Comparative transcriptome analysis of B. oleracea L. var. italica and B. macrocarpa Guss. genotypes under drought stress: de novo vs reference genome assembly

Abstract

Drought stress influences plant growth and development affecting some physiological processes during the growing cycle. The improvement of the drought stress resistance of the plant will allow the reduction of the water requirements of the crops, representing the new frontier for agriculture, as consequence of the ongoing climatic changes. The individuation of genetic features useful for enhancing the reduction of water use and the plant drought resistance will be one of the key strategy for providing enough food for the foreseen increment of the global population. Nowadays, the cultivars used for modern agriculture show a narrow genetic diversity due to the domestication process carried out of each crop, resulting with a less adaptation to the environmental conditions affected by both antropic activities and the climatic change in act. Among the several grown species, Brassica oleracea L. (n = 9) crops are particularly vulnerable to the adverse effects of water deficiency. Transcriptomic analysis is a powerful tool that allows researchers to identify genes and pathways, that are activated or repressed in response to each specific stress, elucidating the complex regulatory networks that underlie the correspondent response. To individuate the differentially expressed genes we compared two drought-sensitive B. oleracea L. var. botritis x italica Sicilian landraces and two drought-tolerant B. macrocarpa Guss populations grown in ordinary irrigation regimes and in water deficit conditions. Their transcriptome was obtained by a RNAseq approach. The individuated sensible and tolerant drought stress genotypes showed significant difference for H₂O₂ content, leaf area and SPAD index (Soil Plant Analysis Development). For better identify crucial genes and pathways associated with drought stress response of both the sensible and tolerant genotypes a thorough evaluation of both de novo assembly and reference B. oleracea var. italica genome-based assembly was conducted. The comparison of the transcriptomes allowed to identify the crucial genes and pathways associated with tolerance to drought stress in Brassica oleracea L. crops. As main results, we individuated one gene coding transcription factor showing opposite behavior in the sensitive and tolerant signatures. The adoption of two transcriptome assembly methods provided a more comprehensive dataset, enabling an unbiased interpretation of the outcomes.