title: 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.
authors.affiliation: Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
authors.forename: Namrata
authors.initials: N
authors.lastname: Singh
authors.forename: Trang T M
authors.initials: TT
authors.lastname: Dang
authors.forename: Georgina V
authors.initials: GV
authors.lastname: Vergara
authors.forename: Dev Mani
authors.initials: DM
authors.lastname: Pandey
authors.forename: Darlene
authors.initials: D
authors.lastname: Sanchez
authors.forename: C N
authors.initials: CN
authors.lastname: Neeraja
authors.forename: Endang M
authors.initials: EM
authors.lastname: Septiningsih
authors.forename: Merlyn
authors.initials: M
authors.lastname: Mendioro
authors.forename: Evelyn Mae
authors.initials: EM
authors.lastname: Tecson-Mendoza
authors.forename: Abdelbagi M
authors.initials: AM
authors.lastname: Ismail
authors.forename: David J
authors.initials: DJ
authors.lastname: Mackill
authors.forename: Sigrid
authors.initials: S
authors.lastname: Heuer
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000483:Alleles; D000595:Amino Acid Sequence; D001483:Base Sequence; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D005819:Genetic Markers; D005966:Glucuronidase / Q000378:metabolism; D006239:Haplotypes / Q000235:genetics; D008969:Molecular Sequence Data; D009928:Organ Specificity / Q000235:genetics; D012275:Oryza / Q000235:genetics* / Q000502:physiology*; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D036226:Seedlings / Q000235:genetics; D012639:Seeds / Q000235:genetics; D016019:Survival Analysis; D013997:Time Factors; D014867:Water / Q000502:physiology*
chemical_list: D005819:Genetic Markers; D010940:Plant Proteins; D014867:Water; D005966:Glucuronidase