title: Comparative analysis of the inverted repeat of a chalcone synthase pseudogene between yellow soybean and seed coat pigmented mutants.
abstract: In soybean, the I gene inhibits pigmentation over the entire seed coat, resulting in yellow seeds. It is thought that this suppression of seed coat pigmentation is due to naturally occurring RNA silencing of chalcone synthase genes (CHS silencing). Fully pigmented seeds can be found among harvested yellow seeds at a very low percentage. These seed coat pigmented (scp) mutants are generated from yellow soybeans by spontaneous recessive mutation of the I gene. A candidate for the I gene, GmIRCHS, contains a perfect inverted repeat (IR) of a CHS pseudogene (pseudoCHS3) and transcripts of GmIRCHS form a double-stranded CHS RNA that potentially triggers CHS silencing. One CHS gene, ICHS1, is located 680 bp downstream of GmIRCHS. Here, the GmIRCHS-ICHS1 cluster was compared in scp mutants of various origins. In these mutants, sequence divergence in the cluster resulted in complete or partial loss of GmIRCHS in at least the pseudoCHS3 region. This result is consistent with the notion that the IR of pseudoCHS3 is sufficient to induce CHS silencing, and further supports that GmIRCHS is the I gene.
authors.affiliation: Faculty of Agriculture and Life Sciences, Hirosaki University , 3 Bunkyo-cho, Hirosaki, Aomori 036-8561 , Japan.
authors.forename: Mineo
authors.initials: M
authors.lastname: Senda
authors.affiliation: Faculty of Agriculture and Life Sciences, Hirosaki University , 3 Bunkyo-cho, Hirosaki, Aomori 036-8561 , Japan.
authors.forename: Satsuki
authors.initials: S
authors.lastname: Nishimura
authors.affiliation: Faculty of Agriculture and Life Sciences, Hirosaki University , 3 Bunkyo-cho, Hirosaki, Aomori 036-8561 , Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Kasai
authors.affiliation: Research Support Center, National Agricultural Research Center for Tohoku Region , Yotsuya, Daisen, Akita 014-0102 , Japan.
authors.forename: Setsuzo
authors.initials: S
authors.lastname: Yumoto
authors.affiliation: National Agricultural Research Organization (NARO) Western Region Agricultural Research Center , 1-3-1 Senyu, Zentsuji, Kagawa 765-8508 , Japan.
authors.forename: Yoshitake
authors.initials: Y
authors.lastname: Takada
authors.affiliation: Hokkaido Research Organization Tokachi Agricultural Experiment Station , S9-2 Shinsei, Memuro, Kasai, Hokkaido 082-0081 , Japan.
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Tanaka
authors.affiliation: Hokkaido Research Organization Kitami Agricultural Experiment Station , 52 Yayoi, Kunneppu, Tokoro, Hokkaido 099-1406 , Japan.
authors.forename: Shizen
authors.initials: S
authors.lastname: Ohnishi
authors.affiliation: Niigata Agricultural Research Institute , 857 Nagakura-machi, Nagaoka, Niigata 940-0826 , Japan.
authors.forename: Tomohisa
authors.initials: T
authors.lastname: Kuroda
keywords: CHS genes; RNA silencing; inverted repeat; mutant; seed coat pigmentation; soybean