title: CACTA-superfamily transposable element is inserted in MYB transcription factor gene of soybean line producing variegated seeds.
abstract: The R gene of soybean, presumably encoding a MYB transcription factor, controls seed coat color. The gene consists of multiple alleles, R (black), r-m (black spots and (or) concentric streaks on brown seed), and r (brown seed). This study was conducted to determine the structure of the MYB transcription factor gene in a near-isogenic line (NIL) having r-m allele. PCR amplification of a fragment of the candidate gene Glyma.09G235100 generated a fragment of about 1 kb in the soybean cultivar Clark, whereas a fragment of about 14 kb in addition to fragments of 1 and 1.4 kb were produced in L72-2040, a Clark 63 NIL with the r-m allele. Clark 63 is a NIL of Clark with the rxp and Rps1 alleles. A DNA fragment of 13 060 bp was inserted in the intron of Glyma.09G235100 in L72-2040. The fragment had the CACTA motif at both ends, imperfect terminal inverted repeats (TIR), inverse repetition of short sequence motifs close to the 5' and 3' ends, and a duplication of three nucleotides at the site of integration, indicating that it belongs to a CACTA-superfamily transposable element. We designated the element as Tgm11. Overall nucleotide sequence, motifs of TIR, and subterminal repeats were similar to those of Tgm1 and Tgs1, suggesting that these elements comprise a family.
authors.affiliation: a Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8518 Japan.
authors.forename: Fan
authors.initials: F
authors.lastname: Yan
authors.affiliation: a Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8518 Japan.
authors.forename: Shaokang
authors.initials: S
authors.lastname: Di
authors.affiliation: a Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8518 Japan.|b National Institute of Crop Science, Tsukuba, Ibaraki, 305-8518 Japan.
authors.forename: Ryoji
authors.initials: R
authors.lastname: Takahashi
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D001483:Base Sequence; D004251:DNA Transposable Elements / Q000235:genetics*; D017343:Genes, Plant; D056426:Genetic Loci; D007438:Introns; D008969:Molecular Sequence Data; D009154:Mutation; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D012639:Seeds / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D030262:Soybean Proteins / Q000096:biosynthesis / Q000235:genetics*; D013025:Glycine max / Q000235:genetics* / Q000378:metabolism; D020079:Terminal Repeat Sequences; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D030262:Soybean Proteins; D014157:Transcription Factors
keywords: CACTA-superfamily transposable element; Glycine max; R gene; couleur de la graine; gène R; seed coat color; soya; soybean; élément transposable de la superfamille CACTA