The ARF, GH3, and Aux/IAA gene families in castor bean (Ricinus communis L.): Genome-wide identification and expression profiles in high-stalk and dwarf strains

The auxin-related gene family adjusts auxin balance and the hormone signaling pathways in plants. The ARF (Auxin response factor), GH3 (Gretchen Hagen 3), and Aux/IAA (Auxin/indole-3-acetic acid) gene families, three key components of the auxin signaling pathway, are ubiquitous in plants and function as regulators of plant growth and response to stress. Although members of ARF, GH3, and Aux/IAA gene families have been identified in several plant species, they have not been identified in castor bean (Ricinus communis L.), a non-edible oil crop. In this study, bioinformatics methods were used and 18 ARF, seven GH3 and 19 Aux/IAA putative genes were identified in castor bean. Detailed sequence characterizations, multiple sequence alignment, and exon-intron structures revealed that the three auxin-related family members have high conservation. Phylogenetic trees constructed with 67 ARF, 38 GH3, and 78 Aux/IAA genes from castor bean, Arabidopsis thaliana, and rice (Oryza sativa L.) indicated that members within same group showed structural conservation, although some divergence occurred in different groups. Cis-regulatory element analysis of promoter regions showed that the ARF, GH3, and Aux/IAA genes have diverse functions in growth and development. Expression pattern analysis based on RNA-seq and qRT-PCR showed that one RcARF, three RcGH3, and four RcIAA genes were differentially expressed between high-stalk and dwarf castor, suggesting functions in castor growth. The present study provides useful information for functional analysis of ARF, GH3, and Aux/IAA genes and suggest that members of these gene families would be candidate for castor molecular breeding.