Abstract
Rice has the natural morphological adaptation to germinate and elongate its coleoptile under submerged flooding conditions. The phenotypic deviation associated with the tolerance to submergence at the germination stage could be due to natural variation. However, the molecular basis of this variation is still largely unknown. A comprehensive understanding of gene regulation of different genotypes that have diverse rates of coleoptile elongation can provide significant insights into improved rice varieties. To do so, publicly available transcriptome data of five rice genotypes, which have different lengths of coleoptile elongation under submergence tolerance, were analyzed. The aim was to identify the correlation between promoter architecture, associated with transcriptional and hormonal regulation, in diverse genotype groups of rice that have different rates of coleoptile elongation. This was achieved by identifying the putative cis-elements present in the promoter sequences of genes upregulated in each group of genotypes (tolerant, highly tolerant, and extremely tolerant genotypes). Promoter analysis identified transcription factors (TFs) that are common and unique to each group of genotypes. The candidate TFs that are common in all genotypes are MYB, bZIP, AP2/ERF, ARF, WRKY, ZnF, MADS-box, NAC, AS2, DOF, E2F, ARR-B, and HSF. However, the highly tolerant genotypes interestingly possess binding sites associated with HY5 (bZIP), GBF3, GBF4 and GBF5 (bZIP), DPBF-3 (bZIP), ABF2, ABI5, bHLH, and BES/BZR, in addition to the common TFs. Besides, the extremely tolerant genotypes possess binding sites associated with bHLH TFs such as BEE2, BIM1, BIM3, BM8 and BAM8, and ABF1, in addition to the TFs identified in the tolerant and highly tolerant genotypes. The transcriptional regulation of these TFs could be linked to phenotypic variation in coleoptile elongation in response to submergence tolerance. Moreover, the results indicate a cross-talk between the key TFs and phytohormones such as gibberellic acid, abscisic acid, ethylene, auxin, jasmonic acid, and brassinosteroids, for an altered transcriptional regulation leading to differences in germination and coleoptile elongation under submergence. The information derived from the current in silico analysis can potentially assist in developing new rice breeding targets for direct seeding.
Highlights
Rice is one of the major cereal crops and staple food in Southeast Asian countries
Promoter regions of common genes upregulated in diverse genotypes of rice germination and coleoptile elongation in response to submergence tolerance contain cis-elements/transcription factors (TFs) binding sites that are responsible for the regulation of genes associated with various hormone signaling as well as metabolic pathways
Putative cis-elements that are present in all genotypes are found to be associated with many known TFs such as MYB, Basic Leucine Zipper (bZIP), APETALA2/Ethylene-Responsive Element (AP2/ethylene-response factor (ERF)), ARF, WRKY, Zinc Finger (ZnF), MADS-box, NAC, AS2, DNA-Binding with One Finger (DOF), E2 factor (E2F), ARR-B, and Heat Shock Factor (HSF) (Tables 1-3)
Summary
Rice is one of the major cereal crops and staple food in Southeast Asian countries. In most of these countries, people sow seeds in the flooded rice fields through direct seeding that helps in reducing cost and manpower. Rice has the natural morphological adaptation to germinate and elongate its coleoptile under submerged flooding condition and even in anoxic conditions. This coleoptile reaches the surface of water to get O2 for aerobic respiration to get sufficient energy for the development of roots and shoots (Narsai et al, 2015). There is phenotypic variation in coleoptile elongation and the tolerance to submergence at the germination stage among different genotypes and which could be due to natural variation. A comprehensive understanding of the gene regulation of different genotypes tolerant to submergence/flooding can provide a significant
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