Genome-wide identification and expression profiling of YUCCA family genes responsive to exogenous hormones and abiotic stress in peanut

Abstract

The YUC family encodes rate-limiting enzymes for tryptophan-dependent auxin biosynthesis, yet its genomic organization and regulatory landscape in peanut—a major oilseed crop with complex polyploid genome—remain largely unexplored. Here, we address this gap by systematically identifying 89 YUC genes across diploid and tetraploid Arachis genomes and dissecting their evolutionary dynamics and expression plasticity. Phylogenetic reconstruction reveals five conserved clades, while synteny analysis demonstrates that segmental duplications, followed by strong purifying selection, drove the family expansion, implying functional constraints. Promoter cis-element profiling associates these genes with hormonal, stress, and light signals, suggesting their integration into multiple environmental cues. Leveraging transcriptome atlas across 34 tissues, we uncover spatiotemporally diversified expression, with specific members showing stress- and hormone-responsive patterns. Notably, qRT-PCR validation under PEG, NaCl, abscisic acid (ABA), gibberellin (GA₃), and 6-benzylaminopurine (6-BA) identifies AhYUC18 and AhYUC29 as two consistently responsive candidates across genotypes, pointing to their potential as nodal regulators in balancing growth and stress survival. Collectively, this study establishes a comprehensive evolutionary and regulatory framework for the peanut YUC family, and provides prioritized gene targets for functional dissection and breeding toward improved stress resilience without compromising yield.