title: Single nucleotide polymorphisms and haplotype diversity in rice sucrose synthase 3.
abstract: Rice sucrose synthase 3 (RSUS3) is expressed predominantly in rice seed endosperm and is thought to play an important role in starch filling during the milky stage of rice seed ripening. Because the genetic diversity of this locus is not known yet, the full sequence of RSUS3 from 43 rice varieties was amplified to examine the distribution of DNA polymorphisms. A total of 254 sequence variants, including SNPs and insertion/deletions, were successfully identified in the 7733 bp sequence that comprises the promoter, exons and introns, and 3' downstream nontranscribed region (NTR). Eleven haplotypes were distinguished among the 43 rice varieties based on nucleotide variation in the 3 defined regions (5' NTR, transcript, and 3' NTR). The promoter region showed evidence of a base change on a cis-element that might influence the functional role of the motif in seed-specific expression. The genetic diversity of the RSUS3 gene sequences in the rice germplasm used in this study appears to be the result of nonrandom processes. Analysis of polymorphism sites indicated that at least 11 recombinations have occurred, primarily in the transcribed region. This finding provides insight into the development of a cladistic approach for establishing future genetic association studies of the RSUS3 locus.
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
authors.forename: Puji
authors.initials: P
authors.lastname: Lestari
authors.forename: Gian
authors.initials: G
authors.lastname: Lee
authors.forename: Tae-Ho
authors.initials: TH
authors.lastname: Ham
authors.lastname: Reflinur
authors.forename: Mi-Ok
authors.initials: MO
authors.lastname: Woo
authors.forename: Rihua
authors.initials: R
authors.lastname: Piao
authors.forename: Wenzhu
authors.initials: W
authors.lastname: Jiang
authors.forename: Sang Ho
authors.initials: SH
authors.lastname: Chu
authors.forename: Joohyun
authors.initials: J
authors.lastname: Lee
authors.forename: Hee-Jong
authors.initials: HJ
authors.lastname: Koh
mesh_terms: D020413:3' Untranslated Regions; D001208:Asia; D001483:Base Sequence; D002874:Chromosome Mapping; D017931:DNA Primers / Q000235:genetics; D056625:Endosperm / Q000235:genetics*; D005091:Exons; D017343:Genes, Plant; D056426:Genetic Loci; D014644:Genetic Variation; D005964:Glucosyltransferases / Q000737:chemistry / Q000235:genetics*; D006239:Haplotypes; D007438:Introns; D007527:Isoenzymes / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D017384:Sequence Deletion
chemical_list: D020413:3' Untranslated Regions; D017931:DNA Primers; D007527:Isoenzymes; D005964:Glucosyltransferases; C022699:sucrose synthase