Genetic Interaction of SEEDSTICK, GORDITA and AUXIN RESPONSE FACTOR 2 during Seed Development

Seed development is under the control of complex and coordinated molecular networks required for the formation of its different components. The seed coat development largely determines final seed size and shape, in addition to playing a crucial role in protecting the embryo and promoting germination. In this study, we investigated the role of three transcription factors known to be active during seed development in Arabidopsis thaliana: SEEDSTICK (STK) and GORDITA (GOA), two MADS-domain proteins, and AUXIN RESPONSE FACTOR 2 (ARF2), belonging to the ARF family. Through a reverse genetic approach, we characterized the seed phenotypes of all the single, double and triple loss-of-function mutants in relation to seed size/shape and the effects on metabolic pathways occurring in the seed coat. This approach revealed that dynamic networks involving these TFs are active throughout ovule and seed development, affecting the formation of the seed coat. Notably, while the genetic interaction among these genes results in synergies that control the promotion of cell expansion in the seed coat upon pollination and production of proanthocyanidins, functional antagonists arise in the control of cell proliferation and release of mucilage.

The F-box protein AFF1 regulates ARF protein accumulation to regulate auxin response

Auxin critically regulates nearly every aspect of plant growth and development. Auxin-driven transcriptional responses are mediated through the AUXIN RESPONSE FACTOR (ARF) family of transcription factors. Although ARF protein stability is regulated via the 26S proteasome, molecular mechanisms underlying ARF stability and turnover are unknown. Here, we report the identification and functional characterization of an F-box E3 ubiquitin ligase, which we have named AUXIN RESPONSE FACTOR F-BOX1 (AFF1). AFF1 directly interacts with ARF19 and regulates its accumulation. Mutants defective in AFF1 display ARF19 protein hyperaccumulation, attenuated auxin responsiveness, and developmental defects. Together, our data suggest a new mechanism, namely control of ARF protein stability, in regulating auxin response.

Characterization of cotton ARF factors and the role of GhARF2b in fiber development

BackgroundCotton fiber is a model system for studying plant cell development. At present, the functions of many transcription factors in cotton fiber development have been elucidated, however, the roles of auxin response factor (ARF) genes in cotton fiber development need be further explored.ResultsHere, we identify auxin response factor (ARF) genes in three cotton species: the tetraploid upland cottonG. hirsutum, which has 73 ARF genes, and its putative extent parental diploidsG. arboreumandG. raimondii, which have 36 and 35 ARFs, respectively. Ka and Ks analyses revealed that inG. hirsutum ARFgenes have undergone asymmetric evolution in the two subgenomes. The cotton ARFs can be classified into four phylogenetic clades and are actively expressed in young tissues. We demonstrate thatGhARF2b, a homolog of the ArabidopsisAtARF2, was preferentially expressed in developing ovules and fibers. Overexpression ofGhARF2bby a fiber specific promoter inhibited fiber cell elongation but promoted initiation and, conversely, its downregulation by RNAi resulted in fewer but longer fiber. We show that GhARF2b directly interacts with GhHOX3 and represses the transcriptional activity of GhHOX3 on target genes.ConclusionOur results uncover an important role of the ARF factor in modulating cotton fiber development at the early stage.

Genome-Wide Identification Analysis of The Auxin Response Factor Gene Family (ARF) in Zizania Latifolia and its Role in Swelling Stem Formation After Ustilago Esculenta Infection

Background: Auxin signalling plays a crucial role in plant growth and development. Although the auxin response factor (ARF) gene family has been studied in some plant species, its structural features, molecular evolution, and expression profile in Zizania latifolia (Z. latifolia) are still not clear.Results: Our study identified 33 putative YSL genes from the whole Z. latifolia genome. Furthermore, a comprehensive overview of the ZlARFs was undertaken, including phylogenetic relationship, gene structures, conserved domains, synteny, Ka/Ks, motifs, and subcellular locations of the gene product. Synteny analyses and the calculation of Ka/Ks values suggested that all 57 orthologous/paralogous gene pairs between Z. latifolia and Z. latifolia, Z. latifolia and Oryza sativa have experienced strong purifying selection. The phylogenetic analysis of ARFs indicated that the ZlARFs can be divided into 6 classes and that most ZlARFs from Z. latifolia have closer relationships with Oryza sativa than with Arabidopsis. RNA-Seq data and qRT-PCR analyses showed that ZlARF genes were expressed in TDF treatment and U. esculenta infection, while some ZlARFs exhibited high expression levels only in U. esculenta infection. Meanwhile, the interaction networks and gene ontology (GO) term of the ZlARF genes were constructed and 23 ZlARF co-expressed genes were identified, most of which were down-regulated involve auxin-activated signalling pathway in after swelling stem formation. Transcriptome analysis results verified the relevant functions of ARF genes, and most ZlARF genes regulated physiological processes in response to differential cell expansion. Conclusion: Comprehensive bioinformation analysis of the auxin response factor gene family (ARF) in Z. latifolia and its association with swelling stem formation after U. esculenta infection. The bioinformatic and RNA-Seq analyses provided valuable information for further study on the regulation of the growth and development of swelling stem formation by ZlARFs in Z. latifolia.