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

Niharika Sharma,Ute Baumann,Bernd Mueller-Roeber,Slobodan Ruzicic,Trang Minh Dang,Sigrid Heuer,Namrata Singh

doi:10.1186/s12284-017-0192-z

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.

Highlights

Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia
Submergence tolerance 1 (Sub1) was identified from the aus-type rice landrace FR13A (Flood Resistance 13A) and it provided a breakthrough in the understanding of submergence tolerance mechanisms, enabling markerassisted breeding of submergence-tolerant rice (Fukao et al, 2006; Xu et al, 2006; Singh, Mackill, and Ismail, 2009; Bailey-Serres et al, 2010; Mackill et al, 2012)
In order to investigate the difference between submergence tolerance as mediated by the strong allele SUB1A1 and the weak allele SUB1A-2, expression of 2487 rice transcription factor (TF) genes was quantified by Quantitative real-time PCR (qPCR) in internodes of submerged and non-submerged control plants

Summary

Introduction

Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Rice production is constraint by submergence stress during the rainy season with complete submergence and water stagnation affecting about 20 million hectares of rice fields in the tropics, causing significant yield and economic losses, and food insecurity (Septiningsih et al, 2012). Rice fields can be flooded with several meters of water for weeks and plants die within a few days from lack of oxygen and impaired photosynthesis (Gibbs and Greenway, 2003; Fukao and Bailey-Serres, 2004). Sub was identified from the aus-type rice landrace FR13A (Flood Resistance 13A) and it provided a breakthrough in the understanding of submergence tolerance mechanisms, enabling markerassisted breeding of submergence-tolerant rice (Fukao et al, 2006; Xu et al, 2006; Singh, Mackill, and Ismail, 2009; Bailey-Serres et al, 2010; Mackill et al, 2012). Sub rice varieties are widely grown across Asia enhancing plant survival in flooded fields with yield advantages of one ton per hectare or more (Septiningsih et al, 2009; Mackill et al, 2012)

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