Genomics of flooding stress tolerance: exploiting natural variation in Arabidopsis thaliana

Water is indispensable for plants. However, both extremes of it, in terms of availability, whether limited (i.e., drought) or excessive (i.e., flooding) are lethal for a plant. The incidence of flooding events, in particular, have increased in the past five decades due to the effect of anthropogenically induced climate change on the global precipitation cycle . Due to the flooding sensitivity of most crop species, this environmental stress causes major losses of crop yield and negatively impacts food production. Hence, the development of tolerant but high yielding varieties is essential. Past research on plant responses to flooding have provided considerable insight into the adaptive responses of relatively flood-tolerant plant species such as rice and Rumex. However, much still needs to be learnt about the (i) the relationship between gene regulation and plant survival and (ii) the genes and mechanisms that determine variation in tolerance to submergence. In the current study, we used the plant model species, Arabidopsis thaliana (Arabidopsis) with a well-characterized genome to identify the genetic components governing the adaptive response to submergence stress. Subsequent translation of thisobtained genomic knowledge from Arabidopsis to crops can aid marker-assistant breeding programs to develop high yielding crop varieties with improved survival under submerged conditions. To achieve our objective, we first exploited the natural variation among a set of 86 Arabidopsis accessions (Chapter 2). Our results demonstrated a considerable natural variation among Arabidopsis accessions for submergence tolerance and allowed the selection of a set of three most tolerant and three most sensitive genotypes. Next, we made a molecular comparison of the response of these six accessions to complete submergence to identify the genetic components that may underlie the observed variation in tolerance. We also characterized the organ-specific submergence-induced molecular adjustments by comparing the hypoxic shoot transcriptome (