title: A recessive allele for delayed flowering at the soybean maturity locus E9 is a leaky allele of FT2a, a FLOWERING LOCUS T ortholog.
abstract: BACKGROUND
  Understanding the molecular mechanisms of flowering and maturity is important for improving the adaptability and yield of seed crops in different environments. In soybean, a facultative short-day plant, genetic variation at four maturity genes, E1 to E4, plays an important role in adaptation to environments with different photoperiods. However, the molecular basis of natural variation in time to flowering and maturity is poorly understood. Using a cross between early-maturing soybean cultivars, we performed a genetic and molecular study of flowering genes. The progeny of this cross segregated for two maturity loci, E1 and E9. The latter locus was subjected to detailed molecular analysis to identify the responsible gene.
  
  
  RESULTS
  Fine mapping, sequencing, and expression analysis revealed that E9 is FT2a, an ortholog of Arabidopsis FLOWERING LOCUS T. Regardless of daylength conditions, the e9 allele was transcribed at a very low level in comparison with the E9 allele and delayed flowering. Despite identical coding sequences, a number of single nucleotide polymorphisms and insertions/deletions were detected in the promoter, untranslated regions, and introns between the two cultivars. Furthermore, the e9 allele had a Ty1/copia-like retrotransposon, SORE-1, inserted in the first intron. Comparison of the expression levels of different alleles among near-isogenic lines and photoperiod-insensitive cultivars indicated that the SORE-1 insertion attenuated FT2a expression by its allele-specific transcriptional repression. SORE-1 was highly methylated, and did not appear to disrupt FT2a RNA processing.
  
  
  CONCLUSIONS
  The soybean maturity gene E9 is FT2a, and its recessive allele delays flowering because of lower transcript abundance that is caused by allele-specific transcriptional repression due to the insertion of SORE-1. The FT2a transcript abundance is thus directly associated with the variation in flowering time in soybean. The e9 allele may maintain vegetative growth in early-flowering genetic backgrounds, and also be useful as a long-juvenile allele, which causes late flowering under short-daylength conditions, in low-latitude regions.
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan. zhaochen_1112@126.com.
authors.forename: Chen
authors.initials: C
authors.lastname: Zhao
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan. take-ryo@res.agr.hokudai.ac.jp.
authors.forename: Ryoma
authors.initials: R
authors.lastname: Takeshima
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan. zhu622@res.agr.hokudai.ac.jp.
authors.forename: Jianghui
authors.initials: J
authors.lastname: Zhu
authors.affiliation: The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China. xumeilan_1984@yahoo.co.jp.
authors.forename: Meilan
authors.initials: M
authors.lastname: Xu
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan. satomasa@res.agr.hokudai.ac.jp.
authors.forename: Masako
authors.initials: M
authors.lastname: Sato
authors.affiliation: Faculty of Agriculture, Saga University, Saga, 840-0027, Japan. nabemame@cc.saga-u.ac.jp.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Watanabe
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan. kanazawa@res.agr.hokudai.ac.jp.
authors.forename: Akira
authors.initials: A
authors.lastname: Kanazawa
authors.affiliation: The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China. liubh@neigaehrb.ac.cn.
authors.forename: Baohui
authors.initials: B
authors.lastname: Liu
authors.affiliation: The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China. kongfj@iga.ac.cn.
authors.forename: Fanjiang
authors.initials: F
authors.lastname: Kong
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan. tetsuyay@res.agr.hokudai.ac.jp.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Yamada
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan. jabe@res.agr.hokudai.ac.jp.
authors.forename: Jun
authors.initials: J
authors.lastname: Abe
mesh_terms: D000483:Alleles; D035264:Flowers / Q000235:genetics* / Q000254:growth & development; D017343:Genes, Plant; D005808:Genes, Recessive; D013025:Glycine max / Q000235:genetics* / Q000254:growth & development