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We determined the molecular basis of three soybean lines that vary in seed coat color at the  R  locus which is thought to encode a MYB transcription factor. RM55- r m   is homozygous for a mutable allele ( r m  ) that specifies black and brown striped seeds; RM30- R*  is a stable black revertant isoline derived from the mutable line; and RM38- r  has brown seed coats due to a recessive  r  allele shown to translate a truncated MYB protein. Using long range PCR, 454 sequencing of amplicons, and whole genome re-sequencing, we determined that the variegated RM55- r m   line had a 13 kb CACTA subfamily transposon insertion (designated  TgmR* ) at a position 110 bp from the beginning of Intron2 of the  R  locus, Glyma09g36983. Although the MYB encoded by  R  was expressed at only very low levels in older seed coats of the black revertant RM30- R*  line, it upregulated expression of anthocyanidin synthase genes ( ANS2, ANS3 ) to promote the synthesis of anthocyanins. Surprisingly, the RM30- R*  revertant also carried the 13 kb  TgmR*  insertion in Intron2. Using RNA-Seq, we showed that intron splicing was accurate, albeit at lower levels, despite the presence of the 13 kb  TgmR*  element. As determined by whole genome methylation sequencing, we demonstrate that the  TgmR*  sequence was relatively more methylated in RM30- R*  than in the mutable RM55- r m   progenitor line. The stabilized and more methylated RM30- R*  revertant line apparently lacks effective binding of a transposae to its subterminal repeats, thus allowing intron splicing to proceed resulting in sufficient MYB protein to stimulate anthocyanin production and thus black seed coats. In this regard, the  TgmR*  element in soybean resembles McClintock's  Spm- suppressible and change-of-state alleles of maize. This comparison explains the opposite effects of the  TgmR*  element on intron splicing of the MYB gene in which it resides depending on the methylation state of the element.

plos one

Methylation Affects Transposition and Splicing of a Large CACTA Transposon from a MYB Transcription Factor Regulating Anthocyanin Synthase Genes in Soybean Seed Coats