From Embryo to Adult: Low Temperatures Affect Phase Transitions of Allium sativum L. from Germination to Flowering

Michael, Tomer E. Ben; Rozenblat, Liraz; Faigenboim, Adi; Shemesh-Mayer, Einat; Forer, Itzhak; Peters, Rachel M.; Klein, Joshua D.; Rabinowitch, Haim D.; Kamenetsky-Goldstein, Rina

doi:10.3390/agronomy10111651

Cited by 3 publications

(3 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Flowering and seed-setting genotype #87 was selected in 2004 from a segregating seedling population and then clonally propagated at the Agricultural Research Organization (ARO), Volcani Center, Israel. For transcriptome sequencing, tissue was sampled from vegetative and reproductive organs at different stages of plant development and after cold-storage treatments (Additional le 4: Table S2), [11,12,19,51].…”

Section: Plant Materials and Transcriptome Datamentioning

confidence: 99%

“…The gray boxes represent the reads for expression of the transcriptome sequence of the individual owers [51] upstream and downstream of the genomic sequence of AsLFY2. C Transcriptome analysis of AsLFYs in vegetative and reproductive tissues and seeds of garlic [11,12,19,51]. The expression values were computed as FPKM, and used to create a heat map by one minus Pearson correlation, using MORPHEUS (https://software.broadinstitute.org/morpheus).…”

Section: Phylogenetic Analysis and Multiple Sequence Alignmentmentioning

confidence: 99%

“…Similar to many other plant species, garlic development is signi cantly affected by regulation of genes of the phosphatidylethanolamine-binding protein (PEBP) family [12,15,18,19]. This family is conserved from prokaryotes to eukaryotes and is classi ed into three main groups: Mother of FT and TFL1 (MFT)like, FLOWERING LOCUS T (FT)-like, and TERMINAL FLOWER1/ CENTRORADIALIS (TFL1/CEN)-like genes [20].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Integrated genomic and transcriptomic elucidation of flowering in garlic

Shemesh-Mayer

Faigenboim

Ben-Michael

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Plant Materials and Transcriptome Datamentioning

confidence: 99%

Section: Phylogenetic Analysis and Multiple Sequence Alignmentmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Integrated genomic and transcriptomic elucidation of flowering in garlic

Shemesh-Mayer

Faigenboim

Ben-Michael

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Genome resequencing reveals the evolutionary history of garlic reproduction traits

Wang,

Shemesh-Mayer,

Zhang

et al. 2023

Horticulture Research

View full text Add to dashboard Cite

The propagation of cultivated garlic relies on vegetative cloves, thus flowers become non-essential for reproduction in this species, driving the evolution of reproductive-feature derived traits. To obtain insights into the evolutionary alteration of reproductive traits in the clonally propagated garlic, the evolutionary histories of two main reproduction-related traits, garlic bolting and flower differentiation, were explored by genome analyses using 134 accessions displaying wide diversity in these two traits. Resequencing identified 272.8 million variations in the garlic genome, 198.0 million of which represent novel variants. Population analysis identified five garlic groups that have evolved into two clades. Gene expression, single-cell RNA sequencing, and genome-wide trait association analyses have identified numerous candidates that correlate with reproductive transition and flower development, some of which display distinct selection signatures. Selective forces acting on the B-box zinc finger protein-encoding Asa2G00291.1, the global transcription factor group E protein-encoding Asa5G01527.1, and VERNALIZATION INSENSITIVE 3-like Asa3G03399.1 appear to be representative of the evolution of garlic bolting. Plenty of novel genomic variations and trait-related candidates represent valuable resources for biological studies of garlic. Numerous selective signatures from genes associated with the two chosen reproductive traits provide important insights into the evolutionary history of reproduction in this clonally propagated crop.

show abstract

Integrated Genomic and Transcriptomic Elucidation of Flowering in Garlic

Shemesh-Mayer

Faigenboim

Michael

et al. 2022

IJMS

View full text Add to dashboard Cite

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.

show abstract

From Embryo to Adult: Low Temperatures Affect Phase Transitions of Allium sativum L. from Germination to Flowering

Cited by 3 publications

References 57 publications

Integrated genomic and transcriptomic elucidation of flowering in garlic

Integrated genomic and transcriptomic elucidation of flowering in garlic

Genome resequencing reveals the evolutionary history of garlic reproduction traits

Integrated Genomic and Transcriptomic Elucidation of Flowering in Garlic

Contact Info

Product

Resources

About