Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses

Genotype-by-Environment Effects of Cis-Variations in the Atgl Promoter Mediate the Divergent Pattern of Phenotypic Plasticity for Temperature Adaptation in Two Congeneric Oyster Species

Phenotypic plasticity plays an essential role in adaptive evolution. However, the molecular mechanisms of how genotype-by-environment interaction (G × E) effects shape phenotypic plasticity in marine organisms remain poorly understood. The crucial temperature-responsive trait triacylglycerol (TAG) content and its major gene adipose triglyceride lipase (Atgl) expression have divergent plastic patterns in two congeneric oyster species (Crassostrea gigas and Crassostrea angulata) to adapt to relative-cold/northern and relative-warm/southern habitats, respectively. In this study, eight putative loci were identified in the Atgl promoter region (cis-variations) between wild C. gigas and C. angulata that exhibited differential environmental responsiveness (G × E). The G and G × E effects of each locus were further dissected by measuring the Atgl gene expression of different genotypes in response to temperature changes at the cellular and organismal levels. Two transcription factors, non-environmentally responsive non-POU domain-containing octamer-binding protein (Nono) and environmentally responsive heterogeneous nuclear ribonucleoprotein K (Hnrnpk), were screened for binding to g.-1804 (G locus) and g.-1919 (G + G × E locus), respectively. The specificity of Nono binding to the C. angulata allele mediated the G effects of g.-1804, and the lower environmental sensitivity of Hnrnpk in C. angulata mediated the G × E effects of g.-1919, jointly regulating the trade-offs between higher constitutive and lower plastic expression of Atgl gene expression in C. angulata. This study served as an experimental case to reveal how the genetic variations with G and (or) G × E effects propagate into the divergent pattern of plasticity in environmental adaptive traits, which provides new insights into predicting the adaptability of marine organisms to future climate changes.

Diversity of Major Yield Traits and Nutritional Components Among Greenhouse Grown Chickpea (Cicer arietinum L.) Breeding Lines, Landraces, and Cultivars of Different Origins

This study analyzed the diversity of major yield traits and nutritional components across 122 chickpea breeding lines, cultivars, and landraces of different origins. All parameters showed significant variations, with a variance ranging from 4.61% in days to maturity (DM) to 43.04% in oleic acid. Six accessions, including CP021, CP022, CP026, CP037, CP066, and CP109, outperformed in yield traits and nutritional value. Origin significantly affected all phenotypic traits except total fatty acid contents, with Indian and Ukrainian accessions demonstrating contrasting performances. Most traits, except for the number of seeds per pod (SPP), palmitic acid, and total fatty acid contents, differed significantly among breeding lines, cultivars, and landraces. Breeding lines were the earliest to flower and to mature with average days to flowering (DF) of 50.23 days and DM of 101.50 days. They also had the highest average SPP, number of pods per plant (PPP), total seeds per plant (TSPP), total protein, crude fiber, dietary fiber, linoleic acid, and linolenic acid contents making them preferable for high yield and nutrition. Hierarchical cluster analysis classified the chickpea accessions into seven clusters, showing significant variations in yield traits and nutritional components. Principal component and Pearson's correlation analyses indicated positive correlations between DM and DF, and between SPP, PPP, and TSPP. Nutritional components also displayed varying associations, with a notable negative correlation between oleic and linoleic acids, the two essential fatty acids. Overall, this study showed the diversity of key phenotypic traits in chickpea breeding lines, cultivars, and landraces of different origins. The significant effects of genotype and origin differences on these traits could be used as a basis for future metabolomics and genomics research.

Clinical value of macrogenome next-generation sequencing on infections

Intracranial infection (ICI) is a frequent and serious complication after neurosurgery. Macrogenome next-generation sequencing (mNGS) technology can provide reference for clinical diagnosis and treatment of ICI. This work aimed to explore the application value of mNGS technology in analyzing the clinical characteristics of human immunodeficiency virus (HIV) infection and ICI after neurosurgery. A total of 60 patients with ICI were enrolled as the research objects, all patients underwent routine cerebrospinal fluid analysis and traditional pathogen detection, followed by mNGS genome analysis. Using clinical diagnosis of ICI as the gold standard, the sensitivity, specificity, positive predictive value, and negative predictive value for both detection methods were calculated. Receiver operating characteristic curves were constructed to assess the area under the curve (AUC) for evaluating the clinical value of mNGS in suspected intracranial infectious pathogen diagnosis. Results showed a positivity rate of 71.67% (43 cases) with mNGS compared to 28.33% (17 cases) with traditional pathogen detection methods, demonstrating a significant difference (P < 0.05). The sensitivity of mNGS for detecting ICIs was 83.7%, significantly higher than the 34.88% observed with traditional methods (P < 0.05). The pathogen detection rate of mNGS was higher than traditional methods (P = 0.002), with an AUC of 0.856 (95% CI: 0.638-0.967), significantly greater than the AUC of 0.572 (95% CI: 0.350-0.792) for traditional methods (P < 0.05). mNGS successfully identified microorganisms such as Cryptococcus, Propionibacterium, Staphylococcus, Corynebacterium, Micrococcus, and Candida associated with ICIs. These findings underscore the clinical applicability of mNGS technology in analyzing the characteristics of HIV infection and ICI post-neurosurgical procedures. This technology enables more accurate diagnosis and treatment of ICIs, providing valuable insights for developing effective therapeutic strategies.

Extraction, Modification, Biofunctionality, and Food Applications of Chickpea (Cicer arietinum) Protein: An Up-to-Date Review

Plant-based proteins have gained popularity in the food industry as a good protein source. Among these, chickpea protein has gained significant attention in recent times due to its high yields, high nutritional content, and health benefits. With an abundance of essential amino acids, particularly lysine, and a highly digestible indispensable amino acid score of 76 (DIAAS), chickpea protein is considered a substitute for animal proteins. However, the application of chickpea protein in food products is limited due to its poor functional properties, such as solubility, water-holding capacity, and emulsifying and gelling properties. To overcome these limitations, various modification methods, including physical, biological, chemical, and a combination of these, have been applied to enhance the functional properties of chickpea protein and expand its applications in healthy food products. Therefore, this review aims to comprehensively examine recent advances in Cicer arietinum (chickpea) protein extraction techniques, characterizing its properties, exploring post-modification strategies, and assessing its diverse applications in the food industry. Moreover, we reviewed the nutritional benefits and sustainability implications, along with addressing regulatory considerations. This review intends to provide insights into maximizing the potential of Cicer arietinum protein in diverse applications while ensuring sustainability and compliance with regulations.

Genetic mapping and transcriptome profiling of a chickpea (Cicer arietinum L.) mutant identifies a novel locus (CaEl) regulating organ size and early vigor

Chickpea is among the top three legumes produced and consumed worldwide. Early plant vigor, characterized by good germination and rapid seedling growth, is an important agronomic trait in many crops including chickpea, and shows a positive correlation with seed size. In this study, we report a gamma-ray-induced chickpea mutant with a larger organ and seed size. The mutant (elm) exhibits increased early vigor and contains higher proline that contributes to a better tolerance under salt stress at germination, seedling, and early vegetative phase. The trait is governed as monogenic recessive, with wild-type allele being incompletely dominant over the mutant. Genetic mapping of this locus (CaEl) identified it as a previously uncharacterized gene (101503252) in chromosome 1 of the chickpea genome. There is a deletion of this gene in the mutant with a complete loss of expression. In silico analysis suggests that the gene is present as a single copy in chickpea and related legumes of the galegoid clade. In the mutant, cell division and expansion are affected. Transcriptome profiling identified differentially regulated transcripts related to cell division, expansion, cell wall organization, and metabolism in the mutant. The mutant can be exploited in chickpea breeding programs for increasing plant vigor and seed size.

SSR Genotyping and Marker-Trait Association with Yield Components in a Kazakh Germplasm Collection of Chickpea (Cicer arietinum L.)

Genetic diversity and marker-trait association with yield-related components were assessed in 39 chickpea accessions from a germplasm collection with either spring or autumn-sown seeds in South-Eastern Kazakhstan. Chickpea accessions originated from Azerbaijan, Germany, Kazakhstan, Moldova, Russia, Türkiye, Ukraine, Syria, and the International Center for Agricultural Research in the Dry Areas (ICARDA). Eleven SSR markers were used for molecular genotyping. Yield and yield components were evaluated in nine traits in experiments with spring and autumn seed sowing. The number of alleles of polymorphic markers varied from 2 to 11. The greatest polymorphism was found in the studied chickpea genotypes using SSR marker TA22 (11 alleles), while NCPGR6 and NCPGR12 markers were monomorphic. In the studied chickpea accessions, unique alleles of the SSR loci TA14, TA46, TA76s, and TA142 were found that were not previously described by other authors. An analysis of correlation relationships between yield-related traits in chickpea revealed the dependence of yield on plant height, branching, and the setting of a large number of beans. These traits showed maximal values in experiments with chickpea plants from autumn seed sowing. An analysis of the relationship between the SSR markers applied and morphological yield-related traits revealed several informative markers associated with important traits, such as plant height, height to first pod, number of branches, number of productive nodes, number of pods per plant, hundred seed weight, seed weight per plant, and seed yield.

Prioritization of Physio-Biochemical Selection Indices and Yield-Attributing Traits toward the Acquisition of Drought Tolerance in Chickpea (Cicer arietinum L.)

Chickpea is widely grown in rainfed areas of developing countries because of its nutritional abundance and adaptability. To overcome the environmental effect of drought on yield, a characteristic-linked selection strategy is proved as well-thought-out and advantageous for the development of drought-tolerant cultivars. To precisely understand the contribution of various physio-biochemical and yield-attributing traits toward drought tolerance in chickpea (Cicer arietinum L.), forty chickpea genotypes were evaluated in the years 2020-2021 and 2021-2022 under normal irrigated as well as drought-stressed conditions. Among the studied genotypes, genotype ICC4958 retained the highest chl content (0.55 mg g-1 FW), minimal electrolyte leakage, and superoxide dismutase (1.48 U/mg FW) and peroxidase (2.21 µmol/min/g FW) activities while cultivar JG11 maintained the maximum relative water content and proline accumulation. The principal-component-based biplots prioritized the physio-biochemical and yield-accrediting characteristics based on their association significance and contribution to terminal drought tolerance. Under drought stress, grain yield per plant was depicted to have a strongly positive association with canopy temperature depression, catalase, superoxide dismutase, and peroxidase activities as well as total soluble sugar, proline, and chlorophyll content, along with the numbers of pods and biological yield per plant. These identified physio-biochemical and yield-attributing traits can be further deployed to select drought-tolerant chickpea genotypes for the breeding of climate-smart chickpea genotypes.

Embryo Rescue in Plant Breeding

Embryo rescue (ER) techniques are among the oldest and most successful in vitro tissue culture protocols used with plant species. ER refers to a series of methods that promote the development of an immature or lethal embryo into a viable plant. Intraspecific, interspecific, or intergeneric crosses allow the introgression of important alleles of agricultural interest from wild species, such as resistance or tolerance to abiotic and biotic stresses or morphological traits in crops. However, pre-zygotic and post-zygotic reproductive barriers often present challenges in achieving successful hybridization. Pre-zygotic barriers manifest as incompatibility reactions that hinder pollen germination, pollen tube growth, or penetration into the ovule occurring in various tissues, such as the stigma, style, or ovary. To overcome these barriers, several strategies are employed, including cut-style or graft-on-style techniques, the utilization of mixed pollen from distinct species, placenta pollination, and in vitro ovule pollination. On the other hand, post-zygotic barriers act at different tissues and stages ranging from early embryo development to the subsequent growth and reproduction of the offspring. Many crosses among different genera result in embryo abortion due to the failure of endosperm development. In such cases, ER techniques are needed to rescue these hybrids. ER holds great promise for not only facilitating successful crosses but also for obtaining haploids, doubled haploids, and manipulating the ploidy levels for chromosome engineering by monosomic and disomic addition as well substitution lines. Furthermore, ER can be used to shorten the reproductive cycle and for the propagation of rare plants. Additionally, it has been repeatedly used to study the stages of embryonic development, especially in embryo-lethal mutants. The most widely used ER procedure is the culture of immature embryos taken and placed directly on culture media. In certain cases, the in vitro culture of ovule, ovaries or placentas enables the successful development of young embryos from the zygote stage to maturity.

Potentials of genotypes, morpho-physio-biochemical traits, and growing media on shelf life and future prospects of gene editing in tomatoes

Background: To study the genetic basis of the impact of genotypes and morpho-physio-biochemical traits under different organic and inorganic fertilizer doses on the shelf life attribute of tomatoes, field experiments were conducted in randomized block designs during the rabi seasons of 2018-2019 and 2019-2020. The experiment comprised three diverse nutrient environments [T1-organic; T2-inorganic; T3-control (without any fertilizers)] and five tomato genotypes with variable growth habits, specifically Angoorlata (Indeterminate), Avinash-3 (semi-determinate), Swaraksha (semi-determinate), Pusa Sheetal (semi-determinate), and Pusa Rohini (determinate). Results: The different tomato genotypes behaved apparently differently from each other in terms of shelf life. All the genotypes had maximum shelf life when grown in organic environments. However, the Pusa Sheetal had a maximum shelf life of 8.35 days when grown in an organic environment and showed an increase of 12% over the control. The genotype Pusa Sheetal, organic environment and biochemical trait Anthocyanin provides a promise as potential contributor to improve the keeping quality of tomatoes. Conclusion: The genotype Pusa Sheetal a novel source for shelf life, organic environment, and anthocyanin have shown promises for extended shelf life in tomatoes. Thus, the identified trait and genotype can be utilized in tomato improvement programs. Furthermore, this identified trait can also be targeted for its quantitative enhancement in order to increase tomato shelf life through a genome editing approach. A generalized genome editing mechanism is consequently suggested.

Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella

Prunus tenella is a rare and precious relict plant in China. It is an important genetic resource for almond improvement and an indispensable material in ecological protection and landscaping. However, the research into molecular breeding and genetic evolution has been severely restricted due to the lack of genome information. In this investigation, we created a chromosome-level genomic pattern of P. tenella, 231 Mb in length with a contig N50 of 18.1 Mb by Hi-C techniques and high-accuracy PacBio HiFi sequencing. The present assembly predicted 32,088 protein-coding genes, and an examination of the genome assembly indicated that 94.7% among all assembled transcripts were alignable to the genome assembly; most (97.24%) were functionally annotated. By phylogenomic genome comparison, we found that P. tenella is an ancient group that diverged approximately 13.4 million years ago (mya) from 13 additional closely related species and about 6.5 Mya from the cultivated almond. Collinearity analysis revealed that P. tenella is highly syntenic and has high sequence conservation with almond and peach. However, this species also exhibits many presence/absence variants. Moreover, a large inversion at the 7588 kb position of chromosome 5 was observed, which may have a significant association with phenotypic traits. Lastly, population genetic structure analysis in eight different populations indicated a high genetic differentiation among the natural distribution of P. tenella. This high-quality genome assembly provides critical clues and comprehensive information for the systematic evolution, genetic characteristics, and functional gene research of P. tenella. Moreover, it provides a valuable genomic resource for in-depth study in protection, developing, and utilizing P. tenella germplasm resources.

Unclasping potentials of genomics and gene editing in chickpea to fight climate change and global hunger threat

Genomics and genome editing promise enormous opportunities for crop improvement and elementary research. Precise modification in the specific targeted location of a genome has profited over the unplanned insertional events which are generally accomplished employing unadventurous means of genetic modifications. The advent of new genome editing procedures viz; zinc finger nucleases (ZFNs), homing endonucleases, transcription activator like effector nucleases (TALENs), Base Editors (BEs), and Primer Editors (PEs) enable molecular scientists to modulate gene expressions or create novel genes with high precision and efficiency. However, all these techniques are exorbitant and tedious since their prerequisites are difficult processes that necessitate protein engineering. Contrary to first generation genome modifying methods, CRISPR/Cas9 is simple to construct, and clones can hypothetically target several locations in the genome with different guide RNAs. Following the model of the application in crop with the help of the CRISPR/Cas9 module, various customized Cas9 cassettes have been cast off to advance mark discrimination and diminish random cuts. The present study discusses the progression in genome editing apparatuses, and their applications in chickpea crop development, scientific limitations, and future perspectives for biofortifying cytokinin dehydrogenase, nitrate reductase, superoxide dismutase to induce drought resistance, heat tolerance and higher yield in chickpea to encounter global climate change, hunger and nutritional threats.

Prospects of microgreens as budding living functional food: Breeding and biofortification through OMICS and other approaches for nutritional security

Nutrient deficiency has resulted in impaired growth and development of the population globally. Microgreens are considered immature greens (required light for photosynthesis and growing medium) and developed from the seeds of vegetables, legumes, herbs, and cereals. These are considered "living superfood/functional food" due to the presence of chlorophyll, beta carotene, lutein, and minerals like magnesium (Mg), Potassium (K), Phosphorus (P), and Calcium (Ca). Microgreens are rich at the nutritional level and contain several phytoactive compounds (carotenoids, phenols, glucosinolates, polysterols) that are helpful for human health on Earth and in space due to their anti-microbial, anti-inflammatory, antioxidant, and anti-carcinogenic properties. Microgreens can be used as plant-based nutritive vegetarian foods that will be fruitful as a nourishing constituent in the food industryfor garnish purposes, complement flavor, texture, and color to salads, soups, flat-breads, pizzas, and sandwiches (substitute to lettuce in tacos, sandwich, burger). Good handling practices may enhance microgreens'stability, storage, and shelf-life under appropriate conditions, including light, temperature, nutrients, humidity, and substrate. Moreover, the substrate may be a nutritive liquid solution (hydroponic system) or solid medium (coco peat, coconut fiber, coir dust and husks, sand, vermicompost, sugarcane filter cake, etc.) based on a variety of microgreens. However integrated multiomics approaches alongwith nutriomics and foodomics may be explored and utilized to identify and breed most potential microgreen genotypes, biofortify including increasing the nutritional content (macro-elements:K, Ca and Mg; oligo-elements: Fe and Zn and antioxidant activity) and microgreens related other traits viz., fast growth, good nutritional values, high germination percentage, and appropriate shelf-life through the implementation of integrated approaches includes genomics, transcriptomics, sequencing-based approaches, molecular breeding, machine learning, nanoparticles, and seed priming strategiesetc.

Mining legume germplasm for genetic gains: An Indian perspective

Legumes play a significant role in food and nutritional security and contribute to environmental sustainability. Although legumes are highly beneficial crops, it has not yet been possible to enhance their yield and production to a satisfactory level. Amid a rising population and low yield levels, per capita average legume consumption in India has fallen by 71% over the last 50 years, and this has led to protein-related malnutrition in a large segment of the Indian population, especially women and children. Several factors have hindered attempts to achieve yield enhancement in grain legumes, including biotic and abiotic pressures, a lack of good ideotypes, less amenability to mechanization, poorer responsiveness to fertilizer input, and a poor genetic base. Therefore, there is a need to mine the approximately 0.4 million ex situ collections of legumes that are being conserved in gene banks globally for identification of ideal donors for various traits. The Indian National Gene Bank conserves over 63,000 accessions of legumes belonging to 61 species. Recent initiatives have been undertaken in consortia mode with the aim of unlocking the genetic potential of ex situ collections and conducting large-scale germplasm characterization and evaluation analyses. We assume that large-scale phenotyping integrated with omics-based science will aid the identification of target traits and their use to enhance genetic gains. Additionally, in cases where the genetic base of major legumes is narrow, wild relatives have been evaluated, and these are being exploited through pre-breeding. Thus far, >200 accessions of various legumes have been registered as unique donors for various traits of interest.