Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice

Abstract

BackgroundFlooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown.ResultsNineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which can partly explain the observed differential TF gene expression.ConclusionThis study identified new gene targets with the potential to further enhance submergence tolerance in rice and provides insights into novel aspects of SUB1A-mediated tolerance.Electronic supplementary materialThe online version of this article (doi: 10.1186/s12284-017-0192-z) contains supplementary material, which is available to authorized users.

Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice

“…9 ). Stress-responsive cis -elements DRE as well as phytohormone-responsive elements including ABRE have all been implicated in response to submergence [ 89 ].…”

Comprehensive transcriptomic analysis of three varieties with different brown planthopper-resistance identifies leaf sheath lncRNAs in rice

“…The heat shock factor (HSF) gene, OsHsfC2a (OsR498G0203284300.01/LOC_Os02g13800), has been reported to have increased expression under a few abiotic stresses, i.e. heat, cold, oxidative stress, submergence [ 73 , 74 ] as well as drought and desiccation [ 75 , 76 ]. This transcription factor also showed response to brassinosteroids (BR), SA and abscisic acid (ABA) [ 75 , 76 ].…”

A NAC transcription factor OsNAC3 positively regulates ABA response and salt tolerance in rice

“…Interestingly, OsSUB12 (Submergence Tolerance 12), encoding an ethylene-responsive transcription factor, is homologous to OsSUB1A that mediates rice submergence stress tolerance [ 44 ]. Furthermore, analysis of cis-acting elements showed that there are many abiotic stress response-related elements, such as MYB binding sites, W-boxes, and ABRE (ABA-responsive element), in the promoter region of OsNAC3 .…”