Improvement Of Horticultural Crops Research Articles

HortGenome Search Engine, a universal genomic search engine for horticultural crops

Abstract Horticultural crops comprising fruit, vegetable, ornamental, beverage, medicinal and aromatic plants play essential roles in food security and human health, as well as landscaping. With the advances of sequencing technologies, genomes for hundreds of horticultural crops have been deciphered in recent years, providing a basis for understanding gene functions and regulatory networks and for the improvement of horticultural crops. However, these valuable genomic data are scattered in warehouses with various complex searching and displaying strategies, which increases learning and usage costs and makes comparative and functional genomic analyses across different horticultural crops very challenging. To this end, we have developed a lightweight universal search engine, HortGenome Search Engine (HSE; http://hort.moilab.net), which allows querying genes, functional annotations, protein domains, homologs, and other gene-related functional information of more than 500 horticultural crops. In addition, four commonly used tools, including ‘BLAST’, ‘Batch Query’, ‘Enrichment analysis’, and ‘Synteny Viewer’, have been developed for efficient mining and analysis of these genomic data.

From Sequencing to Genome Editing in Cucurbitaceae: Application of Modern Genomic Techniques to Enhance Plant Traits

The availability of genome-sequencing and genome-editing techniques has increased the applicability of innovative solutions, opening up revolutionary prospects for developments in horticultural plant breeding. The Cucurbitaceae family is a group of plants of great importance in horticulture due to their high nutritional and economic value. These plants serve as important models for elucidating the principles of plant development and refining yield improvement strategies. While traditional breeding approaches have made significant contributions to the production of cucurbits, they have also been limited by the reduced genetic diversity and lower rates of variation inherent in these species. This comprehensive review summarises the latest developments in genome editing in cucurbits. It covers various aspects of enhancing plant traits to resist biotic stresses such as pathogenic fungi and viruses, as well as abiotic stresses such as adverse climate change, especially stresses caused by drought and salinity. This study focused on improvements in plant quality and on the optimisation of plant architecture, sex determination of flowers and fruit features. This review provides insights that may hold great promise for the future of horticultural crop improvement and serves as an important reference for the advancement of genome-sequencing and gene-editing technologies in cucurbits.

A Comprehensive Review of CRISPR/Cas9 Based Strategies in Horticultural Crop Modification

The introduction of CRISPR/Cas9 gene editing technology represents a groundbreaking advancement in the realm of horticulture. It provides a precise and effective means for making targeted genetic alterations in a wide range of plant species. This abstract delves into the diverse applications of CRISPR/Cas9 within the domain of horticultural crops, with a particular emphasis on its crucial role in tackling issues related to climate change. This review paper outlines the diverse applications of CRISPR/Cas9 in horticulture, including trait improvement for enhanced stress tolerance, disease resistance, and yield optimization. It highlights specific examples of successful CRISPR-edited horticultural crops and their contributions to climate adaptation. Furthermore, it discusses the potential of CRISPR/Cas9 in accelerating the development of new crop varieties tailored to thrive in changing climatic conditions. Additionally, the ethical and regulatory considerations surrounding the use of CRISPR/Cas9 in horticulture are addressed, as they play a crucial role in determining the broader adoption of this technology. Balancing the benefits of climate-resilient crop development with potential environmental and societal implications remains a critical aspect of its application. In conclusion, the transformative potential of CRISPR/Cas9 in horticultural crop improvement and its role in addressing climate-related challenges. By harnessing the power of genetic editing, horticulturalists can create more productive crops and better equipped to withstand the uncertainties of a changing climate. However, this technology's responsible and ethical use is imperative to ensure its long-term sustainability and benefit to society.

Quality trait improvement in horticultural crops: OMICS and modern biotechnological approaches.

Horticultural crops are an essential part of food and nutritional security. Moreover, these form an integral part of the agricultural economy and have enormous economic potential. They are a rich source of nutrients that are beneficial to human health. Plant breeding of horticultural crops has focussed primarily on increasing the productivity and related traits of these crops. However, fruit and vegetable quality is paramount to their perishability, marketability, and consumer acceptance. The improved nutritional value is beneficial to underprivileged and undernourished communities. Due to a declining genetic base, conventional plant breeding does not contribute much to quality improvement as the existing natural allelic variations and crossing barriers between cultivated and wild species limit it. Over the past two decades, 'omics' and modern biotechnological approaches have made it possible to decode the complex genomes of crop plants, assign functions to the otherwise many unknown genes, and develop genome-wide DNA markers. Genetic engineering has enabled the validation of these genes and the introduction of crucial agronomic traits influencing various quality parameters directly or indirectly. This review discusses the significant advances in the quality improvement of horticultural crops, including shelf life, aroma, browning, nutritional value, colour, and many other related traits.

The SlWRKY6-SlPROPEP-SlPep module confers tomato resistance to Phytophthora infestans

Tomato constitutes a primary agricultural industry, but its production is severely impaired by Phytophthora infestans (P. infestans). Although identifying numerous resistance genes, the molecular mechanisms underlying tomato resistance to P. infestans remain elusive. Here, we identified SlPep, a plant elicitor peptide that confers resistance to P. infestans in tomato. SlPep originates from the C terminus of the precursor protein, SlPROPEP, in tomato. The expression of SlPROPEP was transcriptionally induced upon P. infestans infection. And, transiently overexpressing of SlPROPEP enhanced tomato resistance by elevating the levels of reactive oxygen species and pathogenesis-related genes, whereas silencing of SlPROPEP impaired resistance. Moreover, we demonstrated that SlWRKY6 could enhance tomato resistance via up-regulating the expression of SlPROPEP. Additionally, we observed that the exogenous application of SlPep promoted jasmonic acid and ethylene contents, inducing tomato resistance towards P. infestans. Overall, our findings shed light on the molecular roles of the SlWRKY6-SlPROPEP-SlPep module in tomato-P. infestans interactions, providing novel insights into horticultural crop improvement.

CRISPR / Cas 9 assisted genome editing technology for the improvement of Horticultural crops

Horticultural crops produce a wide range of useful goods for humans. There has been an increase in research focus on horticulture crop enhancement, particularly in terms of production and quality. The use of genome editing to enhance horticulture crops has seen a sharp rise in recent years due to the advancement and benefits of genome-editing technology. Here, we provide a brief overview of the various genome-editing techniques applied in horticulture research, with a particular emphasis on CRISPR/CRISPR-associated 9 (Cas9)-mediated genome editing. We also provide an overview of recent developments in the use of genome editing to enhance horticulture crops. Breeding and the rapidly growing field of genome editing will significantly boost the quantity and quality of horticulture crops.

Multi-environment genomic prediction for soluble solids content in peach (Prunus persica).

Genotype-by-environment interaction (G × E) is a common phenomenon influencing genetic improvement in plants, and a good understanding of this phenomenon is important for breeding and cultivar deployment strategies. However, there is little information on G × E in horticultural tree crops, mostly due to evaluation costs, leading to a focus on the development and deployment of locally adapted germplasm. Using sweetness (measured as soluble solids content, SSC) in peach/nectarine assessed at four trials from three US peach-breeding programs as a case study, we evaluated the hypotheses that (i) complex data from multiple breeding programs can be connected using GBLUP models to improve the knowledge of G × E for breeding and deployment and (ii) accounting for a known large-effect quantitative trait locus (QTL) improves the prediction accuracy. Following a structured strategy using univariate and multivariate models containing additive and dominance genomic effects on SSC, a model that included a previously detected QTL and background genomic effects was a significantly better fit than a genome-wide model with completely anonymous markers. Estimates of an individual’s narrow-sense and broad-sense heritability for SSC were high (0.57–0.73 and 0.66–0.80, respectively), with 19–32% of total genomic variance explained by the QTL. Genome-wide dominance effects and QTL effects were stable across environments. Significant G × E was detected for background genome effects, mostly due to the low correlation of these effects across seasons within a particular trial. The expected prediction accuracy, estimated from the linear model, was higher than the realised prediction accuracy estimated by cross-validation, suggesting that these two parameters measure different qualities of the prediction models. While prediction accuracy was improved in some cases by combining data across trials, particularly when phenotypic data for untested individuals were available from other trials, this improvement was not consistent. This study confirms that complex data can be combined into a single analysis using GBLUP methods to improve understanding of G × E and also incorporate known QTL effects. In addition, the study generated baseline information to account for population structure in genomic prediction models in horticultural crop improvement.

MicroRNAs: emerging regulators in horticultural crops.

Horticulture is one of the oldest agricultural practices with great popularity throughout the world. Horticultural crops include fruits, vegetables, ornamental plants, as well as medicinal and beverage plants. They are cultivated for food, specific nutrition, and medical use, or for aesthetic pleasure. MicroRNAs (miRNAs), which constitute a major class of endogenous small RNAs in plants, affect a multitude of developmental and physiological processes by imparting sequence specificity to gene regulation. Over the past decade, tens of thousands of miRNAs have been identified in more than 100 horticultural crops and their critical roles in regulating quality development of diverse horticultural crops have been demonstrated. Here, we review how miRNAs have emerged as important regulators and promising tools for horticultural crop improvement.

The transcriptional coactivator CmMBF1c is required for waterlogging tolerance in Chrysanthemum morifolium.

Waterlogging is one of the most serious abiotic stressors affecting Chrysanthemum morifolium during its lifespan. However, the molecular mechanisms underlying the waterlogging tolerance of chrysanthemum remain unclear. In this study, we discovered that the transcriptional coactivator MULTIPROTEIN BRIDGING FACTOR 1c (CmMBF1c) was significantly induced by waterlogging stress in chrysanthemums. Promoter sequence analysis and transient dual-luciferase assay using chrysanthemum protoplasts showed that the waterlogging-tolerant cultivar 'Nannongxuefeng' carried more response elements involved in waterlogging and hypoxia stress compared with the waterlogging-sensitive cultivar 'Qinglu', conferring on 'Nannongxuefeng' a stronger hypoxia responsive activity and higher CmMBF1c expression under waterlogging conditions. Subcellular localization and transcriptional activity assays showed that CmMBF1c protein was localized to the nucleus and had no transcriptional activation activity. Overexpression of CmMBF1c in 'Qinglu' enhanced its waterlogging tolerance by promoting its reactive oxygen species (ROS) scavenging ability and maintaining low ROS levels. However, RNAi-mediated knockdown of CmMBF1c in cultivar 'Nannongxuefeng' resulted in the opposite tendency. Yeast two-hybrid screening and tobacco bimolecular fluorescence complementation assays revealed that CmHRE2, a pivotal regulator of hypoxia response, could interact with CmMBF1c. In summary, this study demonstrates that CmMBF1c improves chrysanthemum waterlogging tolerance by regulating its ROS signaling pathway and interacting with CmHRE2. These findings together offer, to our knowledge, new mechanistic insights into chrysanthemum waterlogging tolerance and provide a rational foundation for future research on the genetic improvement of horticultural crops for waterlogging stress tolerance.

Role of plant tissue culture in improvement of horticultural crops

Role of plant tissue culture in improvement of horticultural crops

CRISPR Cas-9: A genome editing tool for the improvement of horticultural crops: A review

Horticultural crops, being a prime source of essential nutrients, staple food and foreign exchange for a large part of human population, exhibit a unique status among growers and consumers. Ever increasing population across the world and changing climate conditions are badly affecting food security. Urgent needed improvement of production and enhanced adaptation to changing environmental conditions of horticultural crops seems unlikely to be met by conventional breeding technologies. Fortunately, one of the modern molecular techniques namely “clustered regularly interspaced short palindromic repeat (CRISPR)” technology has opened a new window to genetically improve these crops. Employing CRISPR technology, many crops for instance tomato, potato, watermelon and grapes have been successfully genetically engineered in order to improve their nutritional value and enhance adaptability towards changing climates. In the same way, resistance against many potential diseases have been developed modifying the genetics of certain horticultural crops. In this mini review, we have briefly discussed the successful CRISPR-Cas9 based studies conducted in horticultural crops and tried to present valuable source for the horticulturists working on biotic and abiotic stresses.

Genetic improvement of horticultural crops mediated by CRISPR/Cas: a new horizon of possibilities

ABSTRACT The burden of the current global challenge involving food security lies in the need to improve crop production. In this regard, biotechnology stands out as an essential tool to generate plants able to cope with pests, diseases, and harsh climatic conditions, and more efficient in the use of natural resources. An advanced approach to create genetic variability in a precise and targeted way, the genome-editing technique CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR associated proteins), has drawn the attention of breeders. The genome editing CRISPR/Cas system relies on a guiding RNA that directs a nuclease to generate a double-strand break (DSB) at a target DNA, activating the cell repair systems and eventually leading to deletions or insertions of nucleotides. Therefore, CRISPR/Cas is a toolbox to achieve many goals, from basic science investigations to the development of crops with improved agronomic traits, with potential to bring innovative solutions to food production. The CRISPR/Cas system has been applied in a large number of plants, including some horticultural species. In this review, we present details of the CRISPR/Cas natural and artificial systems, its possibilities as a biotechnological tool, advantages over other breeding techniques, regulatory issues, and its applicability in horticultural crops, as well as future challenges.

CRISPR/Cas9 Mediated Genome Engineering for Improvement of Horticultural Crops.

Horticultural crops are an important part of agriculture for food as well as nutritional security. However, several pests and diseases along with adverse abiotic environmental factors pose a severe threat to these crops by affecting their quality and productivity. This warrants the effective and accelerated breeding programs by utilizing innovative biotechnological tools that can tackle aforementioned issues. The recent technique of genome editing by Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated 9 (CRISPR/Cas9) has greatly advanced the breeding for crop improvement due to its simplicity and high efficiency over other nucleases such as Zinc Finger Nucleases and Transcription Activator Like Effector Nucleases. CRISPR/Cas9 tool contains a non-specific Cas9 nuclease and a single guide RNA that directs Cas9 to the specific genomic location creating double-strand breaks and subsequent repair process creates insertion or deletion mutations. This is currently the widely adopted tool for reverse genetics, and crop improvement in large number of agricultural crops. The use of CRISPR/Cas9 in horticultural crops is limited to few crops due to lack of availability of regeneration protocols and sufficient sequence information in many horticultural crops. In this review, the present status of applicability of CRISPR/Cas9 in horticultural crops was discussed along with the challenges and future potential for possible improvement of these crops for their yield, quality, and resistance to biotic and abiotic stress.

Genetic engineering strategies for biotic and abiotic stress tolerance and quality enhancement in horticultural crops: a comprehensive review.

Genetic engineering technique offers myriads of applications in improvement of horticultural crops for biotic and abiotic stress tolerance, and produce quality enhancement. During last two decades, a large number of transgenic horticultural crops has been developed and more are underway. A number of genes including natural and synthetic Cry genes, protease inhibitors, trypsin inhibitors and cystatin genes have been used to incorporate insect and nematode resistance. For providing protection against fungal and bacterial diseases, various genes like chitinase, glucanase, osmotin, defensin and pathogenesis-related genes are being transferred to many horticultural crops world over. RNAi technique has been found quite successful in inducing virus resistance in horticultural crops in addition to coat protein genes. Abiotic stresses such as drought, heat and salinity adversely affect production and productivity of horticultural crops and a number of genes encoding for biosynthesis of stress protecting compounds including mannitol, glycine betaine and heat shock proteins have been employed for abiotic stress tolerance besides various transcription factors like DREB1, MAPK, WRKY, etc. Antisense gene and RNAi technologies have revolutionized the pace of improvement of horticultural crops, particularly ornamentals for color modification, increasing shelf-life and reducing post-harvest losses. Precise genome editing tools, particularly CRISPR/Cas9, have been efficiently applied in tomato, petunia, citrus, grape, potato and apple for gene mutation, repression, activation and epigenome editing. This review provides comprehensive overview to draw the attention of researchers for better understanding of genetic engineering advancements in imparting biotic and abiotic stress tolerance as well as on improving various traits related to quality, texture, plant architecture modification, increasing shelf-life, etc. in different horticultural crops.

Strategies for Improvement of Horticultural Crops against Abiotic Stresses

Strategies for Improvement of Horticultural Crops against Abiotic Stresses

Somaclonal variations and their applications in horticultural crops improvement.

The advancements made in tissue culture techniques has made it possible to regenerate various horticultural species in vitro as micropropagation protocols for commercial scale multiplication are available for a wide range of crops. Clonal propagation and preservation of elite genotypes, selected for their superior characteristics, require high degree of genetic uniformity amongst the regenerated plants. However, plant tissue culture may generate genetic variability, i.e., somaclonal variations as a result of gene mutation or changes in epigenetic marks. The occurrence of subtle somaclonal variation is a drawback for both in vitro cloning as well as germplasm preservation. Therefore, it is of immense significance to assure the genetic uniformity of in vitro raised plants at an early stage. Several strategies have been followed to ascertain the genetic fidelity of the in vitro raised progenies comprising morpho-physiological, biochemical, cytological and DNA-based molecular markers approaches. Somaclonal variation can pose a serious problem in any micropropagation program, where it is highly desirable to produce true-to-type plant material. On the other hand, somaclonal variation has provided a new and alternative tool to the breeders for obtaining genetic variability relatively rapidly and without sophisticated technology in horticultural crops, which are either difficult to breed or have narrow genetic base. In the present paper, sources of variations induced during tissue culture cycle and strategies to ascertain and confirm genetic fidelity in a variety of in vitro raised plantlets and potential application of variants in horticultural crop improvement are reviewed.

Application of somatic hybridization for the improvement of horticultural crops

<p>Somatic hybridization (SH) using protoplast fusion is a promising tool to produce symmetrical and asymmetrical polyploidy somatic hybrids in many agricultural crops. The technique of SH could facilitate conventional breeding by providing of novel lines so as to use them as elite breeding materials in conventional crosses for both scion and rootstock improvement. Further, SH can overcome those problems associated with sexual hybridization viz., sexual incompatibility, nucellar embryogenesis, and male/female sterility. Successful exploitation of SH in horticultural crops mainly comes from transfer of resistance genes for biotic and abiotic stresses from related species in several horticultural crops, <em>viz</em>., citrus, potato, brinjal, tomato, mango, avocado, banana, strawberry, pear, cherry etc. Unlike transgenic technology, SH is not affected by legal formalities and able to transfer uncloned multiple genes. However, certain boundaries and limitations of SH restricts its use over sexual hybridization but, envisage of new genomic technologies providing better insight into the plant genomes will increase the potentiality of SH in betterment of agriculture.</p>

Genome-editing technologies and their potential application in horticultural crop breeding.

Plant breeding, one of the oldest agricultural activities, parallels human civilization. Many crops have been domesticated to satisfy human's food and aesthetical needs, including numerous specialty horticultural crops such as fruits, vegetables, ornamental flowers, shrubs, and trees. Crop varieties originated through selection during early human civilization. Other technologies, such as various forms of hybridization, mutation, and transgenics, have also been invented and applied to crop breeding over the past centuries. The progress made in these breeding technologies, especially the modern biotechnology-based breeding technologies, has had a great impact on crop breeding as well as on our lives. Here, we first review the developmental process and applications of these technologies in horticultural crop breeding. Then, we mainly describe the principles of the latest genome-editing technologies and discuss their potential applications in the genetic improvement of horticultural crops. The advantages and challenges of genome-editing technologies in horticultural crop breeding are also discussed.

Temporal and spatial control of gene expression in horticultural crops.

Biotechnology provides plant breeders an additional tool to improve various traits desired by growers and consumers of horticultural crops. It also provides genetic solutions to major problems affecting horticultural crops and can be a means for rapid improvement of a cultivar. With the availability of a number of horticultural genome sequences, it has become relatively easier to utilize these resources to identify DNA sequences for both basic and applied research. Promoters play a key role in plant gene expression and the regulation of gene expression. In recent years, rapid progress has been made on the isolation and evaluation of plant-derived promoters and their use in horticultural crops, as more and more species become amenable to genetic transformation. Our understanding of the tools and techniques of horticultural plant biotechnology has now evolved from a discovery phase to an implementation phase. The availability of a large number of promoters derived from horticultural plants opens up the field for utilization of native sequences and improving crops using precision breeding. In this review, we look at the temporal and spatial control of gene expression in horticultural crops and the usage of a variety of promoters either isolated from horticultural crops or used in horticultural crop improvement.

A strategy for developing representative germplasm sets for systematic QTL validation, demonstrated for apple, peach, and sweet cherry

Horticultural crop improvement would benefit from a standardized, systematic, and statistically robust procedure for validating quantitative trait loci (QTLs) in germplasm relevant to breeding programs. Here, we describe and demonstrate a strategy for developing reference germplasm sets of perennial, clonally propagated crops, especially those with long juvenile periods. Germplasm is chosen to efficiently represent important members of larger pedigree-connected genepools. To facilitate validation of multiple QTLs, genome-wide representation of alleles is optimized for designated important breeding parents (IBPs) by estimating average allelic representation in relatives. The strategy and arising principles were demonstrated in a simulated germplasm set. Strong statistical power can be achieved with a carefully chosen germplasm set composed of IBPs, their numerous unselected progenies and close relatives, and all available founders and intermediate ancestors. Crop Reference Sets were developed in the marker-assisted breeding (MAB)-enabling “RosBREED” project as a base resource for QTL validation in US breeding germplasm of apple (Malus × domestica), peach (Prunus persica), and sweet cherry (Prunus avium) consisting of 467, 452, and 268 individuals, respectively. These sets adequately represent the most designated IBPs, have distinct advantages for QTL validation over other germplasm arrangements of equal size, and are recommended as a base resource for QTL validation by breeders of these US crops. The strategy described here can be used to develop efficient reference germplasm sets suiting other breeding genepools or to calculate the statistical power for QTL validation of germplasm sets already established.