Genomic architecture of promoters and transcriptional regulation of candidate genes in rice involved in tolerance to anaerobic germination

Global climate change has significant impacts on rice production due to flooding caused by heavy rainfall which has serious implications in rice growing areas of Southeast Asia. In these areas, direct seeding is preferred as it saves labour, cost, energy and water. Hence, the unique ability of rice seeds to germinate under anaerobic condition is important to achieve direct seeding. A number of candidate genes associated with anaerobic germination have been identified through genome-wide association studies (GWAS) based on single nucleotide polymorphism (SNP) markers. These candidate genes could be regulated by unique transcriptional regulatory mechanisms that enable them to tolerate anaerobic stress. However, the molecular basis of this transcriptional regulation is essentially unknown. Hence, a comprehensive understanding of the gene regulation of these candidate genes can provide important insights towards improved rice varieties for direct seeding. To fill this gap, publicly available novel candidate genes [Os01g0911700 (OsVP1), Os05g0560900 (OsGA2ox8), Os05g0562200 (OsDi19–1) and Os06g0548200] associated with anaerobic germination tolerance were selected and analysed. The genomic architecture of the promoters of these genes was defined by performing putative cis-elements enrichment analysis. Promoter analysis identified putative cis-elements linked to transcription factors (TFs) such as MYB, bZIP, AP2/ERF, EIN3, ABI3, ABR1, ARF, WRKY, bHLH, BES1/BZR1, ZnF, NAC, DOF, AS2, HSF, HD-Zip, TCP, MADS-box, ARR-B, E2F and GATA. Interestingly, putative cis-elements associated with unique TFs possibly related to epigenetic effect such as MYB3R, TSO1, TCX2/SOL2, TCX3/SOL1 and ASHR1; regulation of lipid metabolism associated with AHL and, regulation of sugar and fatty acid metabolism associated with WRI1 were also identified. Besides, the analysis also provides useful information on the crosstalk between key TFs and phytohormones such as GA, ABA, ethylene, auxin, JA and BR for unique transcriptional regulation leading to coleoptile elongation of rice during anaerobic germination tolerance. The current in silico analysis can provide information and contribute to the development of new rice varieties for direct seeding.