TaARF4 genes are linked to root growth and plant height in wheat

Background and Aims Auxin response factors (ARFs) as transcription activators or repressors have important roles in plant growth and development, but knowledge about the functions of wheat ARF members is limited. A novel ARF member in wheat (Triticum aestivum), TaARF4, was identified, and its protein function, haplotype geographic distribution and allelic frequencies were investigated. Methods Tissue expression of TaARF4 was analysed by real-time PCR. Sub-cellular localization was performed using green fluorescent protein (GFP)-tagged TaARF4. Ectopic expression of TaARF4-A in arabidopsis was used to study its functions. Electrophoretic mobility shift assays (EMSAs), chromatin immunoprecipitation (ChIP) analyses and gene expression were performed to detect TaARF4 target genes. A dCAPS (derived cleaved amplified polymorphic sequence) marker developed from TaARF4-B was used to identify haplotypes and association analysis between haplotypes and agronomic traits. Key Results TaARF4-A was constitutively expressed and its protein was localized in the nucleus. Ectopic expression of TaARF4-A in arabidopsis caused abscisic acid (ABA) insensitivity, shorter primary root length and reduced plant height (PH). Through expression studies and ChIP assays, TaARF4-A was shown to regulate HB33 expression which negatively responded to ABA, and reduced root length and plant height by repressing expression of Gretchen Hagen 3 (GH3) genes that in turn upregulated indole-3-acetic acid content in arabidopsis. Association analysis showed that TaARF4-B was strongly associated with PH and root depth at the tillering, jointing and grain fill stages. Geographic distribution and allelic frequencies suggested that TaARF4-B haplotypes were selected in Chinese wheat breeding programmes. An amino acid change (threonine to alanine) at position 158 might be the cause of phenotype variation in accessions possessing different haplotypes. Conclusions Ectopic expression and association analysis indicate that TaARF4 may be involved in root length and plant height determination in wheat. This work is helpful for selection of wheat genotypes with optimal root and plant architecture.