In silico analysis of the regulatory gene families for proanthocyanidins biosynthesis in the genus Gossypium L.

Abstract

The flavonoid pigments provide cotton cultivars with various shades of the naturally colored fiber. Despite of the deep knowledge about the flavonoids biosynthesis pathway in cotton, the genetic features underlying its control are not fully understood. Particularly, data on regulatory genes for the proanthocyanidins (PAs) branch are incomplete for the genus Gossypium L. Here we report results of comprehensive in silico analysis of the R2R3-Myb, bHLH-Myc and WD40 regulatory gene families, involved in the biosynthesis of flavonoid pigment PAs in cotton. For the first time, we identified regulatory genes R2R3-Myb, bHLH-Myc and WD40, including paralogous and homoeologous copies, among all sequenced diploid and allotetraploid cotton species: G. hirsutum L., G. barbadence L., G. raimondii L. and G. arboreum L. All duplication events occurred in the genome of the common diploid ancestor of the genus Gossypium and were supported by a negative evolution (Ka/Ks < 1). However, the GhTTG1/GhTTG3 genes are proved to be the most conservative and predominantly supported by selection, while GhTT2/GhMYB10 and GhTT8 are more variable and suitable for further analysis. The thorough study has suggested that all genes, with the exception of GhTT8-A2, possibly involved in the PAs biosynthesis. Therefore, information about structural organization and functionality of the all MBW genes in cotton genome is represented here. Revealing of the allelic diversities among identified genes, associating with contrast phenotype, may be useful for marker-assisted selection or genome editing for creation of naturally colored cotton cultivars with agriculturally valuable traits.