Identification and Expression Profiles of Auxin-Related Gene Families Involved in Fiber Development in Jute (Corchorus capsularis)

The ARF (Auxin response factor), GH3 (Gretchen Hagen 3), and Aux/IAA (Auxin/indole-3-acetic acid) gene families are key components in auxin signaling pathway and function as regulators of growth in plants. However, this research is rarely reported in jute, which severely limits the understandings of mechanisms involved in fiber development. In this study, 13 ARF, 12 GH3 and 20 Aux/IAA putative genes were identified in the whole genome of jute. Exon-intron structures revealed the high conservation among these auxin-related gene family members. Chromosomal localization and synteny analysis showed that segmental duplication contributed to the expansion of CcARF, CcGH3 and CcIAA gene families. Phylogenetic and conserved motif analysis revealed that they have distinct functional and CcARF, CcGH3 and CcIAA-specific domains, respectively. The expression pattern analysis based on RNA-seq and qRT-PCR indicated that 7 CcARF, 5 CcGH3, and 14 CcIAA genes showed higher expression in stem barks than leaves at the vigorous vegetative growth stage in an elite cultivar Huangma 179 with normal plant height, respectively, suggesting they might regulate the development of bast fiber. Moreover, the expression of 5 CcARF, 4 CcGH3, and 12 CcIAA genes was differentially expressed in stem barks of a typical GA3 sensitive dwarf germplasm in comparison to Huangma 179. The cis-element analysis showed that promoters of 4 CcARF, 3 CcGH3, and 7 CcIAA genes had 1 to 3 cis-elements involved in gibberellin-responsiveness, giving a hint that they could respond to endogenous gibberellin accumulation in Huangma 179 and form a complicated network to regulate hormone regulatory network and plant height. This study provides useful information for functional analysis of ARF, GH3, and Aux/IAA genes, which would be taken as candidates for genetic improvement of bast fiber quality in jute.