Genome-wide identification of peanut PIF family genes and their potential roles in early pod development.

Peanut is typically a geocarpic plant. The developing gynophore ('peg') in air could not swell normally until it buries into soil, indicating light-to-dark conversion is necessary for early pod development in peanut. As the subfamily of basic helix-loop-helix (bHLH) transcription factors, phytochrome interacting factors (PIFs) are key regulators involved in light signaling pathways, and play crucial roles in plant growth and development. In the current study, a total of 14 AhPIFs were identified in cultivated peanut genome (Arachis hypogaea L., AABB), while seven AdPIFs and six AiPIFs were discovered in the two wild diploids (A. duranensis (AA), A. ipaensis (BB)) respectively. Phylogenetic analysis revealed that peanut PIFs were clustered into four distinct clades, and members within the same subgroup had conserved motifs and displayed similar exon-intron distribution patterns. Gene synteny analysis indicated most of the PIFs exhibit one-to-one homology relationship between AA and BB subgenome in A. hypogaea, as well as among the three peanut species. Gene duplication detection showed that segmental duplication and purifying selection contributed to the expansion and evolution of peanut PIF gene family. Transcript profiles combined with subcellular localization analysis suggested AhPIF3A4 and AhPIF3B4 may possibly be involved in regulation of peanut early pod development. This study could further facilitate functional characterization of PIFs in peanut and other legumes.