Genome-wide identification of auxin response factors (ARFs) in three different species of Arachis

The phytohormone auxin is involved in the regulation of plant growth, nutrient acquisition, and response to environmental stimuli. Auxin response factors (ARFs) are transcription factors containing B3 DNA binding domain. ARFs play central role in auxin response, using Aux/IAA proteins as partners. Arachis is a genus within the Dalbergioid clade of papilionoid legumes, which out-branched from other members of papilionoids. Cultivated peanut (Arachis hypogaea L.) is an allotetraploid formed by hybridization of two parental genotypes Arachis duranensis, and Arachis ipaensis merely 10,000 years ago. We have made a genome-wide inventory of all the ARFs present in tetraploid A. hypogaea, as well as in two diploid parental genotypes. Our data show that Arachis contains more ARFs per diploid genome (around 31), compared to other legumes (around 25). We further observed few ARF-like genes which are defective in important domains. Most of the ARFs in tetraploid Arachis are redundant, representing the A and B sub-genomes. Some of the ARFs show expression bias from either A or B sub-genome, while some of the pairs are expressed from both sub-genomes. Many ARFs do not express in any of the conditions for which we have expression data. Finally, few pairs show differential spatio-temporal expression pattern from A and B sub-genomes, indicative of diversification of function. This is the first effort to list all the ARFs from an allotetraploid legume. The list of ARFs in all three species of Arachis will help the scientific community working to understand auxin regulation in crop legumes.