EgLFY, the Eucalyptus grandis homolog of the Arabidopsis gene LEAFY is expressed in reproductive and vegetative tissues

Genetic containment in vegetatively propagated forest trees: CRISPR disruption of LEAFY function in Eucalyptus gives sterile indeterminate inflorescences and normal juvenile development

Eucalyptus is among the most widely planted taxa of forest trees worldwide. However, its spread as an exotic or genetically engineered form can create ecological and social problems. To mitigate gene flow via pollen and seeds, we mutated the Eucalyptus orthologue of LEAFY (LFY) by transforming a Eucalyptus grandis × urophylla wild-type hybrid and two Flowering Locus T (FT) overexpressing (and flowering) lines with CRISPR Cas9 targeting its LFY orthologue, ELFY. We achieved high rates of elfy biallelic knockouts, often approaching 100% of transgene insertion events. Frameshift mutations and deletions removing conserved amino acids caused strong floral alterations, including indeterminacy in floral development and an absence of male and female gametes. These mutants were otherwise visibly normal and did not differ statistically from transgenic controls in juvenile vegetative growth rate or leaf morphology in greenhouse trials. Genes upstream or near to ELFY in the floral development pathway were overexpressed, whereas floral organ identity genes downstream of ELFY were severely depressed. We conclude that disruption of ELFY function appears to be a useful tool for sexual containment, without causing statistically significant or large adverse effects on juvenile vegetative growth or leaf morphology.

Functional analysis of a homologue of the FLORICAULA/LEAFY gene in litchi (Litchi chinensis Sonn.) revealing its significance in early flowering process

Litchi (Litchi chinensis Sonn.) is an important subtropical fruit crop with high commercial value due to its high nutritional values and favorable tastes. However, irregular bearing attributed to unstable flowering is a major ongoing problem for litchi producers. Previous studies indicate that low-temperature is a key factor in litchi floral induction. In order to reveal the genetic and molecular mechanisms underlying the reproductive process in litchi, we had analyzed the transcriptome of buds before and after low-temperature induction using RNA-seq technology. A key flower bud differentiation associated gene, a homologue of FLORICAULA/LEAFY, was identified and named LcLFY (GenBank Accession No. KF008435). The cDNA sequence of LcLFY encodes a putative protein of 388 amino acids. To gain insight into the role of LcLFY, the temporal expression level of this gene was measured by real-time RT-PCR. LcLFY was highly expressed in flower buds and its expression correlated with the floral developmental stage. Heterologous expression of LcLFY in transgenic tobacco plants induced precocious flowering. Meantime, we investigated the sub-cellular localization of LcLFY. The LcLFY-Green fluorescent protein (GFP) fusion protein was found in the nucleus. The results suggest that LcLFY plays a pivotal role as a transcription factor in controlling the transition to flowering and in the development of floral organs in litchi.

Genome-Wide Identification of the MIKC-Type MADS-Box Gene Family in Gossypium hirsutum L. Unravels Their Roles in Flowering

Cotton is one of the major world oil crops. Cottonseed oil meets the increasing demand of fried food, ruminant feed, and renewable bio-fuels. MADS intervening keratin-like and C-terminal (MIKC)-type MADS-box genes encode transcription factors that have crucial roles in various plant developmental processes. Nevertheless, this gene family has not been characterized, nor its functions investigated, in cotton. Here, we performed a comprehensive analysis of MIKC-type MADS genes in the tetraploid Gossypium hirsutum L., which is the most widely cultivated cotton species. In total, 110 GhMIKC genes were identified and phylogenetically classified into 13 subfamilies. The Flowering locus C (FLC) subfamily was absent in the Gossypium hirsutum L. genome but is found in Arabidopsis and Vitis vinifera L. Among the genes, 108 were distributed across the 13 A and 12 of the D genome's chromosomes, while two were located in scaffolds. GhMIKCs within subfamilies displayed similar exon/intron characteristics and conserved motif compositions. According to RNA-sequencing, most MIKC genes exhibited high flowering-associated expression profiles. A quantitative real-time PCR analysis revealed that some crucial MIKC genes determined the identities of the five flower organs. Furthermore, the overexpression of GhAGL17.9 in Arabidopsis caused an early flowering phenotype. Meanwhile, the expression levels of the flowering-related genes CONSTANS (CO), LEAFY (LFY) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) were significantly increased in these lines. These results provide useful information for future studies of GhMIKCs' regulation of cotton flowering.

Cloning and functional identification of the AcLFY gene in Allium cepa

Onion (Allium cepa L.) is one of the important vegetable crops in the world, usually with a two-year life cycle. The bulbs form in the first year after sowing, then bolting and flowering are induced by low temperature in the following year. Previous studies have shown that LEAFY gene is an inflorescence tissue specific gene, and that it is also the ultimate collection channel of all flowering pathway. In this study, using homologous gene cloning and reverse transcription-PCR (RT-PCR), we isolated an inflorescence meristem specific LEAFY cDNA, AcLFY (JX275962), from onion. AcLFY contains a 1119 bp open reading frame, which encodes a putative protein of 372 amino acids, with ∼70% homology to the daffodils LEAFY and >50% homology to LEAFY proteins from other higher plants. Fluorescence quantitative results showed that AcLFY gene has the highest expression level in inflorescence meristem during early bolting, and is still expressed in leaves after the formation of flower organs. Overexpression of AcLFY gene in Arabidopsis thaliana induced early bolting and flowering, whereas knockdown of the endogenous LEAFY gene by RNAi caused a significant delay in bolting. In addition, transgenic plants also exhibited significant morphological changes in rosette leaves, branches, and plant height.

Functional Characterization of PhapLEAFY, a FLORICAULA/LEAFY Ortholog in Phalaenopsis aphrodite

The plant-specific transcription factor LEAFY (LFY) is considered to be a master regulator of flower development in the model plant, Arabidopsis. This protein plays a dual role in plant growth, integrating signals from the floral inductive pathways and acting as a floral meristem identity gene by activating genes for floral organ development. Although LFY occupies an important position in flower development, the functional divergence of LFY homologs has been demonstrated in several plants including monocots and gymnosperms. In particular, the functional roles of LFY genes from orchid species such as Phalaenopsis that contain unique floral morphologies with distinct expression patterns of floral organ identity genes remain elusive. Here, PhapLFY, an ortholog of Arabidopsis LFY from Phalaenopsis aphrodite subsp. formosana, a Taiwanese native monopodial orchid, was isolated and characterized through analyses of expression and protein activity. PhapLFY transcripts accumulated in the floral primordia of developing inflorescences, and the PhapLFY protein had transcriptional autoactivation activity forming as a homodimer. Furthermore, PhapLFY rescues the aberrant floral phenotypes of Arabidopsis lfy mutants. Overexpression of PhapLFY alone or together with PhapFT1, a P. aphrodite subsp. formosana homolog of Arabidopsis FLOWERING LOCUS T (FT) in rice, caused precocious heading. Consistently, a higher Chl content in the sepals and morphological changes in epidermal cells were observed in the floral organs of PhapLFY knock-down orchids generated by virus-induced gene silencing. Taken together, these results suggest that PhapLFY is functionally distinct from RICE FLORICAULA/LEAFY (RFL) but similar to Arabidopsis LFY based on phenotypes of our transgenic Arabidopsis and rice plants.

The floral transcriptome of Eucalyptus grandis

As a step toward functional annotation of genes required for floral initiation and development within the Eucalyptus genome, we used short read sequencing to analyze transcriptomes of floral buds from early and late developmental stages, and compared these with transcriptomes of diverse vegetative tissues, including leaves, roots, and stems. A subset of 4807 genes (13% of protein-coding genes) were differentially expressed between floral buds of either stage and vegetative tissues. A similar proportion of genes were differentially expressed among all tissues. A total of 479 genes were differentially expressed between early and late stages of floral development. Gene function enrichment identified 158 gene ontology classes that were overrepresented in floral tissues, including 'pollen development' and 'aromatic compound biosynthetic process'. At least 40 floral-dominant genes lacked functional annotations and thus may be novel floral transcripts. We analyzed several genes and gene families in depth, including 49 putative biomarkers of floral development, the MADS-box transcription factors, 'S-domain'-receptor-like kinases, and selected gene family members with phosphatidylethanolamine-binding protein domains. Expanded MADS-box gene subfamilies in Eucalyptus grandis included SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), SEPALLATA (SEP) and SHORT VEGETATIVE PHASE (SVP) Arabidopsis thaliana homologs. These data provide a rich resource for functional and evolutionary analysis of genes controlling eucalypt floral development, and new tools for breeding and biotechnology.

Characterization of the sequence and expression pattern of LFY homologues from dogwood species (Cornus) with divergent inflorescence architectures

BACKGROUND AND AIMS

LFY homologues encode transcription factors that regulate the transition from vegetative to reproductive growth in flowering plants and have been shown to control inflorescence patterning in model species. This study investigated the expression patterns of LFY homologues within the diverse inflorescence types (head-like, umbel-like and inflorescences with elongated internodes) in closely related lineages in the dogwood genus (Cornus s.l.). The study sought to determine whether LFY homologues in Cornus species are expressed during floral and inflorescence development and if the pattern of expression is consistent with a function in regulating floral development and inflorescence architectures in the genus.

METHODS

Total RNAs were extracted using the CTAB method and the first-strand cDNA was synthesized using the SuperScript III first-strand synthesis system kit (Invitrogen). Expression of CorLFY was investigated by RT-PCR and RNA in situ hybridization. Phylogenetic analyses were conducted using the maximum likelihood methods implemented in RAxML-HPC v7.2.8.

KEY RESULTS

cDNA clones of LFY homologues (designated CorLFY) were isolated from six Cornus species bearing different types of inflorescence. CorLFY cDNAs were predicted to encode proteins of approximately 375 amino acids. The detection of CorLFY expression patterns using in situ RNA hybridization demonstrated the expression of CorLFY within the inflorescence meristems, inflorescence branch meristems, floral meristems and developing floral organ primordia. PCR analyses for cDNA libraries derived from reverse transcription of total RNAs showed that CorLFY was also expressed during the late-stage development of flowers and inflorescences, as well as in bracts and developing leaves. Consistent differences in the CorLFY expression patterns were not detected among the distinct inflorescence types.

CONCLUSIONS

The results suggest a role for CorLFY genes during floral and inflorescence development in dogwoods. However, the failure to detect expression differences between the inflorescence types in the Cornus species analysed suggests that the evolutionary shift between major inflorescence types in the genus is not controlled by dramatic alterations in the levels of CorLFY gene transcript accumulation. However, due to spatial, temporal and quantitative limitations of the expression data, it cannot be ruled out that subtle differences in the level or location of CorLFY transcripts may underlie the different inflorescence architectures that are observed across these species. Alternatively, differences in CorLFY protein function or the expression or function of other regulators (e.g. TFL1 and UFO homologues) may support the divergent developmental trajectories.

Cloning and characterization of a FLO/LFY ortholog in Gossypium hirsutum L

KEY MESSAGE

GhLFY was cloned from G. hirsutum L. Its expression, subcellular localization, and function were analyzed, as well as the in vivo regulation of GhLFY by the MADS-box protein SOC1 (GhSOC1).

ABSTRACT

Flowering is a very important phase during which plants produce the organs for sexual reproduction. The FLORICAULA/LEAFY (FLO/LFY) homologs play a major role in the initiation of flowering. To understand the mechanism of the transition from the vegetative to reproductive phases in Upland cotton (Gossypium hirsutum L.), we isolated a candidate LFY gene from G. hirsutum L. (GhLFY) that showed a high degree of similarity to other plant homologs of FLO/LFY. qPCR analysis showed that GhLFY was highly expressed in the shoot apex, with substantial upregulation at the third true leaf expansion stage during floral bud differentiation. Subcellular localization studies revealed GhLFY localization in the nucleus. Ectopic expression of the GhLFY coding region in Arabidopsis resulted in early flowering. The expression of the GhLFY coding region under the control of the 35S promoter complemented the lfy-5 mutation in transgenic Arabidopsis lfy-5 mutant plants. Furthermore, a chromatin immunoprecipitation assay revealed that GhLFY may function downstream of GhSOC1 during the initiation of flowering in G. hirsutum L. GhLFY was likely to be regulated by GhSOC1, which binds to the LFY promoter in Arabidopsis. These results suggest that GhLFY is a FLO/LFY ortholog that may be involved in controlling flowering time and floral development.

Isolation of a LEAFY homolog from Populus tomentosa: expression of PtLFY in P. tomentosa floral buds and PtLFY-IR-mediated gene silencing in tobacco (Nicotiana tabacum)

To understand the genetic and molecular mechanisms underlying floral development in Populus tomentosa, we isolated PtLFY, a LEAFY homolog, from a P. tomentosa floral bud cDNA library. DNA gel blot analysis showed that PtLFY is present as a single copy in the genomes of both male and female individuals of P. tomentosa. The genomic copy is composed of three exons and two introns. Relative expression levels of PtLFY in tissues of P. tomentosa were estimated by RT-PCR; our results revealed that PtLFY mRNA is highly abundant in roots and both male and female floral buds. A low level of gene expression was detected in stems and vegetative buds, and no PtLFY-specific transcripts were detected in leaves. PtLFY expression patterns were analyzed during the development of both male and female floral buds in P. tomentosa via real-time quantitative RT-PCR. Continuous, stable and high-level expression of PtLFY-specific mRNA was detected in both male and female floral buds from September 13th to February 25th, but the level of PtLFY transcripts detected in male floral buds was considerably higher than in female floral buds. Our results also showed an inverted repeat PtLFY fragment (PtLFY-IR) effectively blocked flowering of transgenic tobacco plants, and that this effect appeared to be due to post-transcriptional silencing of the endogenous tobacco LFY homologs NFL1 and NFL2.

Quantitative expression analysis of meristem identity genes in Eucalyptus occidentalis: AP1 is an expression marker for flowering

A number of Eucalyptus species exhibit precocious flowering, flowering within a year of germination and often while still exhibiting juvenile foliage. To understand the nature of precocious flowering in Eucalyptus occidentalis, partial homologues of the inflorescence meristem identity gene TERMINAL FLOWER1 and of the floral meristem identity genes LEAFY and APETALA1 (EOTFL1, EOLFY and EOAP1, respectively) were isolated and characterized. The expression patterns of these meristem identity genes during the development of branched and single-stem plants were analysed by quantitative reverse transcriptase PCR. All E. occidentalis plants commenced flowering within 40 weeks of germination. However, the branched plants reached maximum flowering some 5-6 weeks earlier than did single-stem plants. Levels of EOTFL1 and EOLFY expression varied little during the study period irrespective of architecture treatment, whereas expression of EOAP1 reached a peak coincident with peak flowering in both branched and single-stem plants. AP1 is clearly an expression marker for flowering in this species.

Identification of flowering-related genes between early flowering trifoliate orange mutant and wild-type trifoliate orange (Poncirus trifoliata L. Raf.) by suppression subtraction hybridization (SSH) and macroarray

To gain a better understanding of gene expression in early flowering trifoliate orange mutant (precocious trifoliate orange, Poncirus trifoliata L. Raf.), we performed suppression subtractive hybridization, which allowed identification of flowering-related genes in the mutant and the wild type in the juvenile phase. Using macroarray analysis, we identified 125 and 149 non-redundant expressed sequence tags (ESTs) in the forward-subtracted and the reverse-subtracted library. These cDNAs covered a broad repertoire of flowering development related genes, provided helpful information for understanding genetic mechanism underlying the signaling and regulation in transition from the vegetative to reproductive phase. We have investigated the temporal and spatial expression pattern of some SSH-enriched flowering-related genes in the mutant and the wild type. Of these genes, three genes (BARELY ANY MERITED, FLOWERING LOCUS T and TERMINAL FLOWER1) encoding proteins previously reported to be associated with, or involved in, developmental processes in other species were identified and further investigated by in situ hybridization. Specific spatial and/or temporal patterns were detected, and differences were observed between the mutant and the wild type during flower development. Meanwhile, the temporal expression of these genes was further examined by real-time PCR, the results showed that FT and BAM transcripts accumulated to higher levels and TFL1 transcripts accumulated to lower levels in mutant juvenile tissues relative to wild-type juvenile tissues. In the adult stage, FT, BAM and TFL1 expression patterns were closely correlated with flowering development, suggesting that these three genes may play a critical role in the early flowering process of precocious trifoliate orange.

The tropical cedar tree (Cedrela fissilis Vell., Meliaceae) homolog of the Arabidopsis LEAFY gene is expressed in reproductive tissues and can complement Arabidopsis leafy mutants

A homolog of FLORICAULA/LEAFY, CfLFY (for Cedrela fissilis LFY), was isolated from tropical cedar. The main stages of the reproductive development in C. fissilis were documented by scanning electron microscopy and the expression patterns of CfLFY were studied during the differentiation of the floral meristems. Furthermore, the biological role of the CfLFY gene was assessed using transgenic Arabidopsis plants. CfLFY showed a high degree of similarity to other plant homologs of FLO/LFY. Southern analysis showed that CfLFY is a single-copy gene in the tropical cedar genome. Northern blot analysis and in situ hybridization results showed that CfLFY was expressed in the reproductive buds during the transition from vegetative to reproductive growth, as well as in floral meristems and floral organs but was excluded from the vegetative apex and leaves. Transgenic Arabidopsis lfy26 mutant lines expressing the CfLFY coding region, under the control of the LFY promoter, showed restored wild-type phenotype. Taken together, our results suggest that CfLFY is a FLO/LFY homolog probably involved in the control of tropical cedar reproductive development.

The rubber tree (Hevea brasiliensis Muell. Arg.) homologue of the LEAFY/FLORICAULA gene is preferentially expressed in both male and female floral meristems

The rubber tree (Hevea brasiliensis Muell. Arg.) is an important source of natural rubber in tropical regions and, as with many woody species, shows a long juvenile phase. To understand the genetic and molecular mechanisms underlying the reproductive process in rubber trees, H. brasiliensis RRIM600 flower and inflorescence development have been characterized, the rubber tree FLORICAULA/LEAFY (FLO/LFY) orthologue, HbLFY, cloned, and its expression patterns were analysed during vegetative and reproductive development. The rubber tree, similar to other Euphorbiaceae species, produces lateral inflorescences containing male, female, and bisexual flowers. HbLFY is expressed in lateral meristems that give rise to inflorescences and in all flower meristems, consistent with a role in reproductive development. Complementation studies using Arabidopsis lfy mutants indicated that the biological function of LFY might be conserved among Brassicaceae and Euphorbiaceae species.

Identifying Eucalyptus expressed sequence tags related to Arabidopsis flowering-time pathway genes

Flowering initiation depends on the balanced expression of a complex network of genes that is regulated by both endogenous and environmental factors. The timing of the initiation of flowering is crucial for the reproductive success of plants; therefore, they have developed conserved molecular mechanisms to integrate both environmental and endogenous cues to regulate flowering time precisely. Extensive advances in plant biology are possible now that the complete genome sequences of flowering plants is available and plant genomes can be comprehensively compared. Thus, association studies are emerging as powerful tools for the functional identification of genes involved on the regulation of flowering pathways. In this paper we report the results of our search in the Eucalyptus Genome Sequencing Project Consortium (FORESTS) database for expressed sequence tags (ESTs) showing sequence homology with known elements of flowering-time pathways. We have searched the 33,080 sequence clusters in the FORESTS database and identified Eucalyptus sequences that codify putative conserved elements of the autonomous, vernalization-, photoperiod response- and gibberellic acid-controlled flowering-time pathways. Additionally, we have characterized in silico ten putative members of the Eucalyptus homologs to the Arabidopsis CONSTANS family of transcription factors.