Crop Improvement Research Articles

Impact of RNA Enzymes and RNA Protein Complexes in Unleashing RNAInterference for Manyfold Crop Improvements: A Review

RNA interference, which enables more accurate downregulation of gene expression without interfering with the expression of various genes, is a beneficial instrument for gene silencing and a potential gene regulatory strategy in functional genomics that has a big impact on crop progress. Small interfering RNA molecules swift up the RNAi gene silencing machinery, effectually suppressing a target gene. Subsequently transgene proteins not present from genetically modified RNAi plants, it has a sum of rewards over orthodox transgenic methods. Dicer, Drosha which are RNA enzymes, along with protein complexes, RISC and Argonaute, institute at the epicenter of this technology. These explicit RNA binding proteins and ribonucleases regulate the synthesis and production of tiny regulating RNAs. Several latent usages for this ground-breaking process in agriculture have been identified for improving crops, such as the construction of disease-resistant, biotic or abiotic, high-yielding, stress-tolerant and exclusive assortments; enhancement of nutritional quality; removal of allergens and toxins; and postponing the ripening of fruits and vegetables for extended storage periods. This ground-breaking procedure has the latent to be further utilized to pave the way for the creation of environmentally friendly biotech methods for crop protection and enhancement. Improving research and development activities in this auspicious field is imperative to ensure the efficient appropriate and safe application of these instruments as enduring remedies for agricultural enhancement.

Species identification and pollination biology of an economically important true halophyte, Salicornia brachiata Roxb.

Members of the genus Salicornia have gained a global attraction due to their ability to thrive under high saline conditions and as potential candidates in saline agriculture. However, it has been a taxonomically challenging genus for decades since the members show plastic responses to extreme environmental conditions and due to incongruences between morphological and molecular identification methods. While only a handful of commercially grown Salicornia species are fully described, most of the species including S. brachiata, a native species in the Indian sub-continent, Myanmar, and Sri Lanka are poorly described. With the potentials in adapting S. brachiata in saline agriculture, the aim of this study was to establish a morphology and DNA barcode-based species delineation system and to study pollination biology for future crop improvement projects. Tentatively identified S. brachiata plant samples were collected from two populations in Sri Lanka and completely described. GenBank lacked authenticated barcode data for S. brachiata except for one chloroplast genome to which the matK sequence obtained in the present study matched with 100% identity. For the first time, well defined sequences of three barcode regions, ITS, ETS and matK, of S. brachiata were made available for accurate species identification. Reproductive dynamics in different parts of the inflorescence was studied. A facultative xenogamous mating system was recorded for the first time in the genus and while the lower florets in the cladode showed a preference towards outcrossing, the upper florets displayed adaptations for selfing. Data could be effectively utilized in future Salicornia breeding programs.

Methyltransferase 1 (OsMTS1) interacts with hydroxycinnamoyltransferase 1 (OsHCT1) and promotes heading by upregulating heading date 1 (Hd1)

Heading date determines the distribution and yield potentials of rice, and is an ideal target for crop improvement using CRISPR/Cas9 genome editing system. In this study, we reported the loss-of-function of Methyltransferase 1 (MTS1), which promotes heading in rice. Here, we constructed knockouts and overexpression transgenic plants of OsMTS1 in ZH8015 and Nipponbare (NIP) for the first time to validate its heading date function in rice subspecies Oryza sativa ssp. Indica and O. Sativa ssp. Japonica, respectively. The OsMTS1 knockouts in ZH8015 and NIP rice significantly promoted heading date under both natural short days (NSD) and natural long days (NLD) conditions, while the overexpression of OsMTS1 significantly delayed heading date in ZH8015 and NIP rice under both NSD and NLD conditions. Likewise, the complementation transgenic plants displayed late heading date phenotype. OsMTS1 repressed heading through up-regulating Heading date 1 (Hd1) and down-regulating Early heading date 1 (Ehd1) and Heading date 3a (Hd3a). The OsMTS1 protein interacted with OsHCT1 proteins using a yeast two-hybrid (Y2H) assay. The Y2H and overexpression confirmed that OsMTS1 interacted with OsHCT1, which delayed heading by 4.7 days under NLD. Taken together, CRISPR/Cas9, genetic complementation, and overexpression results validated that OsMTS1 represses heading in Indica and Japonica rice under both NLD and NSD conditions. These results demonstrated that OsMTS1 is a useful target for breeding early maturing rice varieties by CRISPR/Cas9 gene editing of the functional allele.

Ensemble and optimization algorithm in support vector machines for classification of wheat genotypes.

This study aimed to classifying wheat genotypes using support vector machines (SVMs) improved with ensemble algorithms and optimization techniques. Utilizing data from 302 wheat genotypes and 14 morphological attributes to evaluate six SVM kernels: linear, radial basis function (RBF), sigmoid, and polynomial degrees 1-3. Various optimization methods, including grid search, random search, genetic algorithms, differential evolution, and particle swarm optimization, were used. The radial basis function kernel achieves the highest accuracy at 93.2%, and the weighted accuracy ensemble further improves it to 94.9%. This study shows the effectiveness of these methods in agricultural research and crop improvement. Notably, optimization-based SVM classification, particularly with particle swarm optimization, saw a significant 1.7% accuracy gain in the test set, reaching 94.9% accuracy. These findings underscore the efficacy of RBF kernels and optimization techniques in improving wheat genotype classification accuracy and highlight the potential of SVMs in agricultural research and crop improvement endeavors.

Genetic Variability, Heritability, Genetic Advance, Path Coefficient Analysis, and Inter-Character Relationships in Colocynth (Citrullus colocynthis [L.] Schrad.) from Southeastern Villages of the Benin Republic

Genetic improvement of crops for important traits requires reliable estimates of genetic variability. heritability and genetic advance of intending parent materials to identify traits useful in planning an efficient breeding program through selection. Hence, the effectiveness of genetic improvement of a crop depends on the variability in the morpho-agronomic traits of individual genotypes. Understanding the variation that exists will allow the breeder to determine strategies to be adopted in his breeding program. The objectives of the present study were to estimate the magnitude of genetic variability and advance, heritability and inter-character relationships by simple correlations and path coefficient analysis in 40 local colocynth genotypes from Southeastern Benin. The experiment was carried out in a randomized complete block design with three replications in three locations for three years. 34 morpho-agronomic traits were observed in each genotype. Analysis of variance revealed that effects of genotype, genotype by year or location and genotype by year by location interactions were significant (p ≤ 0.01 or 0.05) for all the characters. Phenotypic coefficients of variation (PCV) values were relatively greater than genotypic coefficients of variation (GCV) for all traits. High magnitude of phenotypic and genotypic coefficients of variation as well as high heritability along with high genetic advance were recorded particularly for qualitative traits. All yield components, except time to emergence, time to tailspins, leaf limb width, fruit number per plant, fruit width, seed length, seed tegument percentage and stem pubescence texture, had significant and positive correlations with yield attributes represented by thousand-seed weight (TSW) and seed number per plant (SNP). Path coefficient analysis indicated that all the characters (except leaf pubescence texture, stem pubescence texture, fruit design produced by secondary skin color and male flower size) had positive direct effects on TSW and partly SNP. Results suggested that most of the 34 quantitative and qualitative traits studied could be effectively used as selection criteria in the breeding program of Citrullus colocynthis varieties with high yield.

Marker Assisted Selection (MAS) and It's Application in Vegetable Crop Improvement

Vegetable crop breeding has changed dramatically since the early 1980s due to technological breakthroughs, especially high-throughput sequencing and molecular marker technologies, which have made it possible to sequence many plant genomes, create dense genetic maps, and identify important genes and QTLs linked to traits like yield and disease resistance. ..These instruments have expedited genetic research and breeding programs in crops including tomato, pepper, eggplant, and cucumber, establishing marker-assisted selection (MAS) as a crucial component of contemporary breeding. The use of these technologies has improved crop characteristics significantly and is still influencing the development of vegetable crops in the future. .. For instance, in the majority of private and public tomato breeding projects, major-gene disease resistance traits like verticillium wilt and anthracnose are selected for using PCR-based markers such as SCAR and CAPS.Bs5 and Bs6 have broad-spectrum resistance against Xanthomonas spp. against chilli leaf spot thanks to marker-assisted gene pyramiding. Major QTLs associated to SSR marker CAMS451 on chromosome 1 (from Capsicum accession LS2341) and marker ID10-194305124 on chromosome 10 (from C. annuum BVRC1) have been mapped for resistance to Ralstonia bacterial wilt.Constantly searching crop germplasm for new resistance genes or alleles is essential to diversify the gene pool and stop resistance from breaking down. By using marker-assisted selection (MAS), it is possible to combine genes for resistance to different pathogens or several sources of resistance to the same pathogen to create novel cultivars.

Evolution of plant metabolism: the state-of-the-art.

Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and prokaryotic ancestors and further diversified by the unprecedentedly high rates of gene duplication and functionalization experienced in land plants. Unlike prokaryotic microbes, which display frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced relatively few gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner using existing networks as a starting point and under various evolutionary constraints. That said, until recently, the evolution of only a handful of metabolic traits had been extensively investigated and as such, the evolution of metabolism has received a fraction of the attention of, the evolution of development, for example. Advances in metabolomics and next-generation sequencing have, however, recently led to a deeper understanding of how a wide range of plant primary and specialized (secondary) metabolic pathways have evolved both as a consequence of natural selection and of domestication and crop improvement processes. This article is part of the theme issue 'The evolution of plant metabolism'.

Crop Improvement of Moringa oleifera L. through Genotype Screening for the Development of Clonal Propagation Techniques of High-Yielding Clones in Malaysia.

Moringa oleifera L. is a valuable multipurpose tree species widely planted for centuries due to its high medicinal value and antifungal, antiviral, antidepressant, and anti-inflammatory properties in the food industry. However, its cultivation is hindered by production constraints such as the unavailability of planting material and the inadequate number of high-yielding clones. Thus, a study was initiated to select high-yielding clones in terms of growth and chemical content for the mass propagation of superior moringa trees. Screening on high-yielding clones with high astragalin content was conducted through the high-performance liquid chromatography (HPLC) analysis of moringa leaf extract. Selected genotypes were evaluated for their anti-inflammatory potential through in vitro bioactivity assays of leaf methanol extract. The effects of the rooting hormone, rooting substrates, and size of the cutting on the rooting response of branch cuttings of moringa were investigated. Results found that samples collected from different ecological zones of Peninsular Malaysia show significant variation in terms of astragalin content. The extracts were observed to show considerable variation in biological activity against the pro-inflammatory enzymes. The size of the cuttings had significant effects on the rooting of the cuttings as longer cuttings with bigger diameters rooted better than shorter cuttings with smaller diameters. Several genotypes of M. oleifera with superior phenotypic characteristics and bioactive compounds have been identified. Factors affecting the rooting efficiency and optimal conditions of rooting are suggested, which provides valuable information for the propagation of the superior planting material of moringa. This effort will ensure the sustainable production and supply of good quality raw materials for the production of quality end-products for the food and pharmaceutical industry.

Comparative Proteomic Analysis of Wild and Cultivated Amaranth Species Seeds by 2-DE and ESI-MS/MS.

Amaranth is a promising staple food that produces seeds with excellent nutritional quality. Although cultivated species intended for grain production have interesting agronomic traits, relatively little is known about wild species, which can prosper in diverse environments and could be a rich genetic source for crop improvement. This work focuses on the proteomic comparison between the seeds of wild and cultivated amaranth species using polarity-based protein extraction and two-dimensional gel electrophoresis. Differentially accumulated proteins (DAPs) showed changes in granule-bound starch synthases and a wide range of 11S globulin isoforms. The electrophoretic profile of these proteins suggests that they may contain significant phosphorylation as post-translational modifications (PTMs), which were confirmed via immunodetection. These PTMs may impact the physicochemical functionality of storage proteins, with potential implications for seed agronomic traits and food system applications. Low-abundant DAPs with highly variable accumulation patterns are also discussed; these were involved in diverse molecular processes, such as genic regulation, lipid storage, and stress response.

Association Analysis Provides Insights into Molecular Evolution in Salt Tolerance during Tomato Domestication.

Salt stress impairs plant growth and development, generally resulting in crop failure. Tomato domestication gave rise to a dramatic decrease in salt tolerance caused by the genetic variability of the wild ancestors. However, the nature of artificial selection in reducing tomato salt tolerance remains unclear. Here, we generated and analyzed datasets on the survival rates and sodium (Na+) and potassium (K+) concentrations of hundreds of tomato varieties from wild ancestors to contemporary breeding accessions under high salinity. Genome-wide association studies (GWAS) revealed that natural variation in the promoter region of the putative K+ channel regulatory subunit-encoding gene KSB1 (potassium channel beta subunit in Solanum lycopersicum) is associated with survival rates and root Na+/K+ ratios in tomato under salt stress. This variation is deposited in tomato domestication sweeps and contributes to modified expression of KSB1 by salt-induced transcription factor SlHY5 in response to high salinity. We further found that KSB1 interacts with the K+ channel protein KSL1 to maintain cellular Na+ and K+ homeostasis, thus enhancing salt tolerance in tomato. Our findings reveal the crucial role of the SlHY5-KSB1-KSL1 module in regulating ion homeostasis and salt tolerance during tomato domestication, elucidating that selective pressure imposed by humans on the evolutionary process provides insights into further crop improvement.

Identification of a Novel Gene MtbZIP60 as a Negative Regulator of Leaf Senescence through Transcriptome Analysis in Medicago truncatula.

Leaves are the primary harvest portion in forage crops such as alfalfa (Medicago sativa). Delaying leaf senescence is an effective strategy to improve forage biomass production and quality. In this study, we employed transcriptome sequencing to analyze the transcriptional changes and identify key senescence-associated genes under age-dependent leaf senescence in Medicago truncatula, a legume forage model plant. Through comparing the obtained expression data at different time points, we obtained 1057 differentially expressed genes, with 108 consistently up-regulated genes across leaf growth and senescence. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses showed that the 108 SAGs mainly related to protein processing, nitrogen metabolism, amino acid metabolism, RNA degradation and plant hormone signal transduction. Among the 108 SAGs, seven transcription factors were identified in which a novel bZIP transcription factor MtbZIP60 was proved to inhibit leaf senescence. MtbZIP60 encodes a nuclear-localized protein and possesses transactivation activity. Further study demonstrated MtbZIP60 could associate with MtWRKY40, both of which exhibited an up-regulated expression pattern during leaf senescence, indicating their crucial roles in the regulation of leaf senescence. Our findings help elucidate the molecular mechanisms of leaf senescence in M. truncatula and provide candidates for the genetic improvement of forage crops, with a focus on regulating leaf senescence.

Ecogeographic Study of Ipomoea Species in Mauritius, Indian Ocean.

The wild relatives of crops play a critical role in enhancing agricultural resilience and sustainability by contributing valuable traits for crop improvement. Shifts in climatic conditions and human activities threaten plant genetic resources for food and agriculture (PGRFA), jeopardizing contributions to future food production and security. Studies and inventories of the extant agrobiodiversity, in terms of numbers and distribution patterns of species and their genetic diversity, are primordial for developing effective and comprehensive conservation strategies. We conducted an ecogeographic study on Ipomoea species and assessed their diversity, distribution, and ecological preferences across different topographic, altitudinal, geographical, and climatic gradients, at a total of 450 sites across Mauritius. Species distribution maps overlaid with climatic data highlighted specific ecological distribution. Principal Component Analysis (PCA) revealed species distribution was influenced by geographical factors. Regional richness analyses indicated varying densities, with some species exhibiting localized distributions and specific ecological preferences while the other species showed diverse distribution patterns. Field surveys identified 14 species and 2 subspecies out of 21 species and 2 subspecies of Ipomoea reported in Mauritius. A gap in ex situ germplasm collections was observed and several species were identified as threatened. Further investigations and a more long-term monitoring effort to better guide conservation decisions are proposed.

The Future of Genetic Engineering in Crop Improvement and Food Production

The Future of Genetic Engineering in Crop Improvement and Food Production

Enhancing floral diversity: A review of mutation breeding techniques in flower crops

Flower crops encompass a wide range of ornamental annuals and perennials that are commercially cultivated for aesthetic appeal of their floral displays. Mutation induction has been used since the early 20th century to increase genetic diversity and develop new flower varieties with improved yield, quality, adaptation and market value. Mutation experiments have successfully created genetic variability and novel phenotypes in diverse floral species. Mutation breeding, which involves the induction of genetic variations via physical and chemical mutagens, has emerged as a vital technique for enhancing ornamental plant traits, such as flower color, shape, disease resistance and stress tolerance. It explores the types and applications of physical mutagens, such as gamma rays and ion beams and chemical mutagens, such as ethyl methane sulfonate (EMS) and sodium azide (SA). This review provides detailed insights into mutation breeding research conducted on major flower crops (e.g., rose, carnation, chrysanthemum and gerbera). This study also highlights achievements in the development of novel flower varieties, highlights the key challenges faced in mutation breeding programs and identifies gaps in research, particularly concerning the comparative efficacy of different mutagens, environmental impacts and genetic stability of mutated varieties. Furthermore, the impact of mutation breeding on the global flower market is discussed, emphasizing its role in expanding trait diversity, catering to niche markets and enhancing the commercial value of flower crops. Mutation breeding offers significant promise in the development of sustainable and climate-resilient ornamental crops that can meet the needs of emerging markets. This review serves as a valuable resource for students, scientists and breeders interested in leveraging mutation breeding for floral crop improvement.

Metabolic engineering-induced transcriptome reprogramming of lipid biosynthesis enhances oil composition in oat.

The endeavour to elevate the nutritional value of oat (Avena sativa) by altering the oil composition and content positions it as an optimal crop for fostering human health and animal feed. However, optimization of oil traits on oat through conventional breeding is challenging due to its quantitative nature and complexity of the oat genome. We introduced two constructs containing three key genes integral to lipid biosynthesis and/or regulatory pathways from Arabidopsis (AtWRI1 and AtDGAT1) and Sesame (SiOLEOSIN) into the oat cultivar 'Park' to modify the fatty acid composition. Four homozygous transgenic lines were generated with a transformation frequency of 7%. The expression of these introduced genes initiated a comprehensive transcriptional reprogramming in oat grains and leaves. Notably, endogenous DGAT, WRI1 and OLEOSIN genes experienced upregulation, while genes associated with fatty acid biosynthesis, such as KASII, SACPD and FAD2, displayed antagonistic expression patterns between oat grains and leaves. Transcriptomic analyses highlighted significant differential gene expression, particularly enriched in lipid metabolism. Comparing the transgenic oat plants with the wild type, we observed a remarkable increase of up to 34% in oleic acid content in oat grains. Furthermore, there were marked improvements in the total oil content in oat leaves, as well as primary metabolites changes in both oat grains and leaves, while maintaining homeostasis in the transgenic oat plants. These findings underscore the effectiveness of genetic engineering in manipulating oat oil composition and content, offering promising implications for human consumption and animal feeding through oat crop improvement programmes.

Identification and In silico analysis of fungal species from plant pathogens

The study aimed to identify, characterize and analyze fungal species associated with two economically significant plant species, Pongamia pinnata and Asclepias syriaca. Through molecular technique, fungal isolates were identified.The study employed DNA sequencing and phylogenetic analysis to classify the fungal isolates accurately. Furthermore, in silico analyses provided insights into the pathogenicity mechanisms and genetic diversity of the identified fungal species. Functional annotation and pathway analysis elucidated metabolic pathways associated with pathogenesis and host interactions. Overall, our integrated approach provides a comprehensive understand of fungal diversity, evolution, and pathogenicity in P.pinnata and A.syriaca. These findings lay the foundation of future research aimed at developing sustainable strategies for disease management and crop improvement in agricultural systems.

Identification of Key Traits for Yield Improvement in Brinjal Through Correlation and Path Coefficient Analysis

Brinjal (Solanum melongena L.), also known as poor man’s vegetable, is widely distributed and grown in almost all parts of India. The assessment of genetic variation, correlation and path analysis for various yield and yield attributing traits in the available germplasm is crucial for selecting superior genotypes with desired traits such as yield, fruit quality, disease resistance, and adaptability to environmental conditions, thereby enhancing the potential for further crop improvement through breeding. Therefore, the present study was conducted to assess the phenotypic correlation and path coefficient among various yield and yield related traits for 42 genotypes of brinjal at the Horticulture Research Centre, SVPUA&T, Meerut (U.P.), India, over two consecutive Kharif seasons in 2022 and 2023 in Randomized Complete Block Design with three replications. The analysis of variance indicated significant variability across all the traits examined. In general, magnitudes of genotypic correlation coefficient were higher than their corresponding phenotypic correlation coefficient, implying a significant inherent relationship in different pair of traits. Based on the correlation coefficient analysis, fruit yield per plant had significant and positive association with fruit yield per plot, fruit yield per hectare, fruit weight, number of fruits per plant, fruit length and fruit girth both at genotypic and phenotypic levels. Path coefficient analysis showed that the traits viz., number of fruits per plant, fruit weight, fruit girth and fruit length exhibited highest direct effects on fruit yield and also indirectly influenced by the other yield contributing traits of brinjal. It is concluded from the study that these traits may be used as key indices towards the direct selection of elite genotypes for the successful breeding programme for yield improvement of brinjal germplasm.

Modern Plant Breeding Techniques in Crop Improvement and Genetic Diversity: From Molecular Markers and Gene Editing to Artificial Intelligence—A Critical Review

With the development of new technologies in recent years, researchers have made significant progress in crop breeding. Modern breeding differs from traditional breeding because of great changes in technical means and breeding concepts. Whereas traditional breeding initially focused on high yields, modern breeding focuses on breeding orientations based on different crops’ audiences or by-products. The process of modern breeding starts from the creation of material populations, which can be constructed by natural mutagenesis, chemical mutagenesis, physical mutagenesis transfer DNA (T-DNA), Tos17 (endogenous retrotransposon), etc. Then, gene function can be mined through QTL mapping, Bulked-segregant analysis (BSA), Genome-wide association studies (GWASs), RNA interference (RNAi), and gene editing. Then, at the transcriptional, post-transcriptional, and translational levels, the functions of genes are described in terms of post-translational aspects. This article mainly discusses the application of the above modern scientific and technological methods of breeding and the advantages and limitations of crop breeding and diversity. In particular, the development of gene editing technology has contributed to modern breeding research.

Transforming farming: mutational breeding as a sustainable solution for crop improvement in the 21st century

Transforming farming: mutational breeding as a sustainable solution for crop improvement in the 21st century

Differential contributions of double-strand break repair pathways to DNA rearrangements following the irradiation of Arabidopsis seeds and seedlings with ion beams.

DNA rearrangements, including inversions, translocations, and large insertions/deletions (indels), are crucial for crop evolution, domestication, and improvement. The rearrangements are frequently induced by ion beams via the mis-repair of DNA double-strand breaks (DSBs). Unfortunately, how ion beam-induced DSBs are repaired has not been comprehensively analyzed and the mechanisms underlying DNA rearrangements remain unclear. In this study, clonal sectors originating from single mutated cells in carbon ion-irradiated plants were used for whole-genome sequencing analyses after Arabidopsis seeds and seedlings were irradiated. Comparative analyses of the induced mutations (e.g., size and frequency of indels and microhomology at the junctions of the rearrangements) in the irradiated materials suggested that the broken/rejoined DSB ends were more extensively processed in seedlings than in seeds. A mutation to canonical non-homologous end-joining (c-NHEJ), which is a DSB repair pathway with minimal processing of DSB ends, increased the sensitivity to ion beams more in the seeds than in the seedlings, which was consistent with the junction analysis results, indicative of the minor contribution of c-NHEJ to the carbon ion-induced DSB repair in seedlings. Considering the characteristics of the large templated insertions in irradiated seedlings, ion-beam-induced DSBs in seedlings are likely repaired primarily by a polymerase theta-mediated pathway. Polymerase theta-deficient seedlings were more sensitive to ion beams than the c-NHEJ-deficient seedlings, consistent with this hypothesis. This study revealed the key characteristics of ion beam-induced DSBs and the associated repair mechanisms related to the physiological status of the irradiated materials, with implications for elucidating the occurrence and induction of rearrangements.