Plum (Prunus domestica) trees transformed with poplar FT1 result in altered architecture, dormancy requirement, and continuous flowering

Application of new breeding techniques in fruit trees

Climate change and rapid adaption of invasive pathogens pose a constant pressure on the fruit industry to develop improved varieties. Aiming to accelerate the development of better-adapted cultivars, new breeding techniques have emerged as a promising alternative to meet the demand of a growing global population. Accelerated breeding, cisgenesis, and CRISPR/Cas genome editing hold significant potential for crop trait improvement and have proven to be useful in several plant species. This review focuses on the successful application of these technologies in fruit trees to confer pathogen resistance and tolerance to abiotic stress and improve quality traits. In addition, we review the optimization and diversification of CRISPR/Cas genome editing tools applied to fruit trees, such as multiplexing, CRISPR/Cas-mediated base editing and site-specific recombination systems. Advances in protoplast regeneration and delivery techniques, including the use of nanoparticles and viral-derived replicons, are described for the obtention of exogenous DNA-free fruit tree species. The regulatory landscape and broader social acceptability for cisgenesis and CRISPR/Cas genome editing are also discussed. Altogether, this review provides an overview of the versatility of applications for fruit crop improvement, as well as current challenges that deserve attention for further optimization and potential implementation of new breeding techniques.

Genomics insights into flowering and floral pattern formation: regional duplication and seasonal pattern of gene expression in Camellia

BACKGROUND

The formation and domestication of ornamental traits are influenced by various aspects, such as the recognition of esthetic values and cultural traditions. Camellia japonica is widely appreciated and domesticated around the world mainly due to its rich variations in ornamental traits. Ornamental camellias have a diverse range of resources, including different bud variations from Camellia spp. as well as inter- and intra- specific hybridization. Despite research on the formation of ornamental traits, a basic understanding of their genetics and genomics is still lacking.

RESULTS

Here, we report the chromosomal-level reference genome of C. japonica through combining multiple DNA-sequencing technologies and obtain a high-density genetic linkage map of 4255 markers by sequencing 98 interspecific F1 hybrids between C. japonica and C. chekiangoleosa. We identify two whole-genome duplication events in C. japonica: one is a shared ancient γ event, and the other is revealed to be specific to genus Camellia. Based on the micro-collinearity analysis, we find large-scale segmental duplication of chromosome 8, resulting to two copies of the AGAMOUS loci, which may play a key role in the domestication of floral shapes. To explore the regulatory mechanisms of seasonal flowering, we have analyzed year-round gene expression patterns of C. japonica and C. azalea-a sister plant of continuous flowering that has been widely used for cross breeding. Through comparative analyses of gene co-expression networks and annual gene expression patterns, we show that annual expression rhythms of some important regulators of seasonal growth and development, including GIGANTEA and CONSTANS of the photoperiod pathway, have been disrupted in C. azalea. Furthermore, we reveal that the distinctive expression patterns of FLOWERING LOCUS T can be correlated with the seasonal activities of flowering and flushing. We demonstrate that the regulatory module involved in GIGANTEA, CONSTANS, and FLOWERING LOCUS T is central to achieve seasonality.

CONCLUSIONS

Through the genomic and comparative genomics characterizations of ornamental Camellia spp., we propose that duplication of chromosomal segments as well as the establishment of gene expression patterns has played a key role in the formation of ornamental traits (e.g., flower shape, flowering time). This work provides a valuable genomic platform for understanding the molecular basis of ornamental traits.

Effect of heterologous expression of FT gene from Medicago truncatula in growth and flowering behavior of olive plants

Olive (Olea europaea L. subsp. europaea) is one of the most important crops of the Mediterranean Basin and temperate areas worldwide. Obtaining new olive varieties adapted to climatic changing conditions and to modern agricultural practices, as well as other traits such as biotic and abiotic stress resistance and increased oil quality, is currently required; however, the long juvenile phase, as in most woody plants, is the bottleneck in olive breeding programs. Overexpression of genes encoding the 'florigen' Flowering Locus T (FT), can cause the loss of the juvenile phase in many perennials including olives. In this investigation, further characterization of three transgenic olive lines containing an FT encoding gene from Medicago truncatula, MtFTa1, under the 35S CaMV promoter, was carried out. While all three lines flowered under in vitro conditions, one of the lines stopped flowering after acclimatisation. In soil, all three lines exhibited a modified plant architecture; e.g., a continuous branching behaviour and a dwarfing growth habit. Gene expression and hormone content in shoot tips, containing the meristems from which this phenotype emerged, were examined. Higher levels of OeTFL1, a gene encoding the flowering repressor TERMINAL FLOWER 1, correlated with lack of flowering. The branching phenotype correlated with higher content of salicylic acid, indole-3-acetic acid and isopentenyl adenosine, and lower content of abscisic acid. The results obtained confirm that heterologous expression of MtFTa1 in olive induced continuous flowering independently of environmental factors, but also modified plant architecture. These phenotypical changes could be related to the altered hormonal content in transgenic plants.

Regulatory frameworks involved in the floral induction, formation and developmental programming of woody horticultural plants: a case study on blueberries

Flowering represents a crucial stage in the life cycles of plants. Ensuring strong and consistent flowering is vital for maintaining crop production amidst the challenges presented by climate change. In this review, we summarized key recent efforts aimed at unraveling the complexities of plant flowering through genetic, genomic, physiological, and biochemical studies in woody species, with a special focus on the genetic control of floral initiation and activation in woody horticultural species. Key topics covered in the review include major flowering pathway genes in deciduous woody plants, regulation of the phase transition from juvenile to adult stage, the roles of CONSTANS (CO) and CO-like gene and FLOWERING LOCUS T genes in flower induction, the floral regulatory role of GA-DELLA pathway, and the multifunctional roles of MADS-box genes in flowering and dormancy release triggered by chilling. Based on our own research work in blueberries, we highlighted the central roles played by two key flowering pathway genes, FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1, which regulate floral initiation and activation (dormancy release), respectively. Collectively, our survey shows both the conserved and diverse aspects of the flowering pathway in annual and woody plants, providing insights into the potential molecular mechanisms governing woody plants. This paves the way for enhancing the resilience and productivity of fruit-bearing crops in the face of changing climatic conditions, all through the perspective of genetic interventions.

CRISPR/Cas as a Genome-Editing Technique in Fruit Tree Breeding

CRISPR (short for "Clustered Regularly Interspaced Short Palindromic Repeats") is a technology that research scientists use to selectively modify the DNA of living organisms. CRISPR was adapted for use in the laboratory from the naturally occurring genome-editing systems found in bacteria. In this work, we reviewed the methods used to introduce CRISPR/Cas-mediated genome editing into fruit species, as well as the impacts of the application of this technology to activate and knock out target genes in different fruit tree species, including on tree development, yield, fruit quality, and tolerance to biotic and abiotic stresses. The application of this gene-editing technology could allow the development of new generations of fruit crops with improved traits by targeting different genetic segments or even could facilitate the introduction of traits into elite cultivars without changing other traits. However, currently, the scarcity of efficient regeneration and transformation protocols in some species, the fact that many of those procedures are genotype-dependent, and the convenience of segregating the transgenic parts of the CRISPR system represent the main handicaps limiting the potential of genetic editing techniques for fruit trees. Finally, the latest news on the legislation and regulations about the use of plants modified using CRISPR/Cas systems has been also discussed.

A MADS-box gene-induced early flowering pear (Pyrus communis L.) for accelerated pear breeding

There have been a considerable number of studies that have successfully sped up the flowering cycle in woody perennial horticultural species. One particularly successful study in apple (Malus domestica) accelerated flowering using a silver birch (Betula pendula) APETALA1/FRUITFULL MADS-box gene BpMADS4, which yielded a good balance of vegetative growth to support subsequent flower and fruit development. In this study, BpMADS4 was constitutively expressed in European pear (Pyrus communis) to establish whether this could be used as a tool in a rapid pear breeding program. Transformed pear lines flowered within 6-18 months after grafting onto a quince (Cydonia oblonga) rootstock. Unlike the spindly habit of early flowering apples, the early flowering pear lines displayed a normal tree-like habit. Like apple, the flower appearance was normal, and the flowers were fertile, producing fruit and seed upon pollination. Seed from these transformed lines were germinated and 50% of the progeny flowered within 3 months of sowing, demonstrating a use for these in a fast breeding program.

Variation in floral form of CRISPR knock-outs of the poplar homologs of LEAFY and AGAMOUS after FT heat-induced early flowering

Plant migration and gene flow from genetically modified or exotic trees to nearby lands or by crossing with wild relatives is a major public and regulatory concern. Many genetic strategies exist to mitigate potential gene flow; however, the long delay in onset of flowering is a severe constraint to research progress. We used heat-induced FT overexpression to speed assessment of the expected floral phenotypes after CRISPR knockout of poplar homologs of the key floral genes, LEAFY and AGAMOUS. We selected events with previously characterized CRISPR-Cas9 induced biallelic changes then re-transformed them with the Arabidopsis thaliana FLOWERING LOCUS T (AtFT) gene under control of either a strong constitutive promoter or a heat-inducible promoter. We successfully obtained flowering in both a male and female clones of poplar, observing a wide range of inflorescence and floral forms among flowers, ramets, and insertion events. Overall, flowers obtained from the selected LFY and AG targeted events were consistent with what would be predicted for loss-of-function of these genes. LFY-targeted events showed small catkins with leaf-like organs, AG-targeted events had nested floral organs consistent with reduction in floral determinacy and absence of well-formed carpels or anthers. These findings demonstrate the great developmental plasticity of Populus flowers during genetically accelerated flowering, which may be of horticultural value. They also provide an informative early view of floral phenotypes and apparent sterility from knockouts of both these gene targets.

Multiple transcriptome comparisons reveal the essential roles of FLOWERING LOCUS T in floral initiation and SOC1 and SVP in floral activation in blueberry

The flowering mechanisms, especially chilling requirement-regulated flowering, in deciduous woody crops remain to be elucidated. Flower buds of northern highbush blueberry cultivar Aurora require approximately 1,000 chilling hours to bloom. Overexpression of a blueberry FLOWERING LOCUS T (VcFT) enabled precocious flowering of transgenic “Aurora” mainly in non-terminated apical buds during flower bud formation, meanwhile, most of the mature flower buds could not break until they received enough chilling hours. In this study, we highlighted two groups of differentially expressed genes (DEGs) in flower buds caused by VcFT overexpression (VcFT-OX) and full chilling. We compared the two groups of DEGs with a focus on flowering pathway genes. We found: 1) In non-chilled flower buds, VcFT-OX drove a high VcFT expression and repressed expression of a major MADS-box gene, blueberry SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (VcSOC1) resulting an increased VcFT/VcSOC1 expression ratio; 2) In fully chilled flower buds that are ready to break, the chilling upregulated VcSOC1 expression in non-transgenic “Aurora” and repressed VcFT expression in VcFT-OX “Aurora”, and each resulted in a decreased ratio of VcFT to VcSOC1; additionally, expression of a blueberry SHORT VEGETATIVE PHASE (VcSVP) was upregulated in chilled flower buds of both transgenic and non-transgenic’ “Aurora”. Together with additional analysis of VcFT and VcSOC1 in the transcriptome data of other genotypes and tissues, we provide evidence to support that VcFT expression plays a significant role in promoting floral initiation and that VcSOC1 expression is a key floral activator. We thus propose a new hypothesis on blueberry flowering mechanism, of which the ratios of VcFT-to-VcSOC1 at transcript levels in the flowering pathways determine flower bud formation and bud breaking. Generally, an increased VcFT/VcSOC1 ratio or increased VcSOC1 in leaf promotes precocious flowering and flower bud formation, and a decreased VcFT/VcSOC1 ratio with increased VcSOC1 in fully chilled flower buds contributes to flower bud breaking.

The Role of Italy in the Use of Advanced Plant Genomic Techniques on Fruit Trees: State of the Art and Future Perspectives

Climate change is deeply impacting the food chain production, lowering quality and yield. In this context, the international scientific community has dedicated many efforts to enhancing resilience and sustainability in agriculture. Italy is among the main European producers of several fruit trees; therefore, national research centers and universities undertook several initiatives to maintain the specificity of the 'Made in Italy' label. Despite their importance, fruit crops are suffering from difficulties associated with the conventional breeding approaches, especially in terms of financial commitment, land resources availability, and long generation times. The 'new genomic techniques' (NGTs), renamed in Italy as 'technologies for assisted evolution' (TEAs), reduce the time required to obtain genetically improved cultivars while precisely targeting specific DNA sequences. This review aims to illustrate the role of the Italian scientific community in the use of NGTs, with a specific focus on Citrus, grapevine, apple, pear, chestnut, strawberry, peach, and kiwifruit. For each crop, the key genes and traits on which the scientific community is working, as well as the technological improvements and advancements on the regeneration of local varieties, are presented. Lastly, a focus is placed on the legal aspects in the European and in Italian contexts.

Breeding and genetics of disease resistance in temperate fruit trees: challenges and new opportunities

Climate change, large monocultures of disease-susceptible cultivars, overuse of pesticides, and the emergence of new pathogens or pathogenic strains causing economic losses are all major threats to our environment, health, food, and nutritional supply. Temperate tree fruit crops belonging to the Rosaceae family are the most economically important and widely grown fruit crops. These long-lived crops are under attack from many different pathogens, incurring major economic losses. Multiple chemical sprays to control various diseases annually is a common practice, resulting in significant input costs, as well as environmental and health concerns. Breeding for disease resistance has been undertaken primarily in pome fruit crops (apples and pears) for a few fungal and bacterial diseases, and to a lesser extent in some stone fruit crops. These breeding efforts have taken multiple decades due to the biological constraints and complex genetics of these tree fruit crops. Over the past couple of decades, major advances have been made in genetic and physical mapping, genomics, biotechnology, genome sequencing, and phenomics, along with accumulation of large germplasm collections in repositories. These valuable resources offer opportunities to make significant advances in greatly reducing the time needed to either develop new cultivars or modify existing economic cultivars for enhanced resistance to multiple diseases. This review will cover current knowledge, challenges, and opportunities in breeding for disease resistance in temperate tree fruit crops.

Options for the generation of seedless cherry, the ultimate snacking product

This manuscript identifies cherry orthologues of genes implicated in the development of pericarpic fruit and pinpoints potential options and restrictions in the use of these targets for commercial exploitation of parthenocarpic cherry fruit. Cherry fruit contain a large stone and seed, making processing of the fruit laborious and consumption by the consumer challenging, inconvenient to eat 'on the move' and potentially dangerous for children. Availability of fruit lacking the stone and seed would be potentially transformative for the cherry industry, since such fruit would be easier to process and would increase consumer demand because of the potential reduction in costs. This review will explore the background of seedless fruit, in the context of the ambition to produce the first seedless cherry, carry out an in-depth analysis of the current literature around parthenocarpy in fruit, and discuss the available technology and potential for producing seedless cherry fruit as an 'ultimate snacking product' for the twenty-first century.

Promotion of natural flowers by JcFT depends on JcLFY in the perennial woody species Jatropha curcas

Production of normal gametes is necessary for flowering plant reproduction, which involves the transition from vegetative to reproductive stage and floral organ development. Such transitions and floral development are modulated by various environmental and endogenous stimuli and controlled by sophisticated regulatory networks. FLOWERING LOCUS T (FT) and LEAFY (LFY) are two key genes that integrate signals from multiple genetic pathways in Arabidopsis. However, the comprehensive functions and relationship between these two genes in trees are poorly understood. In this study, we found that JcFT played a vital role in regulating the flowering transition in the perennial woody species Jatropha curcas. JcLFY also involved in regulating this transition and controlled floral organ development. The non-flowering phenotype of JcFT-RNAi was rescued successfully by overexpression of JcLFY, while the abnormal flowers produced by JcLFY silencing were not recovered by JcFT overexpression via hybridization. These results indicate that JcFT, in which a mutation leads to a nonflowering phenotype, is the central gene of the floral meristem transition and that JcLFY, in which a mutation leads to striking changes in flowering and often sterility, is the central floral and inflorescence development gene. Moreover, our hybridization results suggest that JcLFY acts downstream of JcFT in Jatropha.

Mobility of FLOWERING LOCUS T protein as a systemic signal in trifoliate orange and its low accumulation in grafted juvenile scions

The long juvenile period of perennial woody plants is a major constraint in breeding programs. FLOWERING LOCUS T (FT) protein is an important mobile florigen signal that induces plant flowering. However, whether FT can be transported in woody plants to shorten the juvenile period is unknown, and its transport mechanism remains unclear. In this study, trifoliate orange FT (ToFT) and Arabidopsis FT (AtFT, which has been confirmed to be transportable in Arabidopsis) as a control were transformed into tomato and trifoliate orange, and early flowering was induced in the transgenic plants. Long-distance and two-way (upward and downward) transmission of ToFT and AtFT proteins was confirmed in both tomato and trifoliate orange using grafting and western blot analysis. However, rootstocks of transgenic trifoliate orange could not induce flowering in grafted wild-type juvenile scions because of the low accumulation of total FT protein in the grafted scions. It was further confirmed that endogenous ToFT protein was reduced in trifoliate orange, and the accumulation of the transported ToFT and AtFT proteins was lower than that in grafted juvenile tomato scions. Furthermore, the trifoliate orange FT-INTERACTING PROTEIN1 homolog (ToFTIP1) was isolated by yeast two-hybrid analysis. The FTIP1 homolog may regulate FT transport by interacting with FT in tomato and trifoliate orange. Our findings suggest that FT transport may be conserved between the tomato model and woody plants. However, in woody plants, the transported FT protein did not accumulate in significant amounts in the grafted wild-type juvenile scions and induce the scions to flower.

How Is Global Warming Affecting Fruit Tree Blooming? "Flowering (Dormancy) Disorder" in Japanese Pear (Pyrus pyrifolia) as a Case Study

Recent climate change has resulted in warmer temperatures. Warmer temperatures from autumn to spring has negatively affected dormancy progression, cold (de)acclimation, and cold tolerance in various temperate fruit trees. In Japan, a physiological disorder known as flowering disorder, which is an erratic flowering and bud break disorder, has recently emerged as a serious problem in the production of the pome fruit tree, Japanese (Asian) pear (Pyrus pyrifolia Nakai). Due to global warming, the annual temperature in Japan has risen markedly since the 1990s. Surveys of flowering disorder in field-grown and greenhouse-grown Japanese pear trees over several years have indicated that flowering disorder occurs in warmer years and cultivation conditions, and the risk of flowering disorder occurrence is higher at lower latitudes than at higher latitudes. Susceptibility to flowering disorder is linked to changes in the transcript levels of putative dormancy/flowering regulators such as DORMANCY-ASSOCIATED MADS-box (DAM) and FLOWERING LOCUS T (FT). On the basis of published studies, we conclude that autumn-winter warm temperatures cause flowering disorder through affecting cold acclimation, dormancy progression, and floral bud maturation. Additionally, warm conditions also decrease carbohydrate accumulation in shoots, leading to reduced tree vigor. We propose that all these physiological and metabolic changes due to the lack of chilling during the dormancy phase interact to cause flowering disorder in the spring. We also propose that the process of chilling exposure rather than the total amount of chilling may be important for the precise control of dormancy progression and robust blooming, which in turn suggests the necessity of re-evaluation of the characteristics of cultivar-dependent chilling requirement trait. A full understanding of the molecular and metabolic regulatory mechanisms of both dormancy completion (floral bud maturation) and dormancy break (release from the repression of bud break) will help to clarify the physiological basis of dormancy-related physiological disorder and also provide useful strategies to mitigate or overcome it under global warming.

Stability of Transgene Inheritance in Progeny of Field-Grown Pear Trees over a 7-Year Period

Breeding woody plants is a very time-consuming process, and genetic engineering tools have been used to shorten the juvenile phase. In addition, transgenic trees for commercial cultivation can also be used in classical breeding, but the segregation of transgenes in the progeny of perennial plants, as well as the possible appearance of unintended changes, have been poorly investigated. We studied the inheritance of the uidA gene in the progeny of field-grown transgenic pear trees for 7 years and the physical and physiological parameters of transgenic seeds. A total of 13 transgenic lines were analyzed, and the uidA gene segregated 1:1 in the progeny of 9 lines and 3:1 in the progeny of 4 lines, which is consistent with Mendelian inheritance for one and two transgene loci, respectively. Rare and random deviations from the Mendelian ratio were observed only for lines with one locus. Transgenic seeds' mass, size, and shape varied slightly, despite significant fluctuations in weather conditions during cultivation. Expression of the uidA gene in the progeny was stable. Our study showed that the transgene inheritance in the progeny of pear trees under field conditions occurs according to Mendelian ratio, does not depend on the environment, and the seed vigor of transgenic seeds does not change.

Efficiency of graft-transmitted JcFT for floral induction in woody perennial species of the Jatropha genus depends on transport distance

FLOWERING LOCUS T (FT) promotes flowering by integrating six genetic pathways. In Arabidopsis, the FT protein is transported from leaves to shoot apices and induces flowering. However, contradictory conclusions about floral induction via graft-transmitted FT in trees were reported in previous studies. We obtained extremely early-flowering transgenic woody Jatropha curcas L. by overexpression of J. curcas FT using Arabidopsis thaliana SUCROSE TRANSPORTER 2 (SUC2) promoter (SUC2:JcFT) and non-flowering transgenic J. curcas by RNA interference (RNAi), which were used to investigate the function of graft-transmitted JcFT in floral induction in woody perennials. Scions from five wild-type species of the Jatropha genus and from JcFT-RNAi transgenic J. curcas were grafted onto SUC2:JcFT rootstocks. Most grafted plants produced flowers in 1-2 months, and the flowering percentage and frequency of various grafted plants decreased with increasing scion length. Consistently, FT protein abundance in scions also decreased with increasing distance from graft junctions to the buds. These findings suggest that FT proteins can be transmitted by grafting and can induce the floral transition in woody perennials, and the efficiency of graft-transmitted JcFT for floral induction depends on the scion length, which may help explain previous seemingly contradictory observations regarding floral induction via graft-transmitted FT in trees.

Advances in genomics and genome editing for breeding next generation of fruit and nut crops

Fruit tree crops are an essential part of the food production systems and are key to achieve food and nutrition security. Genetic improvement of fruit trees by conventional breeding has been slow due to the long juvenile phase. Advancements in genomics and molecular biology have paved the way for devising novel genetic improvement tools like genome editing, which can accelerate the breeding of these perennial crops to a great extent. In this article, advancements in genomics of fruit trees covering genome sequencing, transcriptome sequencing, genome editing technologies (GET), CRISPR-Cas system based genome editing, potential applications of CRISPR-Cas9 in fruit tree crops improvement, the factors influencing the CRISPR-Cas editing efficiency and the challenges for CRISPR-Cas9 applications in fruit tree crops improvement are reviewed. Besides, base editing, a recently emerging more precise editing system, and the future perspectives of genome editing in the improvement of fruit and nut crops are covered.

Metabolic engineering in woody plants: challenges, advances, and opportunities

Woody plant species represent an invaluable reserve of biochemical diversity to which metabolic engineering can be applied to satisfy the need for commodity and specialty chemicals, pharmaceuticals, and renewable energy. Woody plants are particularly promising for this application due to their low input needs, high biomass, and immeasurable ecosystem services. However, existing challenges have hindered their widespread adoption in metabolic engineering efforts, such as long generation times, large and highly heterozygous genomes, and difficulties in transformation and regeneration. Recent advances in omics approaches, systems biology modeling, and plant transformation and regeneration methods provide effective approaches in overcoming these outstanding challenges. Promises brought by developments in this space are steadily opening the door to widespread metabolic engineering of woody plants to meet the global need for a wide range of sustainably sourced chemicals and materials.

Transgenic and genome-edited fruits: background, constraints, benefits, and commercial opportunities

Breeding has been used successfully for many years in the fruit industry, giving rise to most of today's commercial fruit cultivars. More recently, new molecular breeding techniques have addressed some of the constraints of conventional breeding. However, the development and commercial introduction of such novel fruits has been slow and limited with only five genetically engineered fruits currently produced as commercial varieties-virus-resistant papaya and squash were commercialized 25 years ago, whereas insect-resistant eggplant, non-browning apple, and pink-fleshed pineapple have been approved for commercialization within the last 6 years and production continues to increase every year. Advances in molecular genetics, particularly the new wave of genome editing technologies, provide opportunities to develop new fruit cultivars more rapidly. Our review, emphasizes the socioeconomic impact of current commercial fruit cultivars developed by genetic engineering and the potential impact of genome editing on the development of improved cultivars at an accelerated rate.

Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume

BACKGROUND

Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. Though PEBP family genes have been well studied in Arabidopsis and other model species, less is known about these genes in perennial trees.

RESULTS

To understand the evolution of PEBP genes and their functional roles in flowering control, we identified 56 PEBP members belonging to three gene clades (MFT-like, FT-like, and TFL1-like) and five lineages (FT, BFT, CEN, TFL1, and MFT) across nine Rosaceae perennial species. Structural analysis revealed highly conserved gene structure and protein motifs among Rosaceae PEBP proteins. Codon usage analysis showed slightly biased codon usage across five gene lineages. With selection pressure analysis, we detected strong purifying selection constraining divergence within most lineages, while positive selection driving the divergence of FT-like and TFL1-like genes from the MFT-like gene clade. Spatial and temporal expression analyses revealed the essential role of FT in regulating floral bud breaking and blooming in P. mume. By employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module required for dormancy release and blooming in P. mume.

CONCLUSIONS

We have characterized the PEBP family genes in nine Rosaceae species and examined their phylogeny, genomic syntenic relationship, duplication pattern, and expression profiles during flowering process. These results revealed the evolutionary history of PEBP genes and their functions in regulating floral bud development and blooming among Rosaceae tree species.

There is more to flowering than those DAM genes: the biology behind bloom in rosaceous fruit trees

The regulation of bloom time in deciduous fruit trees is an area of increasing interest due to the negative impact of climate change on fruit production. Although flower development has been well-studied in model species, there are many knowledge gaps about this process in perennial fruit trees, whose floral development spans the four seasons and includes many temperature-driven transitions. To develop solutions for minimizing crop loss, a comprehensive research strategy is needed to understand flower development and bloom time in deciduous fruit trees. This approach must incorporate genetic, physiological, and phenological strategies which include morphological and molecular analyses. Here, we describe key floral development events for rosaceae family fruit trees, highlight recent molecular and genetic discoveries, and discuss future directions for this field.

Phased genome sequence of an interspecific hybrid flowering cherry, 'Somei-Yoshino' (Cerasus × yedoensis)

We report the phased genome sequence of an interspecific hybrid, the flowering cherry ‘Somei-Yoshino’ (Cerasus × yedoensis). The sequence data were obtained by single-molecule real-time sequencing technology, split into two subsets based on genome information of the two probable ancestors, and assembled to obtain two haplotype phased genome sequences of the interspecific hybrid. The resultant genome assembly consisting of the two haplotype sequences spanned 690.1 Mb with 4,552 contigs and an N50 length of 1.0 Mb. We predicted 95,076 high-confidence genes, including 94.9% of the core eukaryotic genes. Based on a high-density genetic map, we established a pair of eight pseudomolecule sequences, with highly conserved structures between the two haplotype sequences with 2.4 million sequence variants. A whole genome resequencing analysis of flowering cherries suggested that ‘Somei-Yoshino’ might be derived from a cross between C. spachiana and either C. speciosa or its relatives. A time-course transcriptome analysis of floral buds and flowers suggested comprehensive changes in gene expression in floral bud development towards flowering. These genome and transcriptome data are expected to provide insights into the evolution and cultivation of flowering cherry and the molecular mechanism underlying flowering.

New Plant Breeding Techniques in Citrus for the Improvement of Important Agronomic Traits. A Review

New plant breeding techniques (NPBTs) aim to overcome traditional breeding limits for fruit tree species, in order to obtain new varieties with improved organoleptic traits and resistance to biotic and abiotic stress, and to maintain fruit quality achieved over centuries by (clonal) selection. Knowledge on the gene(s) controlling a specific trait is essential for the use of NPBTs, such as genome editing and cisgenesis. In the framework of the international scientific community working on fruit tree species, including citrus, NPBTs have mainly been applied to address pathogen threats. Citrus could take advantage of NPBTs because of its complex species biology (seedlessness, apomixis, high heterozygosity, and long juvenility phase) and aptitude for in vitro manipulation. To our knowledge, genome editing in citrus via transgenesis has successful for induced resistance to Citrus bacterial canker in sweet orange and grapefruit using the resistance gene CsLOB1. In the future, NPBTs will also be used to improve fruit traits, making them healthier. The regeneration of plants following the application of NPBTs is a bottleneck, making it necessary to optimize the efficiency of current protocols. The strengths and weaknesses of using explants from young in vitro plantlets, and from mature plants, will be discussed. Other major issues addressed in this review are related to the requirement for marker-free systems and shortening the long juvenility phase. This review aims to summarize methods and approaches available in the literature that are suitable to citrus, focusing on the principles observed before the use of NPBTs.

Day length regulates seasonal patterns of stomatal conductance in Quercus species

Vapour pressure deficit is a major driver of seasonal changes in transpiration, but photoperiod also modulates leaf responses. Climate warming might enhance transpiration by increasing atmospheric water demand and the length of the growing season, but photoperiod-sensitive species could show dampened responses. Here, we document that day length is a significant driver of the seasonal variation in stomatal conductance. We performed weekly gas exchange measurements across a common garden experiment with 12 oak species from contrasting geographical origins, and we observed that the influence of day length was of similar strength to that of vapour pressure deficit in driving the seasonal pattern. We then examined the generality of our findings by incorporating day-length regulation into well-known stomatal models. For both angiosperm and gymnosperm species, the models improved significantly when adding day-length dependences. Photoperiod control over stomatal conductance could play a large yet underexplored role on the plant and ecosystem water balances.

Mutagenesis of kiwifruit CENTRORADIALIS-like genes transforms a climbing woody perennial with long juvenility and axillary flowering into a compact plant with rapid terminal flowering

Annualization of woody perennials has the potential to revolutionize the breeding and production of fruit crops and rapidly improve horticultural species. Kiwifruit (Actinidia chinensis) is a recently domesticated fruit crop with a short history of breeding and tremendous potential for improvement. Previously, multiple kiwifruit CENTRORADIALIS (CEN)-like genes have been identified as potential repressors of flowering. In this study, CRISPR/Cas9- mediated manipulation enabled functional analysis of kiwifruit CEN-like genes AcCEN4 and AcCEN. Mutation of these genes transformed a climbing woody perennial, which develops axillary inflorescences after many years of juvenility, into a compact plant with rapid terminal flower and fruit development. The number of affected genes and alleles and severity of detected mutations correlated with the precocity and change in plant stature, suggesting that a bi-allelic mutation of either AcCEN4 or AcCEN may be sufficient for early flowering, whereas mutations affecting both genes further contributed to precocity and enhanced the compact growth habit. CRISPR/Cas9-mediated mutagenesis of AcCEN4 and AcCEN may be a valuable means to engineer Actinidia amenable for accelerated breeding, indoor farming and cultivation as an annual crop.

Agrobacterium-Mediated Transformation of Russian Commercial Plum cv. "Startovaya" (Prunus domestica L.) With Virus-Derived Hairpin RNA Construct Confers Durable Resistance to PPV Infection in Mature Plants

In modern horticulture Plum pox virus (PPV) imposes serious threats to commercial plantations of a wide range of fruit species belonging to genera Prunus. Given the lack of natural genetic resources, which display reliable resistance to PPV infection, there has been considerable interest in using genetic engineering methods for targeted genome modification of stone fruit trees to control Sharka disease caused by PPV. Among the many virus defense mechanisms, RNA interference is shown to be the most promising transgenic disease-control strategy in plant biotechnology. The present study describes the production of transgenic PPV resistant European plum "Startovaya" (P. domestica L.) through the Agrobacterium-mediated transformation of in vitro leaf explants. Due to organogenesis from leaves, the established protocol allows the genetic engineering of the plum genome without losing clonal fidelity of original cultivar. Seven independent transgenic plum lines containing the self-complementary fragments of PPV-CP gene sequence separated by a PDK intron were generated using hpt as a selective gene and uidA as a reporter gene. The transformation was verified through the histochemical staining for β-glucuronidase activity, PCR amplification of appropriate vector products from isolated genomic DNA and Southern blot analysis of hairpin PPV-CP gene fragments. To clarify the virus resistance, plum buds infected by PPV-M strain were grafted onto 1-year-old transgenic plants, which further were grown into mature trees in the greenhouse. As evaluated by RT-PCR, DAS-ELISA, Western blot, ImmunoStrip test, and visual observations, GM plum trees remained uninfected over 9 years. Infected branches that developed from grafted buds displayed obvious symptoms of Sharka disease over the years and maintained the high level of virus accumulation, whereby host transgenic trees had been constantly challenged with the pathogen. Since the virus was unable to spread to transgenic tissues, the stable expression of PPV-derived gene construct encoding intron-spliced hairpin RNAs provided a highly effective protection of plum trees against permanent viral infection. At the same time, this observation indicates the lack of the systemic spread of resistance from GM tissues to an infected plum graft even after years of joint growth.

Agrobacterium-Mediated Transformation of Tree Fruit Crops: Methods, Progress, and Challenges

Genetic engineering based on Agrobacterium-mediated transformation has been a desirable tool to manipulate single or multiple genes of existing genotypes of woody fruit crops, for which conventional breeding is a difficult and lengthy process due to heterozygosity, sexual incompatibility, juvenility, or a lack of natural sources. To date, successful transformation has been reported for many fruit crops. We review the major progress in genetic transformation of these fruit crops made in the past 5 years, emphasizing reproducible transformation protocols as well as the strategies that have been tested in fruit crops. While direct transformation of scion cultivars was mostly used for fruit quality improvement, biotic and abiotic tolerance, and functional gene analysis, transgrafting on genetically modified (GM) rootstocks showed a potential to produce non-GM fruit products. More recently, genome editing technology has demonstrated a potential for gene(s) manipulation of several fruit crops. However, substantial efforts are still needed to produce plants from gene-edited cells, for which tremendous challenge remains in the context of either cell's recalcitrance to regeneration or inefficient gene-editing due to their polyploidy. We propose that effective transient transformation and efficient regeneration are the key for future utilization of genome editing technologies for improvement of fruit crops.

Plant Cellular and Molecular Biotechnology: Following Mariotti's Steps

This review is dedicated to the memory of Prof. Domenico Mariotti, who significantly contributed to establishing the Italian research community in Agricultural Genetics and carried out the first experiments of Agrobacterium-mediated plant genetic transformation and regeneration in Italy during the 1980s. Following his scientific interests as guiding principles, this review summarizes the recent advances obtained in plant biotechnology and fundamental research aiming to: (i) Exploit in vitro plant cell and tissue cultures to induce genetic variability and to produce useful metabolites; (ii) gain new insights into the biochemical function of Agrobacterium rhizogenes rol genes and their application to metabolite production, fruit tree transformation, and reverse genetics; (iii) improve genetic transformation in legume species, most of them recalcitrant to regeneration; (iv) untangle the potential of KNOTTED1-like homeobox (KNOX) transcription factors in plant morphogenesis as key regulators of hormonal homeostasis; and (v) elucidate the molecular mechanisms of the transition from juvenility to the adult phase in Prunus tree species.

VcFT-induced mobile florigenic signals in transgenic and transgrafted blueberries

FLOWERING LOCUS T (FT) can promote early flowering in annual species, but such role has not been well demonstrated in woody species. We produced self and reciprocal grafts involving non-transgenic blueberry (NT) and transgenic blueberry (T) carrying a 35S-driven blueberry FT (VcFT-OX). We demonstrated that the transgenic VcFT-OX rootstock promoted flowering of non-transgenic blueberry scions in the NT (scion):T (rootstock) grafts. We further analyzed RNA-Seq profiles and six groups of phytohormones in both NT:T and NT:NT plants. We observed content changes of several hormone metabolites, in a descending order, in the transgenic NT:T, non-transgenic NT:T, and non-transgenic NT:NT leaves. By comparing differential expression transcripts (DETs) of these tissues in relative to their control, we found that the non-transgenic NT:T leaves had many DETs shared with the transgenic NT:T leaves, but very few with the transgenic NT:T roots. Interestingly, a number of these shared DETs belong to hormone pathway genes, concurring with the content changes of hormone metabolites in both transgenic and non-transgenic leaves of the NT:T plants. These results suggest that phytohormones induced by VcFT-OX in the transgenic leaves might serve as part of the signals that resulted in early flowering in both transgenic plants and the non-transgenic NT:T scions.

Manipulation of Growth and Architectural Characteristics in Trees for Increased Woody Biomass Production

Growth and architectural traits in trees are economically and environmentally important and thus of considerable importance to the improvement of forest and fruit trees. These traits are complex and result from the operation of a number of molecular mechanisms. This review will focus on the regulation of crown architecture, secondary woody growth and adventitious rooting. These traits and processes have significant impact on deployment, management, and productivity of tree crops. The majority of the described work comes from experiments in model plants, poplar, apple, peach, and plum because these species allow functional analysis of the involved genes and have significant genomics resources. However, these studies convincingly show conserved mechanisms for elaboration of specific growth and architectural traits. The conservation of these mechanisms suggest that they can be used as a blueprint for the improvement of these traits and processes in phylogenetically diverse tree crops. We will specifically consider the involvement of flowering time, transcription factors and hormone-associated genes. The review will also discuss the impact of recent technological advances as well as the challenges to the dissection of these traits in trees.

MYBs Drive Novel Consumer Traits in Fruits and Vegetables

Eating plant-derived compounds can lead to a longer and healthier life and also benefits the environment. Innovation in the fresh food sector, as well as new cultivars, can improve consumption of fruit and vegetables, with MYB transcription factors being a target to drive this novelty. Plant MYB transcription factors are implicated in diverse roles including development, hormone signalling, and metabolite biosynthesis. The reds and blues of fruit and vegetables provided by anthocyanins, phlobaphenes, and betalains are controlled by specific R2R3 MYBs. New studies are now revealing that MYBs also control carotenoid biosynthesis and other quality traits, such as flavour and texture. Future breeding techniques may manipulate or create alleles of key MYB transcription factors.

AcFT promotes kiwifruit in vitro flowering when overexpressed and Arabidopsis flowering when expressed in the vasculature under its own promoter

Kiwifruit (Actinidia chinensis) has three FLOWERING LOCUS T (FT) genes, AcFT, AcFT1, and AcFT2, with differential expression and potentially divergent roles. AcFT was previously shown to be expressed in source leaves and induced in dormant buds by winter chilling. Here, we show that AcFT promotes flowering in A. chinensis, despite a short sequence insertion not present in other FT-like genes. A 3.5-kb AcFT promoter region contained all the regulatory elements required to mediate vascular expression in transgenic Arabidopsis thaliana (Arabidopsis). The promoter activation was initially confined to the veins in the distal end of the leaf, before extending to the veins in the base of the leaf, and was detected in inductive and noninductive photoperiods. The 3-kb and 2.7-kb promoter regions of AcFT1 and AcFT2, respectively, demonstrated different activation patterns in Arabidopsis, corresponding to differential expression in kiwifruit. Expression of AcFT cDNA from the AcFT promoter was capable to induce early flowering in transgenic Arabidopsis in noninductive photoperiods. Further, expression of AcFT cDNA fused to the green fluorescent protein was detected in the vasculature and was also capable to advance flowering in noninductive photoperiods. Taken together, these studies implicate AcFT in regulation of kiwifruit flowering time and as a candidate for kiwifruit florigen.

Current achievements and future directions in genetic engineering of European plum (Prunus domestica L.)

In most woody fruit species, transformation and regeneration are difficult. However, European plum (Prunus domestica) has been shown to be amenable to genetic improvement technologies from classical hybridization, to genetic engineering, to rapid cycle crop breeding ('FasTrack' breeding). Since the first report on European plum transformation with marker genes in the early 90 s, numerous manuscripts have been published reporting the generation of new clones with agronomically interesting traits, such as pests, diseases and/or abiotic stress resistance, shorter juvenile period, dwarfing, continuous flowering, etc. This review focuses on the main advances in genetic transformation of European plum achieved to date, and the lines of work that are converting genetic engineering into a contemporary breeding tool for this species.

Generation of advanced fire blight-resistant apple (Malus × domestica) selections of the fifth generation within 7 years of applying the early flowering approach

The approach presented here can be applied to reduce the time needed to introduce traits from wild apples into null segregant advanced selections by one-fourth. Interesting traits like resistances to pathogens are often found within the wild apple gene pool. However, the long juvenile phase of apple seedlings hampers the rapid introduction of these traits into new cultivars. The rapid crop cycle breeding approach used in this paper is based on the overexpression of the birch (Betula pendula) MADS4 transcription factor in apple. Using the early flowering line T1190 and 'Evereste' as source of the fire blight resistance (Fb_E locus), we successfully established 18 advanced selections of the fifth generation in the greenhouse within 7 years. Fifteen individuals showed the habitus expected of a regular apple seedling, while three showed very short internodes. The null segregants possessing a regular habitus maintained the high level of fire blight resistance typical for 'Evereste'. Using SSR markers, we estimated the percentage of genetic drag from 'Evereste' still associated with Fb_E on linkage group 12 (LG12). Eight out of the 18 selections had only 4% of 'Evereste' genome left. Since genotypes carrying the apple scab resistance gene Rvi6 and the fire blight resistance QTL Fb_F7 were used as parents in the course of the experiments, these resistances were also identified in some of the null segregants. One seedling is particularly interesting as, beside Fb_E, it also carries Fb_F7 heterozygously and Rvi6 homozygously. If null segregants obtained using this method will be considered as not genetically modified in Europe, as is already the case in the USA, this genotype could be a very promising parent for breeding new fire blight and scab-resistant apple cultivars in European apple breeding programs.

Bud Dormancy in Perennial Fruit Tree Species: A Pivotal Role for Oxidative Cues

For perennial plants, bud dormancy is a crucial step as its progression over winter determines the quality of bud break, flowering, and fruiting. In the past decades, many studies, based on metabolic, physiological, subcellular, genetic, and genomic analyses, have unraveled mechanisms underlying bud dormancy progression. Overall, all the pathways identified are interconnected in a very complex manner. Here, we review early and recent findings on the dormancy processes in buds of temperate fruit trees species including hormonal signaling, the role of plasma membrane, carbohydrate metabolism, mitochondrial respiration and oxidative stress, with an effort to link them together and emphasize the central role of reactive oxygen species accumulation in the control of dormancy progression.

Identification of Morus notabilis MADS-box genes and elucidation of the roles of MnMADS33 during endodormancy

The MADS-box genes encode transcriptional regulators with various functions especially during floral development. A total of 54 putative Morus notabilis MADS-box genes (MnMADSs) were identified and phylogenetically classified as either type I (17 genes) or type II (37 genes). The detected genes included three FLOWERING LOCUS C-like (MnFLC-like) genes, MnMADS33, MnMADS50, and MnMADS7. MnFLC-like proteins could directly or indirectly repress promoter activity of the mulberry FLOWERING LOCUS T-like (MnFT) gene. Transgenic Arabidopsis thaliana overexpressing MnFLC-like genes exhibited delayed flowering and down-regulated expression of FT and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). The gene expression analyses in floral bud indicated that MnMADS33 expression increased, while MnFT expression decreased during the induction of dormancy in response to cold conditions. Dormancy release resulted in the down-regulation of MnMADS33 expression and the up-regulation of MnFT expression. Furthermore, abscisic acid promoted the transcription of MnMADS33 and MnFT, although the expression level of MnFT gradually decreased. These results are consistent with the hypothesis that MnMADS33 negatively regulated the expression of MnFT to repress dormancy release and flowering in mulberry. This study may be relevant for future investigations regarding the effects of MnMADS genes on mulberry flowering development.

I Want to (Bud) Break Free: The Potential Role of DAM and SVP-Like Genes in Regulating Dormancy Cycle in Temperate Fruit Trees

Bud dormancy is an adaptive process that allows trees to survive the hard environmental conditions that they experience during the winter of temperate climates. Dormancy is characterized by the reduction in meristematic activity and the absence of visible growth. A prolonged exposure to cold temperatures is required to allow the bud resuming growth in response to warm temperatures. In fruit tree species, the dormancy cycle is believed to be regulated by a group of genes encoding MADS-box transcription factors. These genes are called DORMANCY-ASSOCIATED MADS-BOX (DAM) and are phylogenetically related to the Arabidopsis thaliana floral regulators SHORT VEGETATIVE PHASE (SVP) and AGAMOUS-LIKE 24. The interest in DAM and other orthologs of SVP (SVP-like) genes has notably increased due to the publication of several reports suggesting their role in the control of bud dormancy in numerous fruit species, including apple, pear, peach, Japanese apricot, and kiwifruit among others. In this review, we briefly describe the physiological bases of the dormancy cycle and how it is genetically regulated, with a particular emphasis on DAM and SVP-like genes. We also provide a detailed report of the most recent advances about the transcriptional regulation of these genes by seasonal cues, epigenetics and plant hormones. From this information, we propose a tentative classification of DAM and SVP-like genes based on their seasonal pattern of expression. Furthermore, we discuss the potential biological role of DAM and SVP-like genes in bud dormancy in antagonizing the function of FLOWERING LOCUS T-like genes. Finally, we draw a global picture of the possible role of DAM and SVP-like genes in the bud dormancy cycle and propose a model that integrates these genes in a molecular network of dormancy cycle regulation in temperate fruit trees.

Expression patterns of flowering genes in leaves of 'Pineapple' sweet orange [Citrus sinensis (L.) Osbeck] and pummelo (Citrus grandis Osbeck)

BACKGROUND

In citrus the transition from juvenility to mature phase is marked by the capability of a tree to flower and fruit consistently. The long period of juvenility in citrus severely impedes the use of genetic based strategies to improve fruit quality, disease resistance, and responses to abiotic environmental factors. One of the genes whose expression signals flower development in many plant species is FLOWERING LOCUS T (FT).

RESULTS

In this study, gene expression levels of flowering genes CiFT1, CiFT2 and CiFT3 were determined using reverse-transcription quantitative real-time PCR in citrus trees over a 1 year period in Florida. Distinct genotypes of citrus trees of different ages were used. In mature trees of pummelo (Citrus grandis Osbeck) and 'Pineapple' sweet orange (Citrus sinensis (L.) Osbeck) the expression of all three CiFT genes was coordinated and significantly higher in April, after flowering was over, regardless of whether they were in the greenhouse or in the field. Interestingly, immature 'Pineapple' seedlings showed significantly high levels of CiFT3 expression in April and June, while CiFT1 and CiFT2 were highest in June, and hence their expression induction was not simultaneous as in mature plants.

CONCLUSIONS

In mature citrus trees the induction of CiFTs expression in leaves occurs at the end of spring and after flowering has taken place suggesting it is not associated with dormancy interruption and further flower bud development but is probably involved with shoot apex differentiation and flower bud determination. CiFTs were also seasonally induced in immature seedlings, indicating that additional factors must be suppressing flowering induction and their expression has other functions.

Three FT and multiple CEN and BFT genes regulate maturity, flowering, and vegetative phenology in kiwifruit

Kiwifruit is a woody perennial horticultural crop, characterized by excessive vegetative vigor, prolonged juvenility, and low productivity. To understand the molecular factors controlling flowering and winter dormancy, here we identify and characterize the kiwifruit PEBP (phosphatidylethanolamine-binding protein) gene family. Five CEN-like and three BFT-like genes are differentially expressed and act as functionally conserved floral repressors, while two MFT-like genes have no impact on flowering time. FT-like genes are differentially expressed, with AcFT1 confined to shoot tip and AcFT2 to mature leaves. Both act as potent activators of flowering, but expression of AcFT2 in Arabidopsis resulted in a greater impact on plant morphology than that of AcFT1. Constitutive expression of either construct in kiwifruit promoted in vitro flowering, but AcFT2 displayed a greater flowering activation efficiency than AcFT1, leading to immediate floral transition and restriction of leaf development. Both leaf and flower differentiation were observed in AcFT1 kiwifruit lines. Sequential activation of specific PEBP genes in axillary shoot buds during growth and dormancy cycles indicated specific roles in regulation of kiwifruit vegetative and reproductive phenologies. AcCEN and AcCEN4 marked active growth, AcBFT2 was associated with suppression of latent bud growth during winter, and only AcFT was activated after cold accumulation and dormancy release.

Virus-Induced Flowering: An Application of Reproductive Biology to Benefit Plant Research and Breeding

Virus-induced flowering combines fundamental research in reproductive biology with efficient tools for manipulating gene expression in nonmodel systems to accelerate discovery and breeding.

The sweet cherry (Prunus avium) FLOWERING LOCUS T gene is expressed during floral bud determination and can promote flowering in a winter-annual Arabidopsis accession

FT gene is expressed in leaves and buds and is involved in floral meristem determination and bud development in sweet cherry. In woody fruit perennial trees, floral determination, dormancy and bloom, depends on perception of different environmental and endogenous cues which converge to a systemic signaling gene known as FLOWERING LOCUS T (FT). In long-day flowering plants, FT is expressed in the leaves on long days. The protein travels through the phloem to the shoot apical meristem, where it induces flower determination. In perennial plants, meristem determination and flowering are separated by a dormancy period. Meristem determination takes place in summer, but flowering occurs only after a dormancy period and cold accumulation during winter. The roles of FT are not completely clear in meristem determination, dormancy release, and flowering in perennial plants. We cloned FT from sweet cherry (Prunus avium) and analyzed its expression pattern in leaves and floral buds during spring and summer. Phylogenetic analysis shows high identity of the FT cloned sequence with orthologous genes from other Rosaceae species. Our results show that FT is expressed in both leaves and floral buds and increases when the daylight reached 12 h. The peak in FT expression was coincident with floral meristem identity genes expression and morphological changes typical of floral meristem determination. The Edi-0 Arabidopsis ecotype, which requires vernalization to flower, was transformed with a construct for overexpression of PavFT. These transgenic plants showed an early-flowering phenotype without cold treatment. Our results suggest that FT is involved in floral meristem determination and bud development in sweet cherry. Moreover, we show that FT is expressed in both leaves and floral buds in this species, in contrast to annual plants.

Overexpression of blueberry FLOWERING LOCUS T is associated with changes in the expression of phytohormone-related genes in blueberry plants

Flowering locus T (FT) is a primary integrator in the regulation of plant flowering. Overexpressing a blueberry (Vaccinium corymbosum L.) FT gene (VcFT) (herein VcFT-OX) resulted in early flowering and dwarfing in 'Aurora' plants (herein 'VcFT-Aurora'). In this study, we found that VcFT-OX reduced shoot regeneration from leaf explants. To investigate the potential roles of the phytohormone pathway genes associated with VcFT-OX, differentially expressed (DE) genes in leaf tissues of 'VcFT-Aurora' plants were annotated and analyzed using non-transgenic 'Aurora' plants as a control. Three DE floral genes, including the blueberry SUPPRESSOR of Overexpression of constans 1 (VcSOC1) (gibberellin related), Abscisic acid responsive elements-binding factor 2 (VcABF2) and protein related to ABI3/VP1 (VcABI3/VP1) (ethylene-related), are present under both the phytohormone-responsive and the dwarfing-related Gene Ontology terms. The gene networks of the DE genes overall showed the molecular basis of the multifunctional aspects of VcFT overexpression beyond flowering promotion and suggested that phytohormone changes could be signaling molecules with important roles in the phenotypic changes driven by VcFT-OX.

FT and florigen long-distance flowering control in plants

The great hunt for florigen, the universal, long distance flowering regulator proposed by Chailakhan in the 1930s, resulted in the discovery a decade ago that FT-like proteins fulfilled the predictions for florigen. They are small (∼175 amino acids), globular, phosphatidylethanolamine-binding (PEBP) proteins, phloem-expressed, graft-transmissible and able to move to the shoot apex to act as potent stimulators of flowering in many plants. Genes that regulate Arabidopsis FT protein movement and some features of Arabidopsis FT protein that make it an effective florigen have recently been identified. Although floral promotion via graft transmission of FT has not been demonstrated in trees, FT-like genes have been successfully applied to reducing the long juvenile (pre-flowering) phase of many trees enabling fast track breeding.

Opportunities for Products of New Plant Breeding Techniques

Various new plant breeding techniques (NPBT) have a similar aim, namely to produce improved crop varieties that are difficult to obtain through traditional breeding methods. Here, we review the opportunities for products created using NPBTs. We categorize products of these NPBTs into three product classes with a different degree of genetic modification. For each product class, recent examples are described to illustrate the potential for breeding new crops with improved traits. Finally, we touch upon the future applications of these methods, such as cisgenic potato genotypes in which specific combinations of Phytophthora infestans resistance genes have been stacked for use in durable cultivation, or the creation of new disease resistances by knocking out or removing S-genes using genome-editing techniques.

Low temperatures are required to induce the development of fertile flowers in transgenic male and female early flowering poplar (Populus tremula L.)

Until now, artificial early flowering poplar systems have mostly led to the development of sterile flowers. In this study, several strategies aimed at inducting fertile flowers in pHSP::AtFT transgenic poplar were evaluated, in particular the influence of temperature and photoperiod. Our results provide evidence that temperature, and not photoperiod, is the key factor required for the development of fertile flowers in early flowering poplar. Fertile flowers were only obtained when a cold treatment phase of several weeks was used after the heat treatment phase. Heat treatments induced AtFT gene activity through activation of the heat-shock promoter (pHSP). Photoperiod did not show a similar influence on flower fertility as pollen grains were obtained under both long- and short-day conditions. Fertility was confirmed in flowers of both male and female plants. For the first time, crosses were successfully performed with transgenic female early flowering poplar. All mature flowers obtained after 8 weeks of inductive treatments were fertile. Gene expression studies also confirmed that cold temperatures influenced expression of poplar genes homologous to 'pollen development genes' from Arabidopsis thaliana (L.) Heynh. Homology and expression patterns suggested a role for PtTDF1, PtBAM1, PtSERK1/2 and PtMS1 on anther and pollen development in poplar flowers. The system developed in this study allows a fast and very reliable induction of fertile poplar flowers in a very short period of time. The non-reproductive phase, usually 7-10 years, can now be shortened to 6-10 months, and fertile flowers can be obtained independently of the season. This system is a reliable tool for breeding purposes (high-speed breeding technology), genomics and biosafety research.

Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population

In temperate trees, growth resumption in spring time results from chilling and heat requirements, and is an adaptive trait under global warming. Here, the genetic determinism of budbreak and flowering time was deciphered using five related full-sib apple families. Both traits were observed over 3 years and two sites and expressed in calendar and degree-days. Best linear unbiased predictors of genotypic effect or interaction with climatic year were extracted from mixed linear models and used for quantitative trait locus (QTL) mapping, performed with an integrated genetic map containing 6849 single nucleotide polymorphisms (SNPs), grouped into haplotypes, and with a Bayesian pedigree-based analysis. Four major regions, on linkage group (LG) 7, LG10, LG12, and LG9, the latter being the most stable across families, sites, and years, explained 5.6-21.3% of trait variance. Co-localizations for traits in calendar days or growing degree hours (GDH) suggested common genetic determinism for chilling and heating requirements. Homologs of two major flowering genes, AGL24 and FT, were predicted close to LG9 and LG12 QTLs, respectively, whereas Dormancy Associated MADs-box (DAM) genes were near additional QTLs on LG8 and LG15. This suggests that chilling perception mechanisms could be common among perennial and annual plants. Progenitors with favorable alleles depending on trait and LG were identified and could benefit new breeding strategies for apple adaptation to temperature increase.