI was a major driving force behind the 1001 Genomes Consortium, which in 2016 reported the genomes, transcriptomes, and methylomes of over 1000 natural inbred strains of A. thaliana from Europe, Central Asia, North Africa, and North America (two papers in Cell, 2016).
The datasets provide a powerful GWAS platform and an outstanding opportunity to decipher how genetic and epigenetic variation translates into molecular and non-molecular phenotypic variation. For example, DNA methylation correlated strongly with a strain’s geographical origin and climate, supporting the concept that methylation plays a key role in environmental adaptation. The data also provided substantial new insights into the global population structure, migration patterns, and evolutionary history of A. thaliana.
The detailed, curated, and publicly available data resulting from the Consortium’s efforts provide a fantastic resource for the scientific community, which will continue to grow as further sequence information and phenotypic data are added. This resource will greatly advance our knowledge of the evolution of genetic and epigenetic diversity, and will provide unique insights into how plants adapt to variable climates.
Publications:
1001 Genomes Consortium. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 2016; 166:481–491.
Kawakatsu et al. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell 2016; 166:492–505.