Sharma Niharika, Dang Trang Minh, Singh Namrata, Ruzicic Slobodan, Mueller-Roeber Bernd, Baumann Ute, Heuer Sigrid
School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia.
International Rice Research Institute (IRRI), Los Banos, Philippines.
Rice (N Y). 2018 Jan 8;11(1):2. doi: 10.1186/s12284-017-0192-z.
Flooding 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.
Nineteen 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.
This 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.
季节性季风引发的洪水影响了亚洲数百万公顷的水稻种植区。被淹没的水稻植株由于缺氧、光照以及为了露出水面而过度伸长生长，会在一周内死亡。耐淹性最初是在一个稻种类型的水稻地方品种FR13A中被报道的，乙烯响应转录因子（TF）基因SUB1A-1被确定为主要的耐淹基因。不耐淹的水稻品种通常缺乏SUB1A基因，但一些中等耐淹品种，如IR64，携带等位变异体SUB1A-2。到目前为止，这两个等位基因的差异影响尚未得到研究。因此，作为第一步，我们对IR64及其携带SUB1A-1等位基因的耐淹近等基因系IR64-Sub1之间近2500个水稻TF基因的表达进行了定量和比较。在节间研究了基因表达，此前已表明这两个等位基因在节间的表达存在主要差异。
分别在IR64和IR64-Sub1中鉴定出19个和26个对淹水有响应的TF基因。仅发现一个基因在两者中均对淹水有响应，这表明两种基因型在淹水情况下的调控途径不同。这些差异表达基因（DEG）主要包括MYB、NAC、TIFY和锌指TF，大多数基因在淹水时表达下调。在IR64中，而不是在IR64-Sub1中，也存在于Sub1位点的SUB1B和SUB1C被鉴定为对淹水有响应。四个TF对淹水无响应，但表现出组成型的、基因型特异性的差异表达。除乙烯外，大多数已鉴定的对淹水有响应的DEG与调节激素途径有关，即赤霉素（GA）、脱落酸（ABA）和茉莉酸（JA）。对两种基因型的电子启动子分析揭示了等位基因特异性单核苷酸多态性的存在，产生了ABRE、DRE/CRT、CARE和Site II顺式元件，这可以部分解释观察到的TF基因差异表达。
本研究确定了具有进一步提高水稻耐淹性潜力的新基因靶点，并为SUB1A介导的耐受性的新方面提供了见解。
