Integrated genomic and transcriptomic elucidation of flowering in garlic

Abstract Background Commercial cultivars of garlic produce neither flowers nor seeds, and therefore efficient breeding of this important vegetable and medicinal crop is impossible. New avenues for hybridization and seed production were recently opened by the restoration of garlic fertility. The huge genome of garlic was fully sequenced in 2020 but, before that, transcriptome catalogs had been employed as a basis for garlic genetic studies. Here, we provide the conjoint genomic and transcriptome analysis of the regulatory network in flowering garlic genotypes. Results Our genome-wide analysis revealed phosphatidylethanolamine-binding proteins (PEBP) and LEAFY (LFY) genes that were not previously observed at the transcriptome level. Functions of TFL-like genes were reduced and probably replaced by FT-like homologs, whereas homologs of MFT-like genes were not found in the garlic genome. The discovery of three sequences of LFY-like genes in the garlic genome and confirmation of their alternative splicing suggest their key role in garlic florogenesis. It is not yet clear whether only one gene—AsLFY1—acts alone as the "pioneer transcription factor" or AsLFY2 also provides these functions. Conclusions The garlic genome, including key flowering genes, is highly repetitive. The presence of several orthologs of flowering genes that differ in their temporal and spatial expression and co-expression network advocates ongoing evolution in the garlic genome and diversification of gene functions. We propose that the process of fertility deprivation in garlic cultivars is based on the loss of transcriptional functions of the specific genes. Further comparisons of the genome and transcriptome factors in flowering and non-flowering garlic genotypes will clarify the possible evolution of their reproductive traits and contribute to fertility restoration and efficient breeding of this important crop.