Pangenome-wide insights into eukaryotic translation initiation factors (eIF) genes uncover targets for sterility mosaic disease resistance engineering in pigeonpea.

Sterility mosaic disease (SMD) poses a significant threat to pigeonpea production. Although resistant cultivars are widely used, the rapid evolution of viral pathogens often renders host resistance ineffective. Targeting host susceptibility factors-particularly eukaryotic translation initiation factors (eIFs) that many plant viruses exploit for replication-offers a promising alternative. Although eIF proteins are well characterized in several model crops, their roles in pigeonpea remain largely unexplored. In this study, we conducted a comprehensive analysis of the eIF gene family in pigeonpea, supported by a pangenome-wide survey to capture cultivar-specific diversity relevant to SMD response. A total of 52 eIF genes were identified in the reference genome, while 47 homologs were consistently present across the pangenome, representing core gene members. The pangenome analysis also revealed limited sequence-level variation, highlighting strong evolutionary conservation of eIF genes in pigeonpea. Gene copy number, chromosomal distribution, and promoter cis-regulatory elements were characterized through detailed in silico analyses. Expression profiling under PPSMV infection revealed contrasting transcriptional responses: several eIF genes were upregulated in resistant plants, whereas eIF3K, eIF4G, and eIF5A showed higher expression in susceptible genotypes. Variant analysis of the susceptible genotype ICP8863 uncovered 94 polymorphisms across the 52 eIF genes, with seven predicted to have high or moderate functional impact. A stop-gained mutation in eIF3E (Cc_02836) and a frameshift indel in eIF4B (Cc_22348) are predicted to result in truncated, nonfunctional proteins. Additionally, missense mutations in eIF3E (Cc_02836), eIF5B (Cc_04638), eIF2Bδ (Cc_06116), eIF2Bα (Cc_18788), and eIF4B (Cc_22348) may influence protein structure or interaction capacity, potentially compromising antiviral defense. Overall, this study identifies key eIF family members potentially contributing to SMD susceptibility and provides candidate genes for experimental validation to engineer PPSMV resistance in pigeonpea varieties.