Germination of barley after submergence: a genetics and a microbiome approach

I studied barley germination tolerance to short submergence stress through genetic and microbiome approaches. Barley is the most sensitive cereal to submergence, especially during germination. In the past four years, I have phenotyped the WHEALBI barley collection for the trait Submergence Tolerance Index (STI), identifying tolerant and sensitive genotypes to short submergence periods. Through a Genome Wide Association Studies, I was able to identify a laccase as the main responsible of the tolerance variation under the stress. Hence, I show that the differential expression of a specific gene during seed maturation affects the tolerance variation to an abiotic stress during germination. Although differential laccase haplotypes explain the different phenotypes, different seed microbiota can also contribute. Thus, I performed the analysis of a metagenomic 16S rRNA gene amplicon sequencing on tolerant and sensitive barley grains. Obtained results suggest the presence of a dissimilar microbiome availability in tolerant versus sensitive accessions of barley and support the hypothesis that this difference may be responsible of some activities involved in barley germination after submergence. Overall, this works gives an overview in the response of barley to short submergence periods during germination, from the genetics to the microbiome.