Background: The AP2/ERF transcription factor, one of the largest gene families in plants, plays a crucial role in the regulation of growth and development, metabolism, and responses to biotic and abiotic stresses. Castor bean (Ricinus communisL., Euphobiaceae) is one of most important non-edible oilseed crops and its seed oil is broadly used for industrial applications. The available genome provides a great chance to identify and characterize the global information on AP2/ERF transcription factors in castor bean, which might provide insights in understanding the molecular basis of the AP2/ERF family in castor bean.Results: A total of 114 AP2/ERF transcription factors were identified based on the genome in castor bean. According to the number of the AP2/ERF domain, the conserved amino acid residues within AP2/ERF domain, the conserved motifs and gene organization in structure, and phylogenetical analysis, the identified 114 AP2/ERF transcription factors were characterized. Global expression profiles among different tissues using high-throughput sequencing of digital gene expression profiles (DGEs) displayed diverse expression patterns that may provide basic information in understanding the function of the AP2/ERF gene family in castor bean.Conclusions: The current study is the first report on identification and characterization of the AP2/ERF transcription factors based on the genome of castor bean in the family Euphobiaceae. Results obtained from this study provide valuable information in understanding the molecular basis of the AP2/ERF family in castor bean.

Seedlings of large-seeded plants are considered to be able to withstand abiotic stresses efficiently. The molecular mechanisms that underlie the involved signaling crosstalk between the large-seeded trait and abiotic tolerance are, however, largely unknown. Here, we demonstrate the molecular link that integrates plant abscisic acid (ABA) responses to drought stress into the regulation of seed mass. Both loss-of-function mutants of the Auxin Response Factor 2 (ARF2 encoding a transcription factor) and lines overexpressing AINTEGUMENTA (ANT; a transcription factor) under the 35S promoter exhibited large seed and drought-tolerant phenotypes as a result of abnormal ABA–auxin crosstalk signaling pathways in Arabidopsis. The target gene COLD-REGULATED15A (COR15a) was identified as participating in the regulation of seed development with ABA signaling through a negative regulation mechanism that is mediated by ANT. The molecular and genetic evidence presented indicate that ARF2, ANT and COR15A form an ABA-mediated signaling pathway to link modulation of seed mass with drought tolerance. These observations indicate that the ARF2 transcription factor serves as a molecular link that integrates plant ABA responses to drought stress into the regulation of seed mass.

Plant-specific GRAS transcription factors play important roles in regulating growth, development, and stress responses. Castor beans (Ricinus communis) are important non-edible oilseed plants, cultivated worldwide for its seed oils and its adaptability to growth conditions. In this study, we identified and characterized a total of 48 GRAS genes based on the castor bean genome. Combined with phylogenetic analysis, the castor bean GRAS members were divided into 13 distinct groups. Functional divergence analysis revealed the presence of mostly Type-I functional divergence. The gene structures and conserved motifs, both within and outside the GRAS domain, were characterized. Gene expression analysis, performed in various tissues and under a range of abiotic stress conditions, uncovered the potential functions of GRAS members in regulating plant growth development and stress responses. The results obtained from this study provide valuable information toward understanding the potential molecular mechanisms of GRAS proteins in castor beans. These findings also serve as a resource for identifying the genes that allow castor beans to grow in stressful conditions and to enable further breeding and genetic improvements in agriculture.

Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, the triploid endosperm is where gene imprinting occurs most often, but aside from studies on Arabidopsis, little is known about gene imprinting in dicotyledons. In this study, we inspected genomic imprinting in castor bean (Ricinus communis) endosperm, which persists throughout seed development. After mapping out the polymorphic SNP loci between accessions ZB306 and ZB107, we generated deep sequencing RNA profiles of F1 hybrid seeds derived from reciprocal crosses. Using polymorphic SNP sites to quantify allele-specific expression levels, we identified 209 genes in reciprocal endosperms with potential parent-of-origin specific expression, including 200 maternally expressed genes and 9 paternally expressed genes. In total, 57 of the imprinted genes were validated via reverse transcriptase-polymerase chain reaction sequencing, and analysis of the genomic DNA methylation distribution between embryo and endosperm tissues showed significant hypomethylation in the endosperm and an enrichment of differentially methylated regions around the identified genes. Curiously, the expression of the imprinted genes was not tightly linked to DNA methylation. These results largely extended gene imprinting information existing in plants, providing potential directions for further research in gene imprinting.

DNA binding with one finger (Dof) transcription factors are unique in plants, characteristically composed of a Dof domain in structure, functionally involved in mediating many processes of plant growth and development. In this study, we report a genome-wide analysis for Dof gene family in castor bean (Ricinus communis L., Euphorbiaceae) genome. In total, 21 RcDof genes were identified and their constructional characterization, classes and phylogenetic relationships were documented. The expression profiles of the 21 RcDof genes among different tissues were inspected using the high throughput RNA-Seq data. Finally, SqRT-PCR analysis was performed to test the transcriptional responses of the 21 RcDof genes to abscisic acid (ABA) and/or gibberellic acid (GA) signals, resulting in the identification of 18 RcDof genes responsive to ABA and/or GA signals. Thus, this study would provide basic information in understanding the molecular basis of the RcDof family and their potential function in regulating the growth and development of castor bean.