Genes and genome editing tools for breeding desirable phenotypes in ornamentals

The Breeding, Cultivation, and Potential Applications of Ornamental Orchids with a Focus on Phalaenopsis-A Brief Review

The Phalaenopsis genus, a horticulturally vital group within the Orchidaceae, dominates global floriculture markets through strategic cultivar innovation, scalable propagation, and data-driven cultivation. This review systematically examines the breeding, propagation, cultivation management, and potential applications of Phalaenopsis while providing insights into future research directions. The main contents include the following: Breeding innovations-This review outlines the taxonomy of the Phalaenopsis genus and highlights its intergeneric hybridization potential, which offers vast opportunities for developing novel horticultural varieties. By establishing clear breeding objectives, researchers employ diverse breeding strategies, including conventional crossbreeding and biotechnological approaches (e.g., mutation breeding, ploidy manipulation, genetic transformation, and CRISPR/Cas9 editing). Propagation and cultivation management-Analyses of Phalaenopsis tissue culture protocols covering explant selection, media optimization, and regeneration systems are summarized. Key factors for efficient cultivation are discussed, including temperature, light, water, nutrient management, cultivation medium selection, and integrated pest/disease management. Scientific environmental control ensures robust plant growth, synchronized flowering, and high-quality flower production. Emerging applications-Phalaenopsis exhibits promising applications in functional bioactive compound extraction (e.g., antioxidants and antimicrobial agents). This review summarizes current advancements in Phalaenopsis breeding, cultivation, and potential applications. Based on technological progress and market demands, future research directions are proposed to support the sustainable development of the Phalaenopsis industry.

From Flourish to Nourish: Cultivating Soil Health for Sustainable Floriculture

Despite its rapid growth and economic success, the sustainability of the floriculture industry as it is presently conducted is debatable, due to the huge environmental impacts it initiates and incurs. Achieving sustainability requires joint efforts from all stakeholders, a fact that is often neglected in discussions that frequently focus upon economically driven management concerns. This review attempts to raise awareness and collective responsibility among the key practitioners in floriculture by discussing its sustainability in the context of soil health, as soil is the foundation of agriculture systems. Major challenges posed to soil health arise from soil acidification and salinization stimulated by the abusive use of fertilizers. The poisoning of soil biota by pesticide residues and plastic debris due to the excessive application of pesticides and disposal of plastics is another significant issue and concern. The consequence of continuous cropping obstacles are further elucidated by the concept of plant-soil feedback. Based on these challenges, we propose the adoption and implementation of several sustainable practices including breeding stress-resistant and nutrient-efficient cultivars, making sustainable soil management a goal of floriculture production, and the recycling of plastics to overcome and mitigate the decline in soil health. The problems created by flower waste materials are highlighted and efficient treatment by biochar synthesis is suggested. We acknowledge the complexity of developing and implementing the proposed practices in floriculture as there is limited collaboration among the research and operational communities, and the policymakers. Additional research examining the impacts the floriculture industry has upon soils is needed to develop more sustainable production practices that can help resolve the current threats and to bridge the understanding gap between researchers and stakeholders in floriculture.

Convergent evolution of plant prickles by repeated gene co-option over deep time

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses of prickles-sharp epidermal projections-that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus Solanum. Homologs underlie prickle formation across angiosperms that collectively diverged more than 150 million years ago, including rice and roses. By developing new Solanum genetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.

Morphological and molecular analysis of rose cultivars from the Grandiflora and Kordesii garden groups

The breeding of remontant rose cultivars that are resistant to diseases and adverse conditions, with high decorative value and continuous flowering is the most important task during work with the gene pool of garden roses. Currently, intercultivar hybridization within a single garden group has largely outlived its usefulness. It is necessary to breed for highly decorative forms or cultivars that have outstanding resistance, morphological characters and patterns of seasonal rhythms, and use these plants as parental forms in further breeding. This study represents a comparative analysis of rose cultivars from two garden groups, Grandiflora (Gurzuf, Lezginka, Korallovy Syurpriz, Queen Elizabeth, Komsomolsky Ogonyok, Love) and Rosa Kordesii (Letniye Zvyozdy, Dortmund, Gutsulochka). These cultivars proved themselves during many years of testing in harsh climatic conditions. The objectives of the study were to determine the genetic relationship within the groups and to assign phenotypically different cultivars to one or another garden group. The analysis was carried out by morphological, phenological and ISSR markers. According to the phenological observations on the Grandiflora cultivars, Komsomolsky Ogonyok had later budding and flowering stages. Polymorphic data generated from the ISSR markers showed that this cultivar was the most distant from the others and formed a separate cluster on the dendrogram. A comparison of the morphological characters (flower diameter, number of petals, peduncle length, bush height) showed a significant difference ( p < 0.05) between Komsomolsky Ogonyok and the other Grandiflora cultivars. A dendrogram based on a molecular analysis showed a lack of close relationships between Komsomolsky Ogonyok and the Kordesii group, which formed a separate cluster. A pairwise comparison of the morphological characters in Komsomolsky Ogonyok with the Kordesii group revealed a significant ( p <0.05) difference in three of the four characters studied. The exceptions were flower diameter when comparing with Dortmund and Letniye Zvyozdy and peduncle length when comparing with Gutsulochka. Although Komsomolsky Ogonyok has a pattern of seasonal development similar to Dortmund in the Kordesii group, the molecular analysis did not assign the former to this group of roses. The cultivars that have valuable characters that no average rose does and that are phenotypically different from such roses represent the most valuable breeding material.

Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea (Hydrangea macrophylla) and insights into Asterid evolution

The Hydrangea genus belongs to the Hydrangeaceae family, in the Cornales order of flowering plants, which early diverged among the Asterids, and includes several species that are commonly used ornamental plants. Of them, Hydrangea macrophylla is one of the most valuable species in the nursery trade, yet few genomic resources are available for this crop or closely related Asterid species. Two high-quality haplotype-resolved reference genomes of hydrangea cultivars 'Veitchii' and 'Endless Summer' [highest quality at 2.22 gigabase pairs (Gb), 396 contigs, N50 22.8 megabase pairs (Mb)] were assembled and scaffolded into the expected 18 pseudochromosomes. Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants, nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids. Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape, CYP78A5 located on chromosome 4, and a novel gene, BAM3 located on chromosome 17, for causing double flower. Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants, the Asterids.

Robust markers associated with floral traits in roses are suitable for marker-assisted selection across gene pools

We investigated the potential of markers associated with floral traits for parental selection in a cut rose breeding program. We analysed six Kompetitive Allele Specific PCR (KASP) markers for three important floral traits, petal length, petal number and scent, derived from experiments in a garden rose population. The six markers were applied to genotype a collection of 384 parental genotypes used for commercial cut rose breeding. We phenotyped a selection of progeny derived from pairs of parents having either high or low dosages of (contrasting) marker alleles associated with these traits. Significant differences were found between the contrasting progeny groups for each of the traits, although parents with the optimal allele dosage combinations could not always be used for the crosses. This not only supports the robustness of these marker‒trait associations but also demonstrates their potential for commercial rose breeding. It also demonstrates the use of marker information generated in garden rose populations for cut rose breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01438-5.

Genetic Engineering and Genome Editing Advances to Enhance Floral Attributes in Ornamental Plants: An Update

The ornamental horticulture industry is a highly dynamic and rapidly changing market. Constant development of novel cultivars with elite traits is essential to sustain competitiveness. Conventional breeding has been used to develop cultivars, which is often laborious. Biotechnological strategies such as genetic engineering have been crucial in manipulating and improving various beneficial traits that are technically not possible through cross-breeding. One such trait is the highly desired blue-colored flower in roses and chrysanthemums, which can be achieved through transgenic technology. Advances in genome sequencing platforms have enhanced the opportunities to access the whole genome sequence in various ornamentals, facilitating the dissection of the molecular genetics and regulatory controls of different traits. The recent advent of genome editing tools, including CRISPR/Cas9, has revolutionized plant breeding. CRISPR/Cas9-based gene editing offers efficient and highly precise trait modification, contributing to various beneficial advancements. Although genome editing in ornamentals is currently in its infancy, the recent increase in the availability of ornamental genome sequences provides a platform to extend the frontiers of future genome editing in ornamentals. Hence, this review depicts the implication of various commercially valuable ornamental attributes, and details the research attempts and achievements in enhancing floral attributes using genetic engineering and genome editing in ornamental plants.

Review of recent advances in post-harvest techniques for tropical cut flowers and future prospects: Heliconia as a case-study

Aesthetic attributes and easy-to-grow nature of tropical cut flowers (TCFs) have contributedto their potential for increased production. The dearth of information regarding agronomic practices and lack of planting materials are the key hindrances against their fast expansion. Unconventional high-temperature storage requirements and the anatomy of the peduncle contribute topoor vase life performance, while troublesome packaging and transport due to unusual size and structureprimarily cause post-harvest quality deterioration. Nonetheless, the exotic floral structuresconsequently increase market demand, particularly in temperate countries. This boosts studies aimed at overcoming post-harvest hindrances. While a few TCFs (Anthurium, Strelitzia, Alpinia, and a few orchids) are under the spotlight, many others remain behind the veil. Heliconia, an emerging specialty TCF (False Bird-of-Paradise, family Heliconiaceae), is one of them. The structural uniquenessand dazzling hues of Heliconia genotypes facilitate shifting its position from the back to the forefrontof the world floriculture trade. The unsatisfactory state-of-the-art of Heliconia research and the absence of any review exclusively on it are the key impetus for structuring this review. In addition to the aforementioned setbacks, impaired water uptake capacity after harvest, high chilling sensitivity, and the proneness of xylem ducts to microbial occlusion may be counted as a few additional factors that hinder its commercialization. This review demonstrates the state-of-the-art of post-harvest research while also conceptualizing the implementation of advanced biotechnological aid to alleviate the challenges, primarily focusing on Heliconia (the model crop here) along with some relevant literature on its other allied members. Standard harvesting indices, grading, and packaging are also part of the entire post-harvest operational chain, but since these phases are barely considered in Heliconia and the majority of tropical ornamentals except a few, a comprehensive account of these aspects has also been given. The hypothesized cues to nip chilling injury, resorting to different bio-chemical treatments, nano-based technology, and advanced packaging techniques, may help overcome preservation difficulties and propel its transition from niche to the commercial flower market. In a nutshell, readers will gain a comprehensive overview of how optimum post-harvest handling practices can rewardingly characterize this unique group of TCFs as the most remunerative component.

Role of EIN2-mediated ethylene signaling in regulating petal senescence, abscission, reproductive development, and hormonal crosstalk in tobacco

Ethylene plays a pivotal role in a wide range of developmental, physiological, and defense processes in plants. EIN2 (ETHYLENE INSENSITIVE2) is a key player in the ethylene signaling pathway. To characterize the role of EIN2 in processes, such as petal senescence, where it has been found to play important roles along with various other developmental and physiological processes, the tobacco (Nicotiana tabacum) ortholog of EIN2 (NtEIN2) was isolated and NtEIN2 silenced transgenic lines were generated using RNA interference (RNAi). Silencing of NtEIN2 compromised plant defense against pathogens. NtEIN2 silenced lines displayed significant delays in petal senescence, and pod maturation, and adversely affected pod and seed development. This study further dissected the petal senescence in ethylene insensitive lines, that displayed alteration in the pattern of petal senescence and floral organ abscission. Delay in petal senescence was possibly because of delayed aging processes within petal tissues. Possible crosstalk between EIN2 and AUXIN RESPONSE FACTOR 2 (ARF2) in regulating the petal senescence process was also investigated. Overall, these experiments indicated a crucial role for NtEIN2 in controlling diverse developmental and physiological processes, especially in petal senescence.

Tissue Culture in Ornamentals: Cultivation Factors, Propagation Techniques, and Its Application

Ornamentals come in a variety of shapes, sizes, and colors to suit a wide range of climates, landscapes, and gardening needs. Compared to demand, a shortage of plant materials and diversity force the search for solutions for their constant acquisition and improvement to increase their commercial value, respectively. In vitro cultures are a suitable solution to meet expectations using callus culture, somatic embryogenesis, protoplast culture, and the organogenesis of protocorm-like bodies; many of these techniques are commercially practiced. Factors such as culture media, explants, carbohydrates, plant growth regulators, and light are associated with the success of in vitro propagation. Techniques, especially embryo rescue and somatic hybridization, are widely used to improve ornamentals. The development of synthetic seed allows season-independent seed production and preservation in the long term. Despite the advantages of propagation and the improvement of ornamentals, many barriers still need to be resolved. In contrast to propagation and crop developmental studies, there is also a high scope for molecular studies, especially epigenetic changes caused by plant tissue culture of ornamentals. In this review, we have accumulated and discussed an overall update on cultivation factors, propagation techniques in ornamental plant tissue culture, in vitro plant improvement techniques, and future perspectives.

CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement

The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.

A large deletion at the cortex locus eliminates butterfly wing patterning

As the genetic basis of natural and domesticated variation has been described in recent years, a number of hotspot genes have been repeatedly identified as the targets of selection, Heliconius butterflies display a spectacular diversity of pattern variants in the wild and the genetic basis of these patterns has been well-described. Here, we sought to identify the mechanism behind an unusual pattern variant that is instead found in captivity, the ivory mutant, in which all scales on both the wings and body become white or yellow. Using a combination of autozygosity mapping and coverage analysis from 37 captive individuals, we identify a 78-kb deletion at the cortex wing patterning locus, a gene which has been associated with wing pattern evolution in H. melpomene and 10 divergent lepidopteran species. This deletion is undetected among 458 wild Heliconius genomes samples, and its dosage explains both homozygous and heterozygous ivory phenotypes found in captivity. The deletion spans a large 5′ region of the cortex gene that includes a facultative 5′UTR exon detected in larval wing disk transcriptomes. CRISPR mutagenesis of this exon replicates the wing phenotypes from coding knock-outs of cortex, consistent with a functional role of ivory-deleted elements in establishing scale color fate. Population demographics reveal that the stock giving rise to the ivory mutant has a mixed origin from across the wild range of H. melpomene, and supports a scenario where the ivory mutation occurred after the introduction of cortex haplotypes from Ecuador. Homozygotes for the ivory deletion are inviable while heterozygotes are the targets of artificial selection, joining 40 other examples of allelic variants that provide heterozygous advantage in animal populations under artificial selection by fanciers and breeders. Finally, our results highlight the promise of autozygosity and association mapping for identifying the genetic basis of aberrant mutations in captive insect populations.

Flavonoids - flowers, fruit, forage and the future

Flavonoids are plant-specific secondary metabolites that arose early during land-plant colonisation, most likely evolving for protection from UV-B and other abiotic stresses. As plants increased in complexity, so too did the diversity of flavonoid compounds produced and their physiological roles. The most conspicuous are the pigments, including yellow aurones and chalcones, and the red/purple/blue anthocyanins, which provide colours to flowers, fruits and foliage. Anthocyanins have been particularly well studied, prompted by the ease of identifying mutants of genes involved in biosynthesis or regulation, providing an important model system to study fundamental aspects of genetics, gene regulation and biochemistry. This has included identifying the first plant transcription factor, and later resolving how multiple classes of transcription factor coordinate in regulating the production of various flavonoid classes - each with different activities and produced at differing developmental stages. In addition, dietary flavonoids from fruits/vegetables and forage confer human- and animal-health benefits, respectively. This has prompted strong interest in generating new plant varieties with increased flavonoid content through both traditional breeding and plant biotechnology. Gene-editing technologies provide new opportunities to study how flavonoids are regulated and produced and to improve the flavonoid content of flowers, fruits, vegetables and forages.

Reporter genes confer new-to-nature ornamental traits in plants

This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).