Integrated Genomic and Transcriptomic Elucidation of Flowering in Garlic

Abstract

Commercial cultivars of garlic are sterile, and therefore efficient breeding of this crop is impossible. Recent restoration of garlic fertility has opened new options for seed production and hybridization. Transcriptome catalogs were employed as a basis for garlic genetic studies, and in 2020 the huge genome of garlic was fully sequenced. We provide conjoint genomic and transcriptome analysis of the regulatory network in flowering garlic genotypes. The genome analysis revealed phosphatidylethanolamine-binding proteins (PEBP) and LEAFY (LFY) genes that were not found at the transcriptome level. Functions of TFL-like genes were reduced and replaced by FT-like homologs, whereas homologs of MFT-like genes were not found. The discovery of three sequences of LFY-like genes in the garlic genome and confirmation of their alternative splicing suggest their role in garlic florogenesis. It is not yet clear whether AsLFY1 acts alone as the “pioneer transcription factor” or AsLFY2 also provides these functions. The presence of several orthologs of flowering genes that differ in their 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.

Genome-Wide Characterization of PEBP Gene Family and Functional Analysis of TERMINAL FLOWER 1 Homologs in Macadamia integrifolia

“…Flowering is a key process which indicates the transition from vegetative to reproductive growth for plants, and genes of the PEBP family play important roles during this process and in the final plant architecture [ 3 ]. Up to now, the genes of the PEBP family have been identified in many plant species, such as quinoa, perilla, sugarcane, rice, garlic, etc., and the number of PEBP genes varies among these species [ 41 , 42 , 43 , 44 , 45 ]. A total of 13 PEBP family members were identified in M. integrifolia , and they were classified into three subfamilies: MFT-like , FT-like and TFL1-like .…”

Deprivation of Sexual Reproduction during Garlic Domestication and Crop Evolution

“…Low temperatures stimulate cascades of developmental mechanisms in several genetic pathways. The transcripts annotated as vernalization genes play a central role in the flowering pathway's interplay [13,35]. Our genome and transcriptome analyses indicate that several variants of VERNALIZATION INSENSITIVE 3 (VIN3), a key gene in temperature perception and plant response to cold [36], are located in garlic chromosomes 3, 4 and 6.…”

“…Further morpho-physiological studies showed that in some garlic genotypes, flower initiation and bolting (elongation of flower scape) are completely impaired, while others develop small topsets (bulblets) within the inflorescence which compete with flowers for nutrients. Moreover, even if individual flowers succeed in differentiating, seed production might be compromised by male or female sterility, tapetum degeneration, and pollen abortion [11][12][13].…”

“…The recent publication of the full genome sequence [16] of garlic enabled in-depth research on garlic biology [13,19]. Here, we provide phenotypic, genomic, and transcriptomic analyses of several genetic groups of garlic.…”

Comparative Genomics and Functional Genomics Analysis in Plants

“…They further hypothesized that a unique sex determination system exists in these species that differs from Populus and other Salix species. Shemesh-Mayer et al (2022) [ 14 ] presented conjoint genomic and transcriptome analyses of the regulatory network in flowering garlic genotypes and proposed that the process of fertility deprivation in garlic cultivars is based on the loss of the transcriptional functions of the specific genes. Rice and wheat are two of the most important food crops in the world.…”