Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A

Abstract

The major rice quantitative-trait locus Submergence 1 (Sub1) confers tolerance of submergence for about 2 weeks. To identify novel sources of tolerance, we have conducted a germplasm survey with allele-specific markers targeting SUB1A and SUB1C, two of the three transcription-factor genes within the Sub1 locus. The objective was to identify tolerant genotypes without the SUB1A gene or with the intolerant SUB1A-2 allele. The survey revealed that all tolerant genotypes possessed the tolerant Sub1 haplotype (SUB1A-1/SUB1C-1), whereas all accessions without the SUB1A gene were intolerant. Only the variety James Wee with the SUB1A-2 allele was moderately tolerant. However, some intolerant genotypes with the SUB1A-1 allele were identified and RT-PCR analyses were conducted to compare gene expression in tolerant and intolerant accessions. Initial analyses of leaf samples failed to reveal a clear association of SUB1A transcript abundance and tolerance. Temporal and spatial gene expression analyses subsequently showed that SUB1A expression in nodes and internodes associated best with tolerance across representative genotypes. In James Wee, transcript abundance was high in all tissues, suggesting that some level of tolerance might be conferred by high expression of the SUB1A-2 allele. To further assess tissue-specific expression, we have expressed the GUS reporter gene under the control of the SUB1A-1 promoter. The data revealed highly specific GUS expression at the base of the leaf sheath and in the leaf collar region. Specific expression in the growing part of rice leaves is well in agreement with the role of SUB1A in suppressing leaf elongation under submergence.

Waterproofing Crops: Effective Flooding Survival Strategies

“…These two alleles encode proteins that only differ at a single amino acid, Ser-186 in SUB1A-1 and Pro-186 in SUB1A-2, a putative mitogen-activated protein kinase (MPK) phosphorylation site in SUB1A-1 . To further assess the determination of submergence tolerance by SUB1A, Singh et al (2010) evaluated SUB1A genotype and submergence tolerance in 76 rice accessions from a variety of geographic locations. Although tolerance was highly correlated with strong up-regulation of SUB1A-1 mRNA during submergence, there was an imperfect association between tolerance and SUB1A-1.…”

Development of High-Yielding Rice Varieties Suitable for Swampy Lands in Indonesia

“…This result was similar with the finding of Septiningsih et al (2012), where the SUB1A gene in the variety Madabaru, a moderately tolerant variety, was highly expressed under submergence, even though this variety had the 'susceptible' allele SUB1A-2. Likewise, Singh et al (2010) had reported that the susceptible SUB1A-2 allele identified in the variety James Wee was highly expressed under submergence, despite the fact that this variety was moderately tolerant to submergence. Therefore, for a diversity study, in addition to the use of SUB1 DNA markers it is imperative to check the expression of SUB1A to confirm whether SUB1 indeed plays a role in contributing to submergence tolerance.…”

Submergence Tolerant Rice: SUB1’s Journey from Landrace to Modern Cultivar

“…An extensive analysis of diverse rice accessions with different SUB1 haplotype showed that submergence tolerance is associated with variable levels of SUB1A transcript in internodes and nodes at the heading stage (Singh et al 2010). In Nipponbare transgenics expressing the GUS reporter gene under the control of the native SUB1A promoter, GUS activity was specifically induced by submergence in regions of leaves associated with growth, i.e., the leaf base and leaf collar, suggesting that SUB1A might act on the processes of cell division and/or cell elongation in leaves under submergence.…”