Analyses of gene families, allelic variation and VIGS reveal that GheIF3M.2 is significantly associated with dwarfism in upland cotton

Abstract Eukaryotic translation initiation factor 3 (eIF3), the largest eukaryotic initiation factor, regulates mRNA translation initiation. While eIF3 has been extensively studied in various plant species, research on eIF3 in upland cotton remains limited. Sixty-one GheIF3s were identified using a bioinformatics approach, and comprehensive characteristic analysis was conducted in upland cotton. The results revealed that the different subunits of the GheIF3s were strongly conserved in both structural and evolutionary relationships. RNA-seq and qRT‒PCR results revealed that the expression levels of GheIF3L.1 and GheIF3M.2 in early-maturing varieties were significantly greater than those in late-maturing varieties. Furthermore, no single-nucleotide polymorphisms (SNPs) were detected in GheIF3L.1, and a SNP (A05:105181831, T/G) significantly related to the flowering period within the coding sequence of GheIF3M.2 was identified. The flowering time of the varieties carrying the GG allele was significantly earlier than that of the varieties carrying the TT allele, which was verified in both early − flowering and late-flowering varieties via Sanger sequencing. Genetic diversity analysis revealed that the gene region differed between early − and late − maturing varieties, suggesting that artificial selection might have occurred. Virus-induced gene silencing (VIGS) results indicated that the silenced plants (TRV:GheIF3M.2) presented a significant decrease in plant height; inhibited flower bud differentiation; and significantly decreased IAA, GA₃, and BR contents. These analyses elucidated the functions of GheIF3s in upland cotton and provided genetic resources related to plant morphology and early maturity.