Visiting Scientists

Fabiana Rodrigues

Associated to Labex Scientist Alexandre Lima Nepomuceno

Evaluation of soybean wide transcriptome responses during drought and how circadian clock genes are affected.

Research Team: Fabiana Rodrigues (PhD), Frank Harmon (PhD), Alexandre Nepomuceno (PhD).

Objective: Through a genome-wide approach, study and identify transcriptional networks controlled by the clock genes in soybean under drought and normal environments.

Approach: Soybean plants were grown up to V1 developmental stage and after that leaf samples were collected every 4h in a time course of 24h at a 14/10h day/night photoperiod in a 30% (mild stress) Soil Gravimetric Humidity (GH). RNA extractions already started and RNA-Seq libraries will be sequenced using Hi-Seq 2000 at Eurofins MWG Operon.

Results: We are already analyzing the RNAseq results from all the samples. Results from this RNA-Seq experiment will give a genome wide view of how pathways are up/down regulated under different day-time hours and how water deficit interferes with these responses. Novel transcripts, SNPs, alternative splicing variants might be found and these data can be used in new approaches for genetic engineering focused in drought tolerance. Like any other new technology, RNA-Seq might have challenges because of the required assembly of millions of short sequence reads generated by next generation sequencers such as the HiSeq 2000. However, preliminary analysis show that our RNAseq result matches almost perfectly our qPCR results for the genes analyzed. This means that the expression patterns we are observing in the other thousands of genes in the RNAseq results are consistent. Thus, our intention is to use the RNAseq data and identify differentially expressed genes to make genetic constructs to transform A.thaliana and evaluate for abiotic stress tolerance. We plan to focus in regulatory genes (e.g. transcription factors), and in genes without much information about their function, increasing chances of being off-patent by other institutions.