Please use this identifier to cite or link to this item: https://hdl.handle.net/2440/83143
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Type: Journal article
Title: Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A
Author: Singh, N.
Dang, T.
Vergara, G.
Pandey, D.
Sanchez, D.
Neeraja, C.
Septiningsih, E.
Mendioro, M.
Tecson-Mendoza, E.
Ismail, A.
MacKill, D.
Heuer, S.
Citation: Theoretical and Applied Genetics: international journal of plant breeding research, 2010; 121(8):1441-1453
Publisher: Springer
Issue Date: 2010
ISSN: 0040-5752
1432-2242
Statement of
Responsibility: 
Namrata Singh, Trang T. M. Dang, Georgina V. Vergara, Dev Mani Pandey, Darlene Sanchez, C. N. Neeraja, Endang M. Septiningsih, Merlyn Mendioro, Evelyn Mae Tecson-Mendoza, Abdelbagi M. Ismail, David J. Mackill, Sigrid Heuer
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.
Keywords: Seeds
Water
Glucuronidase
Plant Proteins
Genetic Markers
Survival Analysis
Gene Expression Profiling
Adaptation, Physiological
Organ Specificity
Gene Expression Regulation, Plant
Amino Acid Sequence
Base Sequence
Haplotypes
Alleles
Genes, Plant
Time Factors
Molecular Sequence Data
Promoter Regions, Genetic
Oryza
Seedlings
Rights: © Springer-Verlag 2010
DOI: 10.1007/s00122-010-1400-z
Appears in Collections:Agriculture, Food and Wine publications
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