Functional Natural Variation at 2 levels of Complexity: plant growth and cis-regulation – 2Complex

Plant growth is a complex process that integrates internal and external signals in order to optimize the extent and timing of biomass increase. The ability to rapidly adjust to large fluctuations in the environmental conditions is essential to these sessile organisms. If excessive, these fluctuations in the abiotic environment cause stress and acclimative strategies are induced. During evolution plants have developed an array of mechanisms to enable them to minimize the negative effects of unfavourable environmental conditions, representing an unlimited pool of genetic adaptations that largely remains to be understood and exploited. Following a long history of quantitative genetics in crop plants, it now becomes feasible to use naturally-occuring variation contained in Arabidopsis thaliana accessions (lines isolated from natural populations -potentially genetically distant from one another) as the source of quantitative genomics approaches, in which molecular markers enable to localize and identify the regions involved in the control of a trait, the QTLs. Apart from being able to exploit 'in multiple genetic backgrounds' allelic variation that cannot be easily generated by conventional mutagenesis, the (relatively few) success of the QTL studies has often been because of the use of quantitative phenotyping, as opposed to the qualitative gauges used in typical mutant screens. Among the various genetic mechanisms responsible for natural variation that have just started to be revealed, cis-acting regulation is potentially of large impact and it is hypothesized that cis-regulatory sequences might be less constrained in evolution than trans-factors or coding regions. However, these regulatory changes remain more difficult to recognize and confirm. The objective of this project is to clone new genes or alleles responsible for quantitative variation in Arabidopsis. We will apply genome-wide quantitative molecular genetics to both, a very integrative and classical quantitative trait (shoot growth) and a molecular trait a priori more directly linked to the source of variation (gene expression under cis-regulation). We propose to use a combination of our unique high-troughput phenotyping display, fine-mapping, complementation approaches and association genetics to pinpoint a significant number of QTLs and eQTLs to the gene level and identify causative polymorphisms. The analysis of the molecular and functional variation leading to the biomass and/or transcript accumulation phenotype(s) in interaction with the environment will provide clues as to how and where in the pathways adaptation is shaping natural variation and improve our understanding of the transcriptional cis-regulatory code. Moreover, the genes and physiological functions identified here will provide targets for biomass-related breeding programs, as well as participate in building an integrative view of the biology of the species and its evolution.