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Social Impact Statement: The genetic variation of crop wild relatives will be key for our survival, as environmental change represents an increasing global threat for agriculture and food security. Cucurbita lundelliana and Cucurbita okeechobeensis subsp. martinezii are wild relatives of cultivated squashes and pumpkins that could be used for crop improvement. A genomic approach was used to characterize genetic resources in these taxa, that is, to identify candidate sites in the genome involved in responses to abiotic stress, and to understand the roles of gene flow and environmental differentiation in their divergence. This study highlights the importance of conserving these two species as phytogenetic resources for crop improvement. Summary: Crop wild relatives (CWR) are reservoirs of genetic diversity and they are important for the maintenance of crop evolutionary potential. Mexico is the centre of domestication and diversity for many CWR. The genus Cucurbita originated in America, where at least six independent domestication events took place. Nonetheless, Cucurbita CWR have been seldom studied. In the present study, we test the role of incomplete lineage sorting (ILS) and secondary contact in the divergence of C. okeechobeensis subsp. martinezii and C. lundelliana. Additionally, we seek to understand the role of environmental differentiation in their divergence.We obtained 1,638 single nucleotide polymorphisms (SNPs) for 107 individuals from the most recently diverged wild species in this genus, encompassing 25 localities of C. lundelliana and nine localities of C. okeechobeensis subsp. martinezii in Mexico.We found higher genetic variation in C. lundelliana (HE = 0.227) than in C. okeechobeensis subsp. martinezii (HE = 0.187). Each taxon constitutes a well‐differentiated genetic group, with an area of introgression in Pantanos de Centla. We found candidate loci associated to hydric and thermal stress, which could be valuable for crop improvement. Our study supported a scenario of ILS followed by secondary contact, where divergence was probably driven by Pleistocene climate change.These CWR represent important phytogenetic resources for crop improvement given their high levels of genetic variation and differentiation and their SNPs associated to different climatic variables. [ABSTRACT FROM AUTHOR]

Summary: Although forward‐genetics‐metabolomics methods such as mGWAS and mQTL have proven effective in providing myriad loci affecting metabolite contents, they are somehow constrained by their respective constitutional flaws such as the hidden population structure for GWAS and insufficient recombinant rate for QTL. Here, the combination of mGWAS and mQTL was performed, conveying an improved statistical power to investigate the flavonoid pathways in common wheat. A total of 941 and 289 loci were, respectively, generated from mGWAS and mQTL, within which 13 of them were co‐mapped using both approaches. Subsequently, the mGWAS or mQTL outputs alone and their combination were, respectively, utilized to delineate the metabolic routes. Using this approach, we identified two MYB transcription factor encoding genes and five structural genes, and the flavonoid pathway in wheat was accordingly updated. Moreover, we have discovered some rare‐activity‐exhibiting flavonoid glycosyl‐ and methyl‐transferases, which may possess unique biological significance, and harnessing these novel catalytic capabilities provides potentially new breeding directions. Collectively, we propose our survey illustrates that the forward‐genetics‐metabolomics approaches including multiple populations with high density markers could be more frequently applied for delineating metabolic pathways in common wheat, which will ultimately contribute to metabolomics‐assisted wheat crop improvement. [ABSTRACT FROM AUTHOR]

BACKGROUND: Food quality traits related to the genetics of yam influence the acceptability for its consumption. This study aimed at identifying genetic factors underlying sensory and textural quality attributes of boiled and pounded yam, the two dominant food products from white Guinea yam. RESULTS: A genome‐wide association study (GWAS) of a panel of 184 genotypes derived from five multi‐parent crosses population was conducted. The panel was phenotyped for the qualities of boiled and pounded yam using sensory quality and instrument‐based textural profile assays. The genotypes displayed significant variation for most of the attributes. Population differentiation and structure analysis using principal component analysis (PCA) and population structure‐based Bayesian information criteria revealed the presence of four well‐defined clusters. The GWAS results from a multi‐random mixed linear model with kinship and PCA used as covariate identified 13 single‐nucleotide polymorphic (SNP) markers significantly associated with the boiled and pounded yam food qualities. The associated SNP markers explained 7.51–13.04% of the total phenotypic variance with a limit of detection exceeding 4. CONCLUSION: Regions on chromosomes 7 and 15 were found to be associated with boiled and pounded yam quality attributes from sensory and instrument‐based assays. Gene annotation analysis for the regions of associated SNPs revealed co‐localization of several known putative genes involved in glucose export, hydrolysis and glycerol metabolism. Our study is one of the first reports of genetic factors underlying the boiled and pounded yam food quality to pave the way for marker‐assisted selection in white Guinea yam. © 2023 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

The demand for food goods is rising along with the world population growth, which is directly related to the yield of agricultural crops around the world. However, a number of environmental factors, including floods, salinity, moisture, and drought, have a detrimental effect on agricultural production around the world. Among all of these stresses, drought stress (DS) poses a constant threat to agricultural crops and is a significant impediment to global agricultural productivity. Its potency and severity are expected to increase in the future years. A variety of techniques have been used to generate drought-resistant plants in order to get around this restriction. Different crop plants exhibit specific traits that contribute to drought resistance (DR), such as early flowering, drought escape (DE), and leaf traits. We are highlighting numerous methods that can be used to overcome the effects of DS in this review. Agronomic methods, transgenic methods, the use of sufficient fertilizers, and molecular methods such as clustered regularly interspaced short palindromic repeats (CRISPRs)-associated nuclease 9 (Cas9), virus-induced gene silencing (VIGS), quantitative trait loci (QTL) mapping, microRNA (miRNA) technology, and OMICS-based approaches make up the majority of these techniques. CRISPR technology has rapidly become an increasingly popular choice among researchers exploring natural tolerance to abiotic stresses although, only a few plants have been produced so far using this technique. In order to address the difficulties imposed by DS, new plants utilizing the CRISPR technology must be developed. [ABSTRACT FROM AUTHOR]

Crop simulation models are valuable tools for decision making regarding evaluation and crop improvement under different field conditions. CSM-CROPGRO model integrates genotype, environment and crop management portfolios to simulate growth, development and yield. Modeling the safflower response to varied climate regimes are needed to strengthen its productivity dynamics. The main objective of the study was to evaluate the performance of DSSAT-CSM-CROPGRO-Safflower (Version 4.8.2) under diverse climatic conditions. The model was calibrated using the field observations for phenology, biomass and safflower grain yield (SGY) of the year 2016–17. Estimation of genetic coefficients was performed using GLUE (Genetic Likelihood Uncertainty Estimation) program. Simulated results for days to flowering, maturity, biomass at flowering and maturity and SGY were predicted reasonably with good statistical indices. Model evaluation results elucidate phenological events with low root mean square error (6.32 and 6.52) and high d-index (0.95 and 0.96) for days to flowering and maturity respectively for all genotypes and climate conditions. Fair prediction of safflower biomass at flowering and maturity showed low RMSE (887.3 and 564.3 kg ha−1) and high d-index (0.67 and 0.93) for the studied genotypes across the environments. RMSE for validated safflower grain yield (101.8 kg ha−1) and d-index (0.95) depicted that model outperformed for all genotypes and growing conditions. Longer appropriate growing conditions at NARC-Islamabad took optimal duration to assimilate photosynthetic products lead to higher grain yield. Safflower resilience to different environments showed that it can be used as an alternate crop for different agroecological regions. Furthermore, CROPGRO-Safflower model can be used as tool to further evaluate inclusion of safflower in the existing cropping systems of studied regions. [ABSTRACT FROM AUTHOR]

While soybean (Glycine max L.) provides the most important source of vegetable oil and protein, it is sensitive to salinity, which seriously endangers the yield and quality during soybean production. The application of Plant Growth‐Promoting Rhizobacteria (PGPR) to improve salt tolerance for plant is currently gaining increasing attention. Streptomycetes are a major group of PGPR. However, to date, few streptomycetes has been successfully developed and applied to promote salt tolerance in soybean. Here, we discovered a novel PGPR strain, Streptomyces lasalocidi JCM 3373T, from 36 strains of streptomycetes via assays of their capacity to alleviate salt stress in soybean. Microscopic observation showed that S. lasalocidi JCM 3373T does not colonise soybean roots. Chemical analysis confirmed that S. lasalocidi JCM 3373T secretes indole‐3‐carboxaldehyde (ICA1d). Importantly, IAC1d inoculation alleviates salt stress in soybean and modulates its root architecture by regulating the expression of stress‐responsive genes GmVSP, GmPHD2 and GmWRKY54 and root growth‐related genes GmPIN1a, GmPIN2a, GmYUCCA5 and GmYUCCA6. Taken together, the novel PGPR strain, S. lasalocidi JCM 3373T, alleviates salt stress and improves root architecture in soybean by secreting ICA1d. Our findings provide novel clues for the development of new microbial inoculant and the improvement of crop productivity under salt stress. Summary statement: Streptomyces lasalocidi JCM 3373T, selected from 36 species of streptomycetes, alleviates salt tolerance and shapes root architecture by secreting a metabolite‐indole‐3‐carboxaldehyde in soybean. [ABSTRACT FROM AUTHOR]

In crop improvement, delineating inheritance pattern of a character guides a plant breeder to choose appropriate breeding procedure, which enables ease of improving phenotypic expression of the traits. To deduce the inheritance pattern of naked seed or fuzzless character, four parental lines involving two purely naked seed types (DHN‐1 and DHN‐10), one partial naked seed type (SP46CC) and one fully fuzzy type (OSB415) were used to develop three different types of crosses, namely, naked × naked seed type cross (N × N), partial naked × naked seed type cross (PN × N) and fuzzy × naked seed type cross (F × N). We observed that naked trait segregates in the ratio of 11 naked: 5 partial naked in N × N cross, 22 naked: 42 partial naked in PN × N cross and 22 naked: 42 partial naked: 192 fuzzy in F × N cross. Our study reports a novel four‐gene model to understand inheritance nature of naked seed character where the presence of single basic dominant fuzzy gene negates the effect of genes controlling nakedness resulting fuzzy phenotype irrespective of the number of partial fuzzyness/nakedness imparting alleles. This indicates that nakedness is recessive to fuzzyness. Based on our results, we infer observing gradations of nakedness on seeds depends on the presence of number of partial fuzzyness imparting alleles, which led to a conclusion that the trait exhibited dose‐dependent expression with one basic gene for fuzziness. [ABSTRACT FROM AUTHOR]

Premise: Wild species are strategic sources of valuable traits to be introduced into crops through hybridization. For peanut, the 33 currently described wild species in the section Arachis are particularly important because of their sexual compatibility with the domesticated species, Arachis hypogaea. Although numerous wild accessions are carefully preserved in seed banks, their morphological similarities pose challenges to routine classification. Methods: Using a high‐density array, we genotyped 272 accessions encompassing all diploid species in section Arachis. Detailed relationships between accessions and species were revealed through phylogenetic analyses and interpreted using the expertise of germplasm collectors and curators. Results: Two main groups were identified: one with A genome species and the other with B, D, F, G, and K genomes. Species groupings generally showed clear boundaries. Structure within groups was informative, for instance, revealing the history of the proto‐domesticate A. stenosperma. However, some groupings suggested multiple sibling species. Others were polyphyletic, indicating the need for taxonomic revision. Annual species were better defined than perennial ones, revealing limitations in applying classical and phylogenetic species concepts to the genus. We suggest new species assignments for several accessions. Conclusions: Curated by germplasm collectors and curators, this analysis of species relationships lays the foundation for future species descriptions, classification of unknown accessions, and germplasm use for peanut improvement. It supports the conservation and curation of current germplasm, both critical tasks considering the threats to the genus posed by habitat loss and the current restrictions on new collections and germplasm transfer. [ABSTRACT FROM AUTHOR]

Among the many threats to food security, extremes of temperature, and unpredictable changes in temperature such as unseasonal frost or snowfall resulting from climate change have significant impacts on crop productivity and yields. It has been projected that for each increase by 1 °C of the global temperature, agricultural outputs of some staple food crops will decline by up to 3–8%. Alarmingly, reports from the National Aeronautics and Space Administration (NASA) and National Oceanic and Atmospheric Administration (NOAA) have revealed that our earth experienced one of the warmest summers in 2022, indicating that temperature stress is not a threat that can be taken lightly. Global food prices have risen by more than 70% since the middle of 2020, however, the UN Food and Agriculture Organization (FAO) projects that by 2027, the combined effects of climate change, conflict and poverty may lead to an additional rise in food prices by 8.5%. Taken together, the impacts of extreme temperatures on staple food supply amplify the risks of child malnutrition and food insecurity, especially in less-developed countries. This review offers a novel perspective on the intricate interplay between plant responses to heat and cold stresses, aiming to pave the way for innovative and efficient crop improvement programs crucial for ensuring a resilient and sustainable food supply in the face of climate change. A thorough and comprehensive understanding on plant mechanisms can effectively help agricultural industry to produce stress-resilient and climate-tolerant crops. Also, with the assistance from robust breeding techniques and genetic tools, the goal to achieve sustainable food supply chain can be attained. [ABSTRACT FROM AUTHOR]

Plants are among the many creatures that have benefited from the widespread application of the CRISPR-associated Cas system as a genome-editing tool for investigating gene function, identifying disease, and enhancing agricultural yields. Although the CRISPR/Cas systems for DNA editing are widely employed, post-transcriptional manipulation of RNA remains difficult despite the prevalence of Cas9. Type VI CRISPR/Cas systems, which were recently found, allow for precise RNA editing without permanently affecting the genome. Cas13d has been put to good use in RNA-related studies across a wide range of RNA knock-down, and RNA detection without affecting DNA. Regulation of cas13d specificity and activity helps to avoid the off-target effects and immune responses in plants. Cas13d as highly efficient RNA-targeting tools for the virus resistance, gene function studies, disease diagnostics, and crop improvement in plants. However, CRISPR/Cas13d applications in plant RNA biology are just getting started. This article discusses how RNA editing tools derived from the CRISPR/Cas13d system are currently being used and where they may be used in the future for plant research. [ABSTRACT FROM AUTHOR]

Variations in seed yield and essential oil composition of 48 coriander (Coriandrum sativum L.) germplasms collected from various geographical locations in India were evaluated. The variation in seed yield plant−1 (2.52–10.97 g plant−1), essential oil content (0.08–0.56%) and linalool content (49.04–82.14%). Linalool, γ-terpinene, β-pinene, p-cymene, β-myrcene, limonene, geraniol, caryophyllene, geranyl acetate, α-terpineol, citronellol and caryophyllene were detected in one or other germplasm lines. Cluster analysis was done using Ward's method based on the value of all the traits, resulting in 6 distinct groups of germplasms. Among six clusters, the maximum number of accessions was grouped into cluster II (16). The seed yield plant−1 is positively correlated with the number of umbels plant−1, number of umbellets plant−1, number of seeds plant−1, number of primary and secondary branches. The selection of these traits may result in the identification of germplasm with high seed yield. The genetic diversity revealed in this study could be useful for further crop improvement programs in coriander. [ABSTRACT FROM AUTHOR]

Summary: Professor Rajeev K. Varshney's transformative impact on crop genomics, genetics, and agriculture is the result of his passion, dedication, and unyielding commitment to harnessing the potential of genomics to address the most pressing challenges faced by the global agricultural community. Starting from a small town in India and reaching the global stage, Professor Varshney's academic and professional trajectory has inspired many scientists active in research today. His ground‐breaking work, especially his effort to list orphan tropical crops to genomic resource‐rich entities, has been transformative. Beyond his scientific achievements, Professor Varshney is recognized by his colleagues as an exemplary mentor, fostering the growth of future researchers, building institutional capacity, and strengthening scientific capability. His focus on translational genomics and strengthening seed system in developing countries for the improvement of agriculture has made a tangible impact on farmers' lives. His skills have been best utilized in roles at leading research centres where he has applied his expertise to deliver a new vision for crop improvement. These efforts have now been recognized by the Royal Society with the award of the Fellowship (FRS). As we mark this significant milestone in his career, we not only celebrate Professor Varshney's accomplishments but also his wider contributions that continue to transform the agricultural landscape. [ABSTRACT FROM AUTHOR]

SUMMARY: Mung bean (Vigna radiata) stands as a crucial legume crop in Asia, contributing to food security. However, our understanding of the underlying genetic foundation governing domesticated agronomic traits, especially those linked to pod architecture, remains largely unexplored. In this study, we delved into the genomic divergence between wild and domesticated mung bean varieties, leveraging germplasm obtained from diverse sources. Our findings unveiled pronounced variation in promoter regions (35%) between the two mung bean subpopulations, suggesting substantial changes in gene expression patterns during domestication. Leveraging transcriptome analysis using distinct reproductive stage pods and subpopulations, we identified candidate genes responsible for pod and seed architecture development, along with Genome‐Wide Association Studies (GWAS) and Quantitative Trait Locus (QTL) analysis. Notably, our research conclusively confirmed PDH1 as a parallel domesticated gene governing pod dehiscence in legumes. This study imparts valuable insights into the genetic underpinnings of domesticated agronomic traits in mung bean, and simultaneously highlighting the parallel domestication of pivotal traits within the realm of legume crops. Significance Statement: This study elucidates the genetic mechanisms underpinning pod development traits in mung bean, a key crop in Asian agriculture. By focusing on the PDH1 gene, our research reveals its pivotal role in pod dehiscence and contributes to the broader understanding of parallel domestication processes in legumes, providing valuable insights for future crop improvement strategies. [ABSTRACT FROM AUTHOR]

Background: The increasing impacts of heat stress on wheat production due to climate change has entailed the development of heat-resilient crop varieties. To address this, two hundred recombinant inbred lines (RILs) derived from a cross between WH711/WH1021 were evaluated in a randomized block design (RBD) with two replications at CCSHAU, Hisar, during 2018-19 under heat stress and non-stress conditions. Heat stress was induced by altering the date of sowing so that the grain filling stage coincide with heat stress. Results: Heat stress adversely affects RILs performance, as illustrated by alterations in phenotypic traits. Highest coefficients of variations were recorded for TAA, CTD 1, WUE, CTD 2, Cc and A under non-stress and heat stress conditions whereas gs, WUEi and GY under non-stress and SPAD 1, SPAD 2, GY and NDVI 2 under heat-stress conditions recorded moderate estimates of coefficient of variations. CTD 2, TAA, E, WUE and A displayed a significant occurrence of both high heritability and substantial genetic advance under non-stress. Similarly, CTD 2, NDVI 2, A, WUEi, SPAD 2, gs, E, Ci, MDA and WUE exhibited high heritability with high genetic advance under heat-stress conditions. Conclusions: Complementary and duplicate types of interactions with number of controlling genes were observed for different parameters depending on the traits and environments. RILs 41, 42, 59, 74, 75, 180 and 194 were categorized as heat tolerant RILs. Selection preferably for NDVI 1, RWC, TAA, A, E and WUEi to accumulate heat tolerance favorable alleles in the selected RILs is suggested for development of heat resilient genotypes for sustainable crop improvement. The results showed that traits such as such as NDVI, RWC, TAA, A, E, and WUEi, can be effective for developing heat-resilient wheat genotypes and ensuring sustainable crop improvement. [ABSTRACT FROM AUTHOR]

The impact of rising global temperatures on crop yields is a serious concern, and the development of heat-resistant crop varieties is crucial for mitigating the effects of climate change on agriculture. To achieve this, a better understanding of the molecular basis of the thermal responses of plants is necessary. The circadian clock plays a central role in modulating plant biology in synchrony with environmental changes, including temperature fluctuations. Recent studies have uncovered the role of transcriptional activators of the core circadian network in plant temperature responses. This expert view highlights key novel findings regarding the role of the RVE and LNK gene families in controlling gene expression patterns and plant growth under different temperature conditions, ranging from regular diurnal oscillations to extreme stress temperatures. These findings reinforce the essential role of the circadian clock in plant adaptation to changing temperatures and provide a basis for future studies on crop improvement. [ABSTRACT FROM AUTHOR]

SUMMARY Polyamines are involved in several plant physiological processes. In Arabidopsis thaliana, five FAD‐dependent polyamine oxidases (AtPAO1 to AtPAO5) contribute to polyamine homeostasis. AtPAO5 catalyzes the back‐conversion of thermospermine (T‐Spm) to spermidine and plays a role in plant development, xylem differentiation, and abiotic stress tolerance. In the present study, to verify whether T‐Spm metabolism can be exploited as a new route to improve stress tolerance in crops and to investigate the underlying mechanisms, tomato (Solanum lycopersicum) AtPAO5 homologs were identified (SlPAO2, SlPAO3, and SlPAO4) and CRISPR/Cas9‐mediated loss‐of‐function slpao3 mutants were obtained. Morphological, molecular, and physiological analyses showed that slpao3 mutants display increased T‐Spm levels and exhibit changes in growth parameters, number and size of xylem elements, and expression levels of auxin‐ and gibberellin‐related genes compared to wild‐type plants. The slpao3 mutants are also characterized by improved tolerance to drought stress, which can be attributed to a diminished xylem hydraulic conductivity that limits water loss, as well as to a reduced vulnerability to embolism. Altogether, this study evidences conservation, though with some significant variations, of the T‐Spm‐mediated regulatory mechanisms controlling plant growth and differentiation across different plant species and highlights the T‐Spm role in improving stress tolerance while not constraining growth. [ABSTRACT FROM AUTHOR]

This study evaluated the efficacy of phytogenic silver and zinc nanoparticles in improving heat resilience in various wheat varieties. The silver and zinc nanoparticles were synthesized using plant leaf extract and characterized using various techniques. Four wheat varieties (DBW187, Black Wheat, DBW 50, and PBW 621) were subjected to field trials. The random block design was used, and nanoparticles in different concentrations were applied at various growth stages and morphologically, and yield parameters were recorded. UV–vis spectroscopy spectral analysis showed peaks for Ag nanoparticles at 420 nm wavelength and Zn nanoparticles at 240 and 350 nm wavelength, depicting the preliminary confirmation of nanoparticle synthesis. Electron microscopic analysis (TEM and SEM) provided morphological insights and confirmed synthesis of fine-sized particle mostly in a range between 10 and 60 nm. Energy dispersive x-ray analysis confirmed the elemental composition of the synthesized nanoparticles, with Ag and Zn elements detected in their respective samples. It also confirmed the oxide nature of synthesized ZnNPs. Dynamic light scattering analysis provided size distribution profiles, indicating average sizes of approximately 61.8 nm for Ag nanoparticles and 46.5 nm for Zn nanoparticles. The concentrations of Ag and Zn nanoparticles in the samples were found to be 196.3 ppm and 115.14 ppm, respectively, through atomic absorption spectroscopic analysis. Fourier transform infrared spectroscopy analysis revealed characteristic functional groups present in the nanoparticles. The results of field experiments established that Ag nanoparticles at 75 ppm concentration exhibited the most significant enhancements in plant growth. Conversely, Zn nanoparticles at a 100 ppm concentration demonstrated the most substantial improvements in the growth and yield of heat-stressed wheat varieties. The study concludes that optimized concentrations of silver and zinc nanoparticles can effectively improve heat stress resilience in wheat. These findings are promising to enhance abiotic stress resilience in crops. [ABSTRACT FROM AUTHOR]

Background: Jackfruit (Artocarpus heterophyllus) is an economically valuable fruit tree in Uganda. However, the production of jackfruit in Uganda is low. Additionally, because of deforestation, genetic erosion of the resource is predicted before its exploitation for crop improvement and conservation. As a prerequisite for crop improvement and conservation, 100 A. heterophyllus tree isolates from the Kayunga and Luwero districts in Uganda were characterized using 16 morphological and 10 microsatellite markers. Results: The results from the morphological analysis revealed variations in tree height, diameter at breast height (DBH), and crown diameter, with coefficient of variation (CV) values of 20%, 41%, and 33%, respectively. Apart from the pulp taste, variation was also observed in qualitative traits, including tree vigor, trunk surface, branching density, tree growth habit, crown shape, leaf blade shape, fruit shape, fruit surface, flake shape, flake color, flake flavor and pulp consistency/texture. Genotyping revealed that the number of alleles amplified per microsatellite locus ranged from 2 to 5, with an average of 2.90 and a total of 29. The mean observed (Ho) and expected (He) heterozygosity were 0.71 and 0.57, respectively. Analysis of molecular variance (AMOVA) indicated that 81% of the variation occurred within individual trees, 19% among trees within populations and 0% between the two populations. The gene flow (Nm) in the two populations was 88.72. The results from the 'partitioning around medoids' (PAM), principal coordinate analysis (PCoA) and genetic cluster analysis further revealed no differentiation of the jackfruit populations. The Mantel test revealed a negligible correlation between the morphological and genetic distances. Conclusions: Both morphological and genetic analyses revealed variation in jackfruit within a single interbreeding population. This diversity can be exploited to establish breeding and conservation strategies to increase the production of jackfruit and hence boost farmers' incomes. However, selecting germplasm based on morphology alone may be misleading. [ABSTRACT FROM AUTHOR]

SUMMARY Brassica carinata (BBCC) commonly referred to as Ethiopian mustard is a natural allotetraploid containing the genomes of Brassica nigra (BB) and Brassica oleracea (CC). It is an oilseed crop endemic to the northeastern regions of Africa. Although it is under limited cultivation, B. carinata is valuable as it is resistant/highly tolerant to most of the pathogens affecting widely cultivated Brassica species of the U's triangle. We report a chromosome‐scale genome assembly of B. carinata accession HC20 using long‐read Oxford Nanopore sequencing and Bionano optical maps. The assembly has a scaffold N50 of ~39.8 Mb and covers ~1.11 Gb of the genome. We compared the long‐read genome assemblies of the U's triangle species and found extensive gene collinearity between the diploids and allopolyploids with no evidence of major gene losses. Therefore, B. juncea (AABB), B. napus (AACC), and B. carinata can be regarded as strict allopolyploids. We cataloged the nucleotide‐binding and leucine‐rich repeat immune receptor (NLR) repertoire of B. carinata and, identified 465 NLRs, and compared these with the NLRs in the other Brassica species. We investigated the extent and nature of early‐generation genomic interactions between the constituent genomes of B. carinata and B. juncea in interspecific crosses between the two species. Besides the expected recombination between the constituent B genomes, extensive homoeologous exchanges were observed between the A and C genomes. Interspecific crosses, therefore, can be used for transferring disease resistance from B. carinata to B. juncea and broadening the genetic base of the two allotetraploid species. [ABSTRACT FROM AUTHOR]

Tef research has little benefited from omics due to neglect of the crop by the global scientific community. However, the few utilized tools showed promising results. Chromosome-scale assembly of the genome reveals the evolution of tef. The whole-genome sequencing of drought-resurrecting Eragrostis nindensis and desiccation-sensitive Eragrostis curvula shows genes that play key roles in drought responses. A few studies using omics tools have revealed differentially expressed genes, proteins, and metabolites in tef plants exposed to drought. Molecular markers have deciphered diversity in tef germplasm collected from diverse agroecologies in Ethiopia. The application of targeting induced local lesions in genomes resulted in mutant tef lines with a semidwarf stature, which were later bred to locally adapted and high-yielding varieties. Genome editing using 'Green Revolution' genes resulted in a semidwarf and lodging-tolerant tef plant. Tef or teff [ Eragrostis tef (Zucc.) Trotter] is a cereal crop indigenous to the Horn of Africa, where it is a staple food for a large population. The popularity of tef arises from its resilience to environmental stresses and its nutritional value. For many years, tef has been considered an orphan crop, but recent research initiatives from across the globe are helping to unravel its undisclosed potential. Advanced omics tools and techniques have been directed toward the exploration of tef's diversity with the aim of increasing its productivity. In this review, we report on the most recent advances in tef omics that brought the crop into the spotlight of international research. [ABSTRACT FROM AUTHOR]

Understanding historical changes in root depth attributes is needed for crop productivity and sustainability assessments, but such information is rare. We explored whether newer maize (Zea mays L.) hybrids grow roots faster and deeper than older hybrids and quantified the role of management and environment on root trait expression. We measured root front velocity (RFV) and maximum root depth in 11 Bayer Crop Science legacy hybrids released from 1983 to 2017 across five environments in the US Corn Belt during 2021 and 2022. Root depth was measured weekly during vegetative stages with manual probes and the maximum root depth at crop harvest with a Giddings probe. Results indicated that the RFV and maximum root depth slightly increased with the year of hybrid release (0.13% per year, p = 0.1) at 8.7 plants m−2. Historical increases in plant density from 4.7 to 8.7 plants m−2 lowered RFV and maximum root depth, but the new hybrids compensated for this loss, resulting in 4% higher RFV and 3% higher maximum depth when comparing systems from 1983 to 2017. The environment strongly influenced root trait expression (>41%). Rain anomaly and soil bulk density explained a portion of this variation. We found a linear relationship between root depth and leaf number (R2 = 0.95) and a nonlinear relationship between RFV and maximum root depth (R2 = 0.77), which can stimulate crop model improvements. Faster and deeper roots were not correlated with maize yields in our environments. This study enhances our understanding of maize breeding impacts on root traits. Core Ideas: We studied root front velocity (RFV) and maximum root depth in maize hybrids released from 1983 to 2017.RFV and maximum root depth increased by 0.13% per year, a 10‐fold lower increase than grain yield genetic gain.Root depth and collared leaf number were strongly correlated (R2 = 0.95).The environment had the strongest influence on the root depth traits.Faster and deeper roots did not necessarily translate into higher yields. [ABSTRACT FROM AUTHOR]

Longan (Dimocarpus longan Lour.) is an important underutilized fruit crop. There is currently limited information available on the genetic background of longans, which is a key bottleneck in longan improvement. Studies on the extent of genetic variability and genetic divergence are crucial and it can provide relevant information which can be very useful for crop improvement programmes. In the present study, a total of 54 qualitative and quantitative traits were investigated of 20 different longan genotypes to determine the morphological and physiochemical traits that. Results revealed that the significant variability existed in the studied traits except few. Among the qualitative traits petiole colour, leaflet curvature, young leaf colour, mature leaf colour, branching density, leaflet midrib colour, abundance of flower, trunk surface, fruit maturity group, and tree vigour were showed more than the average value of Shannon's diversity index. Higher PCV and GCV recorded for several traits viz., tree volume followed by aril weight, number of fruits per branch, aril/seed weight ratio, trunk girth, TSS acid ratio, aril thickness, number of days from panicle initiation to flowering, titratable acidity, width of inflorescence, length of inflorescence, petiole length, fruit weight, plant height, crown diameter and rachis length. High heritability estimates coupled with high genetic advance as % of mean were recorded for the traits viz., plant height, trunk girth, crown diameter, tree volume, rachis and petiole length, number of days from panicle initiation to flowering, length and width of inflorescence, number of fruits per bunch, fruit, aril and seed weight, aril thickness, fruit colour-a, titratable acidity and TSS acid ratio which is indicative of additive gene action and selection based on these traits would be more reliable. According to the Mahalanobis D2 statistic, twenty diverse genotypes were grouped into eight groups. The presence of genetic divergence was also tested in cluster means by the significant amount of variability for various variables. Therefore, this study's findings imply that these genotypes have variability in terms of fruit quality traits, yield and traits that contribute to yield, and other agronomic traits that could be useful in future crop improvement initiatives. [ABSTRACT FROM AUTHOR]

Mutagenesis is the process of creating mutations in an organism's DNA. Induced mutagenesis can be used to create crops with higher yields, better quality, disease and insect resistance, and stress tolerance, all of which are critical for food security and sustainable agriculture. Physical, biological and chemical mutagens can induce mutations in seeds and other plant propagules, followed by selection for superior agronomic traits in the first generation. The phenotypic stability of agronomic features generated by the mutagenesis process is established in the second and third generations, with the following generations undergoing further evaluation. Only mutant lines exhibiting the desired characteristics are chosen as new varieties or parent lines for a breeding program. New crop varieties are developed around the world utilizing induced mutagenesis techniques such as irradiation or chemical mutagens. In this review, we examine the different approaches to mutagenesis, their applications, challenges and prospects for increasing crop productivity and quality. [ABSTRACT FROM AUTHOR]

• Significant variation among the GWAS panel was recorded for all the traits • 143 MTAs associations were observed for all traits distributed on all chromosomes • Eleven stable QTLs were identified for number of seeds per plant and pods per plant • MLD was utilised to establish correlation between phenotypic traits to loci's Genome wide association study (GWAS) was performed to identify loci associated with three agronomic traits namely seeds per pod, pods per plant and number of seeds per plant of horsegram (Macrotyloma uniflorum). Total 87 accesions of horsegram from different geographical regions of India and one wild relative from Australia were utilised for the genome wide association studies. The genotyping was carried out using genotype-by-sequencing technology and after high quality filtering, minor allele frequency of 0.05, a total of 55,656 quality SNPs were utilised for determining Marker-Trait Association. The LD decay varied across the chromosomes form 8 kb to 300 kb. Further, the population structure analysis has clustered the accession into three subpopulations. All the 88 accessions of horsegram were evaluated at Palampur (32.1109° N, 76.5363° E) and Bajaura (31.8465°N, 77.1605°E) locations of North-Western Himalayan region, India from. In the current study, 143 MTAs associations were observed for seeds per pod distributed on all 8 chromosomes, 2 for pods per plant at chromosomes 2 and 3 and 1 for number of seeds per plant at chromosome 7. However, total 11 stable QTLs (9 for number of seeds per plant and 2 for pods per plant) were also identified. These QTLs can serve as a potential source for marker assisted selection. The genes identified within and in proximity to the stable QTLs will serve as a bridge between genetic information and its practical application for crop improvement. [ABSTRACT FROM AUTHOR]

Background and aims: Intercropping is known to have low fertilizer input but high production efficiency. However, only few studies have explored the nutrient stoichiometry of soil and microbiome under intercropping patterns to understand the mechanisms underlying the improvement in crop production by intercropping. Methods: A field-based experiment (started in 2013) was conducted to explore the effects of intercropping of maize with peanut, soybean, gingelly, and sweet potato on soil microbial resource limitation, and the factors controlling the resource limitation were investigated by exploring functional gene abundance and soil C–N–P stoichiometry. Results: Vector angle (indicator of microbial P limitation) was > 45° in all soil samples. Compared with monocropping, intercropping significantly decreased the vector length and angle. The RC:N-TERC:N was < 0 and the RC:P-TERC:P was > 0 in all soil samples. The RC:P-TERC:P of the monocropping was significantly higher than that of the intercropping soil. Compared with monocropping, the abundances of most of functional genes related to C degradation and fixation, N fixation, nitrification, denitrification, and P activation increased in intercropping soil. Microbial P limitation was associated more with the C–N–P stoichiometric ratios of soil and microbiome than with functional gene abundance. Soil microbial P limitation was notably related to plant N and P uptake and maize yield, regulating by soil microbial N:P, available P:C and P:N ratio. Conclusions: This study demonstrated the mitigation of microbial P limitation by intercropping and highlighted the importance of understanding the promotion of microbial metabolisms by soil resource stoichiometry, which can help in improving maize productivity. [ABSTRACT FROM AUTHOR]

Taro [Colocasia esculenta (L.) Schott var. antiquorum] is an important tuber crop widely cultivated in tropical and sub‐tropical regions, for its corms, leaves, and petioles. Millions of people living in developing countries in Asia, Africa, and Central America, utilise taro as a staple or subsistence food and it plays a very crucial role there for food security, nutritional security, livelihood improvement, and employment generation. It exhibits a capacious range of diversity worldwide regarding plant characteristics. However, its phenology has not yet been described systematically. The present study defines codes and phenological growth stages of taro according to the extended Biologische Bundesanstalt, Bundessortenamnt, and Chemische Industrie (BBCH) scale using a three‐digit numerical coding system for its description. A total of nine principal growth stages were described such as germination (0), leaf development (1), elongation of shoot/stem (2), tuber formation (3), development of inflorescence/spadix (5), flowering (6), development of berries/fruiting (7), ripening of berries and seed development (8) and senescence and beginning of dormancy (9) and further, each of the principal development stages has been partitioned into optional developmental growth stages. Under remarkable circumstances, it is valuable to use mesostages with three‐digit codes for description. The study of extended BBCH scale for taro has immense importance in crop management, crop improvement, germplasm characterisation, and assessment of impact of the climate on phenology under different agro‐climatic conditions for the selection of suitable genotypes. [ABSTRACT FROM AUTHOR]

Bacterial stalk rot (BSR), caused by Dickeya zeae (syn. Erwinia chrysanthemi pv. zeae), has emerged as a significant disease affecting maize crops worldwide. In this study, symptomatic maize plants were collected from diverse agroclimatic zones in India over the period of kharif 2019–2021. Various approaches, including pathogenicity tests, cultural characteristics, biochemical profiling and molecular analysis, were employed to accurately identify the collected bacterial isolates as Dickeya. Pathogenicity assessments were conducted on 40‐day‐old maize plants, following Koch's postulates, as well as through potato maceration assays. Furthermore, cross‐infectivity studies were conducted on rice, potato, tomato and banana plants. Phenotypic and biochemical characterization confirmed that all the isolates belonged to the Dickeya genus. Additionally, PCR amplification of a pel gene fragment, specific to the genus Dickeya, further verified the pathogenic isolates as Dickeya. Molecular characterization studies were performed on four isolates (UKMDZ‐3, PBMDZ‐7, TSMDZ‐11 and HPMDZ‐16), selected to represent distinct maize agroclimatic zones and four states of India, and which caused severe infections on susceptible maize cv. Early Composite. Amplification of six characteristic genome regions (16S rRNA, recN, gyrB, dnaX, recA and dnaJ) from these isolates facilitated individual and concatenated gene phylogenetic analyses, confirming their resemblance to Dickeya zeae. This study represents the first comprehensive molecular analysis of D. zeae isolates from India, providing valuable insights for future crop improvement strategies. The findings contribute to our understanding of the genetic basis of BSR in maize and offer potential avenues for genetic enhancement to mitigate the disease's impact on maize cultivation. [ABSTRACT FROM AUTHOR]

Summary: Plants have evolved a multi‐layered immune system to fight off pathogens. However, immune activation is costly and is often associated with growth and development penalty. In crops, yield is the main breeding target and is usually affected by high disease resistance. Therefore, proper balance between growth and defence is critical for achieving efficient crop improvement. This review highlights recent advances in attempts designed to alleviate the trade‐offs between growth and disease resistance in crops mediated by resistance (R) genes, susceptibility (S) genes and pleiotropic genes. We also provide an update on strategies for optimizing the growth–defence trade‐offs to breed future crops with desirable disease resistance and high yield. [ABSTRACT FROM AUTHOR]

Background: TALE-derived DddA-based cytosine base editors (TALE-DdCBEs) can perform efficient base editing of mitochondria and chloroplast genomes. They use transcription activator-like effector (TALE) arrays as programmable DNA-binding domains and a split version of the double-strand DNA cytidine deaminase (DddA) to catalyze C•G-to-T•A editing. This technology has not been optimized for use in plant cells. Results: To systematically investigate TALE-DdCBE architectures and editing rules, we established a β-glucuronidase reporter for transient assays in Nicotiana benthamiana. We show that TALE-DdCBEs function with distinct spacer lengths between the DNA-binding sites of their two TALE parts. Compared to canonical DddA, TALE-DdCBEs containing evolved DddA variants (DddA6 or DddA11) showed a significant improvement in editing efficiency in Nicotiana benthamiana and rice. Moreover, TALE-DdCBEs containing DddA11 have broader sequence compatibility for non-TC target editing. We have successfully regenerated rice with C•G-to-T•A conversions in their chloroplast genome, as well as N. benthamiana with C•G-to-T•A editing in the nuclear genome using TALE-DdCBE. We also found that the spontaneous assembly of split DddA halves can cause undesired editing by TALE-DdCBEs in plants. Conclusions: Altogether, our results refined the targeting scope of TALE-DdCBEs and successfully applied them to target the chloroplast and nuclear genomes. Our study expands the base editing toolbox in plants and further defines parameters to optimize TALE-DdCBEs for high-fidelity crop improvement. [ABSTRACT FROM AUTHOR]

Background: Climate change has led to severe cold events, adversely impacting global crop production. Eggplant (Solanum melongena L.), a significant economic crop, is highly susceptible to cold damage, affecting both yield and quality. Unraveling the molecular mechanisms governing cold resistance, including the identification of key genes and comprehensive transcriptional regulatory pathways, is crucial for developing new varieties with enhanced tolerance. Results: In this study, we conducted a comparative analysis of leaf physiological indices and transcriptome sequencing results. The orthogonal partial least squares discriminant analysis (OPLS-DA) highlighted peroxidase (POD) activity and soluble protein as crucial physiological indicators for both varieties. RNA-seq data analysis revealed that a total of 7024 and 6209 differentially expressed genes (DEGs) were identified from variety "A" and variety "B", respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of DEGs demonstrated that the significant roles of starch and sucrose metabolism, glutathione metabolism, terpenoid synthesis, and energy metabolism (sucrose and starch metabolism) were the key pathways in eggplant. Weighted gene co-expression network analysis (WGCNA) shown that the enrichment of numerous cold-responsive genes, pathways, and soluble proteins in the MEgrep60 modules. Core hub genes identified in the co-expression network included POD, membrane transporter-related gene MDR1, abscisic acid-related genes, growth factor enrichment gene DELLA, core components of the biological clock PRR7, and five transcription factors. Among these, the core transcription factor MYB demonstrated co-expression with signal transduction, plant hormone, biosynthesis, and metabolism-related genes, suggesting a pivotal role in the cold response network. Conclusion: This study integrates physiological indicators and transcriptomics to unveil the molecular mechanisms responsible for the differences in cold tolerance between the eggplant cold-tolerant variety "A" and the cold-sensitive variety "B". These mechanisms include modulation of reactive oxygen species (ROS), elevation in osmotic carbohydrate and free proline content, and the expression of terpenoid synthesis genes. This comprehensive understanding contributes valuable insights into the molecular underpinnings of cold stress tolerance, ultimately aiding in the improvement of crop cold tolerance. [ABSTRACT FROM AUTHOR]

Plant-specific transcription factors (TFs) are responsible for regulating the genes involved in the development of plant-specific organs and response systems for adaptation to terrestrial environments. This includes the development of efficient water transport systems, efficient reproductive organs, and the ability to withstand the effects of terrestrial factors, such as UV radiation, temperature fluctuations, and soil-related stress factors, and evolutionary advantages over land predators. In rice and Arabidopsis, INDETERMINATE DOMAIN (IDD) TFs are plant-specific TFs with crucial functions, such as development, reproduction, and stress response. However, in tomatoes, IDD TFs remain uncharacterized. Here, we examined the presence, distribution, structure, characteristics, and expression patterns of SlIDDs. Database searches, multiple alignments, and motif alignments suggested that 24 TFs were related to Arabidopsis IDDs. 18 IDDs had two characteristic C2H2 domains and two C2HC domains in their coding regions. Expression analyses suggest that some IDDs exhibit multi-stress responsive properties and can respond to specific stress conditions, while others can respond to multiple stress conditions in shoots and roots, either in a tissue-specific or universal manner. Moreover, co-expression database analyses suggested potential interaction partners within IDD family and other proteins. This study functionally characterized SlIDDs, which can be studied using molecular and bioinformatics methods for crop improvement. [ABSTRACT FROM AUTHOR]

AbstractCassava (Manihot esculenta Crantz) is an important staple crop, especially for resource-poor populations. Cassava-based diets are rich in calories but grossly deficient in essential mineral elements. A field study in southeastern Nigeria aimed at increasing yields and concentrations of bioavailable mineral elements in a β-carotene cassava variety, UMUCASS 38 (TMS 01/1371), through agronomic biofortification. A randomized complete block design experiment in triplicate, with foliar application of Zn (3.0 kg ha−1 Zn as ZnSO4), I (4.0 kg ha−1 I as KI), Se (0.25 kg ha−1 Se as Na2SeO3) and Zn + Se + I in combination at vegetative, tuber initiation and bulking stages of cassava. Results indicated neither phytotoxicity nor altered physical and chemical soil properties. Application of Zn or Zn + Se + I at the vegetative stage significantly increased cassava tuber yields. More Zn, Se, and I accumulated in fresh and processed cassava tuber products (gari, lafun), especially when Zn + Se + I was applied at tuber initiation stage. The combined application of Zn + Se + I consistently outperformed sole applications indicating a synergistic interaction effect between the three elements. It is concluded that in the Zn-deficient soils of southeast Nigeria, yield of cassava root tubers can be significantly increased by foliar application of Zn-containing fertilizer at the vegetative stage, but for optimal accumulation of elemental Zn, Se, and I, a combined Zn + Se + I fertilizer be applied at the tuber initiation stage. [ABSTRACT FROM AUTHOR]

Rice tissue culture is very well established for the Indica and Japonica varieties in white rice. Black rice is recalcitrant for the regeneration due to their pigment. Since, there is a limited genetic transformation protocol available for the black rice so crop improvement efforts have not made so much progress. Here, we have developed an improved, efficient and reliable regeneration protocol for Chakhao amubi cultivar of black rice using mature seeds as an explant and through somatic embryogenesis pathway. The effects of growth regulators, gelling agent, and photoperiod, and various stages of complete protocol is well established. The regeneration protocol developed in this study will be well suited for introducing the agronomical important genes and functional genomic studies in black rice. [ABSTRACT FROM AUTHOR]

The present study focuses on the 1‐aminocyclopropane‐1‐carboxylic acid (ACC) deaminase assay and the rhizospheric interactions affecting enzyme activity. We investigate the efficacy of ACC deaminase‐producing rhizobacterial activity in alleviating salt stress in rice. Among the five selected isolates, only two strains, KFSC2 and PK7, possessed the enzyme activity. The amplification of the acdS gene resulted in gene identification in all five isolates. The newly designed primer in this study was suitable for both Pseudomonas and Enterobacter species. The gene products of KFSC1 and KFSC2 were amplified, sequenced and subsequently submitted to GenBank with accession numbers OQ703930 and OQ798805, respectively. This marks the first‐ever submission of the acdS gene sequence from Pseudomonas aeruginosa to GenBank. The interactive effect of root exudates on ACC deaminase activity was assessed using amino acids, organic acids and sugars. The highest enzyme activity was obtained with aspartic acid and fructose, while organic acids and varying pH levels had negative influences on enzyme activity. Additionally, salt and proline had positive effects. These results indicate that there is a positive interaction occurring among these compounds from plants and root‐colonizing bacteria. The selected strain PK7 had a significant impact on growth parameters. Moreover, yield resulted in 252 kg/hec over the control suggests its future possibility of promising bioformulations. [ABSTRACT FROM AUTHOR]

[Display omitted] • The transcriptome and translatome of 8 tissues of cotton generated large datasets. • De novo transcriptome assembly and ribosome profiling fine-tune cotton genome annotation. • Unannotated translational events including sORFs (uORFs and dORF), and lncRNAs were identified. • Omics integrated analysis of normal fiber ZM24 and short fiber pag1 explored fiber-specific genes. • GhKCS6 overexpression showed greater fiber length than the control and validated our approach. The unavailability of intergenic region annotation in whole genome sequencing and pan-genomics hinders efforts to enhance crop improvement. Despite advances in research, the impact of post-transcriptional regulation on fiber development and translatome profiling at different stages of fiber growth in cotton (G. hirsutum) remains unexplored. We utilized a combination of reference-guided de novo transcriptome assembly and ribosome profiling techniques to uncover the hidden mechanisms of translational control in eight distinct tissues of upland cotton. Our study identified P-site distribution at three-nucleotide periodicity and dominant ribosome footprint at 27 nucleotides. Specifically, we have detected 1,589 small open reading frames (sORFs), including 1,376 upstream ORFs (uORFs) and 213 downstream ORFs (dORFs), as well as 552 long non-coding RNAs (lncRNAs) with potential coding functions, which fine-tune the annotation of the cotton genome. Further, we have identified novel genes and lncRNAs with strong translation efficiency (TE), while sORFs were found to affect mRNA transcription levels during fiber elongation. The reliability of these findings was confirmed by the high consistency in correlation and synergetic fold change between RNA-sequencing (RNA-seq) and Ribosome-sequencing (Ribo-seq) analyses. Additionally, integrated omics analysis of the normal fiber ZM24 and short fiber pag1 cotton mutant revealed several differentially expressed genes (DEGs), and fiber-specific expressed (high/low) genes associated with sORFs (uORFs and dORFs). These findings were further supported by the overexpression and knockdown of GhKCS6 , a gene associated with sORFs in cotton, and demonstrated the potential regulation of the mechanism governing fiber elongation on both the transcriptional and post-transcriptional levels. Reference-guided transcriptome assembly and the identification of novel transcripts fine-tune the annotation of the cotton genome and predicted the landscape of fiber development. Our approach provided a high-throughput method, based on multi-omics, for discovering unannotated ORFs, hidden translational control, and complex regulatory mechanisms in crop plants. [ABSTRACT FROM AUTHOR]

• Fourteen pole-type hyacinth bean genotypes were analyzed for trace elements (Zn, Fe, Mn, and Cu). • Green pod yield was a function of pod weight and width. • 16/DOLP VAR 4 registered highest yield and uptake of Zn, Fe, and Cu. • There was an absence of yield dilution on concentrations of trace elements. • BCDB 5 was screened as most potential genotype for agronomic biofortification while 16/DOLP VAR 4 for genetic biofortification. Trace element malnutrition is a global malaise and remains a concern for humanity. Hyacinth bean (Lablab purpureus L.), an underutilized legume vegetable, could be a suitable option to alleviate such malaise owing to its high content of trace elements. Our study aimed to evaluate phenotypic segregation of some pole-type hyacinth bean genotypes and their logical screening for specific biofortification programs (genetic or agronomic). We observed significantly (P <0.05) higher pod yields in 16/DOLP VAR 4 (344.19 q ha−1), 17/DOLP VAR 1 (283.47 q ha−1), 16/DOLP VAR 2 (280.19 q ha−1), and 16/DOLP VAR 1 (260.22 q ha−1) compared to others. Experimental results also revealed that yield was a function of pod weight and width. Although concentration of trace elements varied significantly (P <0.05) between the genotypes, 16/DOLP VAR 4 showed significantly (P <0.05) greater uptake of Zn (822.12 g ha−1), Fe (2240.28 g ha−1), and Cu (268.42 g ha−1). The relation between the trace elements was antagonistic in most genotypes for Mn and Cu (r = –0.34; P >0.05) followed by Zn and Fe (r = –0.25; P >0.05). Quadrant segregation, based on the relation between yield and uptake of trace elements, identified genotype BCDB 5 (low yield with less uptake potential) as suitable for agronomic biofortification (Zn and Fe) while 16/DOLP VAR 4 (high yield with greater uptake potential) for genetic biofortification (Zn, Fe, Mn, and Cu) program. Since agronomic biofortification offers a scope for additional enrichment of trace elements concentration (particularly Zn and Fe), we conclude that it may be necessitated as an immediate effort to promote the underutilized hyacinth bean in populations with the potential for higher consumption. [ABSTRACT FROM AUTHOR]

Summary: Quantifying the temporal or longitudinal growth dynamics of crops in diverse environmental conditions is crucial for understanding plant development, requiring further modeling techniques.In this study, we analyzed the growth patterns of two different maize (Zea mays L.) populations using high‐throughput phenotyping with a maize population consisting of 515 recombinant inbred lines (RILs) grown in Texas and a hybrid population containing 1090 hybrids grown in Missouri.Two models, Gaussian peak and functional principal component analysis (FPCA), were employed to study the Normalized Green–Red Difference Index (NGRDI) scores. The Gaussian peak model showed strong correlations (c. 0.94 for RILs and c. 0.97 for hybrids) between modeled and non‐modeled temporal trajectories. Functional principal component analysis differentiated NGRDI trajectories in RILs under different conditions, capturing substantial variability (75%, 20%, and 5% for RILs; 88% and 12% for hybrids).By comparing these models with conventional BLUP values, common quantitative trait loci (QTLs) were identified, containing candidate genes of brd1, pin11, zcn8 and rap2. The harmony between these loci's additive effects and growing degree days, as well as the differentiation of RIL haplotypes across growth stages, underscores the significant interplay of these loci in driving plant development. These findings contribute to advancing understanding of plant–environment interactions and have implications for crop improvement strategies. [ABSTRACT FROM AUTHOR]

By 2050, the global population is projected to exceed 9.5 billion, posing a formidable challenge to ensure food security worldwide. To address this pressing issue, mutation breeding in horticultural crops, utilizing physical or chemical methods, has emerged as a promising biotechnological strategy. However, the efficacy of these mutagens can be influenced by various factors, including biological and environmental variables, as well as targeted plant materials. This review highlights the global challenges related to food security and explores the potential of mutation breeding as an indispensable biotechnological tool in overcoming food insecurity. This review also covers the emergence of CRISPR-Cas9, a breakthrough technology offering precise genome editing for the development of high-yield, stress-tolerant crops. Together, mutation breeding and CRISPR can potentially address future food demands. This review focuses into these biotechnological advancements, emphasizing their combined potential to fortify global food security in the face of a booming population. [ABSTRACT FROM AUTHOR]

The seed‐endophytic bacterial community is a potentially beneficial and heritable fraction of the plant microbiome. Its utilization as a sustainable crop improvement strategy could be especially valuable for species such as hemp, where production is being scaled up and new challenges will be faced in managing crop productivity and health. However, little is known about the makeup and variation of the hemp seed microbiome. This study profiled the endophytic bacterial communities harboured by 16 hemp cultivars sourced from commercial suppliers in Europe. A 16S rDNA amplicon sequencing approach identified 917 amplicon sequence variants across samples. Taxonomic classification of sequences revealed 4 phyla and 87 genera to be represented in the dataset. Several genera were widespread while some were specific to one or a few cultivars. Flavobacterium, Pseudomonas, and Pantoea were notable in their high overall abundance and prevalence, but community composition was variable and no one taxon was universally abundant, suggesting a high degree of flexibility in community assembly. Taxonomic composition and alpha diversity differed among cultivars, though further work is required to understand the relative influence of hemp genetic factors on community structure. The taxonomic profiles presented here can be used to inform further work investigating the functional characteristics and potential plant‐growth‐promoting traits of seed‐borne bacteria in hemp. [ABSTRACT FROM AUTHOR]

The investigation was conducted during the rabi season (September 2019 to February 2020) of 2019 to 2020 at the research field of All India Co-ordinated Vegetable Crops, located at Bidhan Chandra Krishi Viswavidyalaya in Kalyani, Nadia, West Bengal, India. The aim of the study was to examine the characteristics of twenty-six chilli genotypes across twelve qualitative traits. The investigation unveiled a broad range of phenotypic variability using Randomized Block Design in three replications. Among the assessed traits, leaf density, leaf shape, fruit shape, plant habit, fruit curvature, and anther colour exhibited the most extensive variations among the genotypes. Conversely, the traits with the least diversity values, all falling below the overall mean, included fruit surface (0.28%), leaf colour (0.42%), stem pubescence (0.42%), stem colour (0.42%), anthocyanin colouration at nodes (0.48%), and leaf pubescence (0.48%). The Shannon-Weiner Diversity Index (H') ranged from 0.28 to 1.07. Of the traits evaluated, leaf density displayed the highest diversity index (1.07), followed by leaf shape (1.05), fruit shape (1.01), plant habit (0.86), fruit curvature (0.69), and anther colour (0.58). The obtained Shannon-Weiner Diversity Index, with an average value of 64.66%, confirmed the presence of significant diversity within the examined chilli genotypes. The results suggest that the indirect selection of chilli parent plants based on a range of morphological characteristics can offer advantages in the management of both biotic and abiotic stresses. The information holds significant value for effective pre-breeding, management, and utilization in crop improvement initiatives, in addition to augmenting the genetic potential of the crop. [ABSTRACT FROM AUTHOR]

Mutants are useful for determining the genes that underlie a given trait. This information is highly useful for developing molecular markers for breeding and is the foundational knowledge required for future genomic crop improvements. The dessert strawberry, Fragaria ×ananassa, is a valuable crop with high potential for increased use in controlled environment agriculture. The genome of the woodland strawberry Fragaria vesca is the dominant genome of the four diploid strawberry subgenomes that contribute to the octoploid F. ×ananassa genome. F. vesca is therefore a useful reference system for determining gene function and should be a useful source of gene diversity for breeding of F. ×ananassa. Chemical mutagenesis of the inbred F. vesca line H4 F7-3 resulted in one M2 line with a smaller stature overall and which produces flowers on very short peduncles close to the crown. This line was named short inflorescence (sin). The sin phenotype results from a single gene recessive mutation that is pleiotropic in that the mutation also affects internode lengths of runners as well as petiole elongation of sin plants. Microscopic characterization revealed that sin peduncles are most likely short because of a failure of cells to elongate. Inflorescences, runners, and petioles of sin plants were found to elongate in response to exogenous gibberellin, indicating that sin could be a gibberellin biosynthesis or transport mutant. A brief characterization of sin plants is presented to facilitate collaborative studies of the line. [ABSTRACT FROM AUTHOR]

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop improvement. To investigate its molecular mechanisms in rice, we performed map-based cloning and characterization of OPEN PANICLE 1 (OP1), a gain-of-function allele of LIGULELESS 1 (LG1), controlling the spread-panicle phenotype. This allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary branch. Increased OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1 (sp1). Knocking out BRASSINOSTEROID UPREGULATED1 (BU1) gene in the background of OP1 complementary plants resulted in compact panicles, suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling pathway. We regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture. [ABSTRACT FROM AUTHOR]

Sustainable agriculture in combination with crop improvement programme is gaining more attention in the scientific field nowadays. With abundance of resources, endophytes offer an environmentally friendly and sustainable approach to increase crop yield, improve soil fertility while protecting the plants from a number of biotic and abiotic stresses. Residing within plant, endophytes are unique group of symbionts that systematically invade the internal environment of host without causing any pathogenic symptoms. Endophytes, which include bacteria, fungi, and viruses, have been shown to have beneficial effects on their hosts, either directly or indirectly. On the other hand, Zingiberaceae is a valuable family of ginger that has a lot of economic benefits. Endophytes isolated from the Zingiberaceae plants are known to promote plant development through the production of phytohormone, 1-aminocyclopropane -1 carboxylic acid (ACC) deaminase, siderophore and also assist the host plant in phosphate solubilization activity. They are also prominent producers of several secondary metabolites with a lot of bioactivities. However, the full potential of endophytes from the Zingiberaceae plants largely remain untapped. Thus, the aim of this review is to discover various types of endophytes isolated from the Zingiberaceae plants, their phytohormone production, nutrient acquisition, biohardening application, secondary metabolites production and bioactivities. The broad knowledge of endophytes from Zingiberaceae plants will provide insight into new economic potentials and determine its future in sustainable agriculture practices. [ABSTRACT FROM AUTHOR]

Molecular markers, including Simple Sequence Repeat (SSR), Single Nucleotide Polymorphism (SNP), and Intron Length Polymorphism (ILP), are widely utilized in crop improvement and population genetics studies. However, these marker resources remain insufficient for Musa species. In this study, we developed genome-wide SSR, SNP, and ILP markers from Musa and its sister species, creating a comprehensive molecular marker repository for the improvement of Musa species. This database contains 2,115,474 SSR, 63,588 SNP, and 91,547 ILP markers developed from thirteen Musa species and two of its relative species. We found that 77% of the SSR loci are suitable for marker development; 38% of SNP markers originated from the genic region, and transition mutations (C↔T; A↔G) were more frequent than transversion. The database is freely accessible and follows a 'three-tier architecture,' organizing marker information in MySQL tables. It has a user-friendly interface, written in JavaScript, PHP, and HTML code. Users can employ flexible search parameters, including marker location in the chromosome, transferability, polymorphism, and functional annotation, among others. These distinctive features distinguish the Musa Marker Database (MMdb) from existing marker databases by offering a novel approach that is tailored to the precise needs of the Musa research community. Despite being an in silico method, searching for markers based on various attributes holds promise for Musa research. These markers serve various purposes, including germplasm characterization, gene discovery, population structure analysis, and QTL mapping. [ABSTRACT FROM AUTHOR]

SUMMARY: Actinidia ('Mihoutao' in Chinese) includes species with complex ploidy, among which diploid Actinidia chinensis and hexaploid Actinidia deliciosa are economically and nutritionally important fruit crops. Actinidia deliciosa has been proposed to be an autohexaploid (2n = 174) with diploid A. chinensis (2n = 58) as the putative parent. A CCS‐based assembly anchored to a high‐resolution linkage map provided a chromosome‐resolved genome for hexaploid A. deliciosa yielded a 3.91‐Gb assembly of 174 pseudochromosomes comprising 29 homologous groups with 6 members each, which contain 39 854 genes with an average of 4.57 alleles per gene. Here we provide evidence that much of the hexaploid genome matches diploid A. chinensis; 95.5% of homologous gene pairs exhibited >90% similarity. However, intragenome and intergenome comparisons of synteny indicate chromosomal changes. Our data, therefore, indicate that if A. deliciosa is an autoploid, chromosomal rearrangement occurred following autohexaploidy. A highly diversified pattern of gene expression and a history of rapid population expansion after polyploidisation likely facilitated the adaptation and niche differentiation of A. deliciosa in nature. The allele‐defined hexaploid genome of A. deliciosa provides new genomic resources to accelerate crop improvement and to understand polyploid genome evolution. Significance Statement: We provide insights into the origin of the hexaploid crop Actinidia deliciosa—a putative autohexaploid. Our data suggest chromosomal rearrangements—indicating that either the species is a segmental allopolyploid, or if a strict autoploid then chromosomal rearrangement occurred following autohexaploidy. Our work also provides a template for the study of high ploidal level (6x genome) auto or segmental alloploid genomes. [ABSTRACT FROM AUTHOR]

The growth and yield of crop plants are threatened by environmental challenges such as water deficit, soil flooding, high salinity, and extreme temperatures, which are becoming increasingly severe under climate change. Stomata contribute greatly to plant adaptation to stressful environments by governing transpirational water loss and photosynthetic gas exchange. Increasing evidence has revealed that stomata formation is shaped by transcription factors, signaling peptides, and protein kinases, which could be exploited to improve crop stress resistance. The past decades have seen unprecedented progress in our understanding of stomata formation, but most of these advances have come from research on model plants. This review highlights recent research in stomata formation in crops and its multifaceted functions in abiotic stress tolerance. Current strategies, limitations, and future directions for harnessing stomatal development to improve crop stress resistance are discussed. [ABSTRACT FROM AUTHOR]

Physaria fendleri is a member of the Brassicaceae that produces in its embryos hydroxy fatty acids, constituents of oils that are very valuable and widely used by industry for cosmetics, lubricants, biofuels, etc. Free of toxins and rich in hydroxy fatty acids, Physaria provides a promising alternative to imported castor oil and is on the verge of being commercialized. This study aims to identify important biochemical step(s) for oil synthesis in Physaria , which may serve as target(s) for future crop improvement. To advance towards this goal, the endosperm composition was analysed by LC-MS/MS to develop and validate culture conditions that mimic the development of the embryos in planta. Using developing Physaria embryos in culture and 13C-labeling, our studies revealed that: (i) Physaria embryos metabolize carbon into biomass with an efficiency significantly lower than other photosynthetic embryos; (ii) the plastidic malic enzyme provides 42% of the pyruvate used for de novo fatty acid synthesis, which is the highest measured so far in developing 'green' oilseed embryos; and (iii) Physaria uses non-conventional pathways to channel carbon into oil, namely the Rubisco shunt, which fixes CO2 released in the plastid, and the reversibility of isocitrate dehydrogenase, which provides additional carbon for fatty acid elongation. [ABSTRACT FROM AUTHOR]

DNA-binding with one finger (Dof) proteins comprise a large family that play central roles in stress tolerance by regulating the expression of stress-responsive genes via the DOFCORE element or by interacting with other regulatory proteins. Although the Dof TF has been identified in a variety of species, its systemic analysis in potato (Solanum tuberosum L.) is lacking and its potential role in abiotic stress responses remains unclear. A total of 36 potential Dof genes in potato were examined at the genomic and transcriptomic levels in this work. Five phylogenetic groups can be formed from these 36 Dof proteins. An analysis of cis-acting elements revealed the potential roles of Dofs in potato development, including under numerous abiotic stress conditions. The cycling Dof factors (CDFs) might be the initial step in the abiotic stress response signaling cascade. In potato, five CDFs (StCDF1/StDof19, StCDF2/StDof4, StCDF3/StDof11, StCDF4/StDof24, and StCDF5/StDof15) were identified, which are homologs of Arabidopsis CDFs. The results revealed that these genes were engaged in a variety of abiotic reactions. Moreover, an expression analysis of StDof genes in two potato cultivars ('Long10′ (drought tolerant) and 'DXY' (drought susceptible)) of contrasting tolerances under drought stress was carried out. Further, a regulatory network mediated by lncRNA and its target Dofs was established. The present study provides fundamental knowledge for further investigation of the roles of Dofs in the adaptation of potato to drought stress, aiming to provide insights into a viable strategy for crop improvement and stress-resistance breeding. [ABSTRACT FROM AUTHOR]

The Tahitian (or Polynesian) chestnut Inocarpus fagifer is distributed widely in tropical South-East Asia and in the Pacific region. It is an important component in traditional agroforestry systems. However, its importance as a food plant has decreased considerably. There is no evidence that the species has ever been domesticated, nor that deliberate breeding and crop improvement is presently taking place. This article aims to provide an overview of the current status of knowledge about its distribution, biology, its past and current cultivation and use as a species in agroforestry systems, and to analyse its future potential for production, commercial use and plant improvement. Inocarpus fagifer grows in lowlands in coastal and near coastal areas, often along rivers. It often forms almost pure stands underneath the canopy trees. Inocarpus fagifer trees are very vigorous and shade-tolerant. They thrive in moist to wet soils. Nearly all parts of the tree have been used for multiple purposes including timber, medicine, and animal fodder. The seed has significant traditional importance as human food, and it plays an important role in the diets of rural communities, in particular during the crop harvesting season. Inocarpus fagifer is mostly disease-free. Reports about the commercial use of I. fagifer remain localised and largely anecdotal. The species retains a good potential for commercial development and for a wider commercial use as an alternative food source. No accessible genebank accessions are available. Fundamental questions on its marketability and genetic potential need to be answered. [ABSTRACT FROM AUTHOR]