Identification of tomato root growth regulatory genes and transcription factors through comparative transcriptomic profiling of different tissues

Abstract

Tomato is an economically important vegetable crop and a model for development and stress response studies. Although studied extensively for understanding fruit ripening and pathogen responses, its role as a model for root development remains less explored. In this study, an Illumina-based comparative differential transcriptomic analysis of tomato root with different aerial tissues was carried out to identify genes that are predominantly expressed during root growth. Sequential comparisons revealed * 15,000 commonly expressed genes and * 3000 genes of several classes that were mainly expressed or regulated in roots. These included 1069 transcription factors (TFs) of which 100 were differentially regulated. Prominent amongst these were members of families encoding Zn finger, MYB, ARM, bHLH, AP2/ ERF, WRKY and NAC proteins. A large number of kinases, phosphatases and F-box proteins were also expressed in the root transcriptome. The major hormones regulating root growth were represented by the auxin, ethylene, JA, ABA and GA pathways with root-specific expression of certain components. Genes encoding carbon metabolism and photosynthetic components showed reduced expression while several protease inhibitors were amongst the most highly expressed. Overall, the study sheds light on genes governing root growth in tomato and provides a resource for manipulation of root growth for plant improvement.

Physiological and Transcriptional Characteristics of Banana Seedlings in Response to Nitrogen Deficiency Stress

“…The participation of transcription factors in the signaling network of plant stress is crucial for nitrogen response factors, ultimately influencing the regulation of target gene expression to modulate root growth [70,71]. Notably, prominent transcription factors, including WRKY, GRAS, MYB, and Zinc finger, have been demonstrated to govern root development in Arabidopsis and rice [72][73][74][75][76]. In Arabidopsis, AtMYB59 controlled the cell cycle of root tip cells, AtWRKY46 modulated lateral root development through ABA signal, AtWRKY23 influenced roots by modifying auxin distribution, and AtZFP5 played a role in root hair development and elongation by mediating cytokinin and ethylene signaling pathways [77][78][79][80].…”