Characteristics of NAC transcription factors in Solanaceae crops and their roles in responding to abiotic and biotic stresses.

As one of the largest transcription factor (TF) families in plants, the NAC (NAM, ATAF1/2, and CUC2) family plays important roles in response pathways to various abiotic and biotic stresses, such as drought, high salinity, low temperature, and pathogen infection. Although, there are a number of reviews on the involvement of NAC TF in plant responses to biotic and abiotic stresses, most of them are focused on the model plants Arabidopsis thaliana and Oryza sativa, and there is a lack of systematic evaluation of specific species. Solanaceae, the world's third most significant cash crop, has been seriously affected by environmental disturbances in recent years in terms of yield and quality, posing a severe threat to global food security. This review focuses on the functional roles of NAC transcription factors in response to external stresses involved in five important Solanaceae crops: tomato, potato, pepper, eggplant and tobacco, and analyzes the affinities between them. It will provide resources for stress-resistant breeding of Solanaceae crops using transgenic technology.

Whole-genome sequencing in medicinal plants: current progress and prospect.

Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.

Deprivation of Sexual Reproduction during Garlic Domestication and Crop Evolution.

Garlic, originating in the mountains of Central Asia, has undergone domestication and subsequent widespread introduction to diverse regions. Human selection for adaptation to various climates has resulted in the development of numerous garlic varieties, each characterized by specific morphological and physiological traits. However, this process has led to a loss of fertility and seed production in garlic crops. In this study, we conducted morpho-physiological and transcriptome analyses, along with whole-genome resequencing of 41 garlic accessions from different regions, in order to assess the variations in reproductive traits among garlic populations. Our findings indicate that the evolution of garlic crops was associated with mutations in genes related to vernalization and the circadian clock. The decline in sexual reproduction is not solely attributed to a few mutations in specific genes, but is correlated with extensive alterations in the genetic regulation of the annual cycle, stress adaptations, and environmental requirements. The regulation of flowering ability, stress response, and metabolism occurs at both the genetic and transcriptional levels. We conclude that the migration and evolution of garlic crops involve substantial and diverse changes across the entire genome landscape. The construction of a garlic pan-genome, encompassing genetic diversity from various garlic populations, will provide further insights for research into and the improvement of garlic crops.

BEL transcription factors in prominent Solanaceae crops: the missing pieces of the jigsaw in plant development.

MAIN CONCLUSION: Understanding BEL transcription factors roles in potato and tomato varies considerably with little overlap. The review suggests reciprocal use of gained results to proceed with the knowledge in both crops The proper development of organs that plants use for reproduction, like fruits or tubers, is crucial for the survival and competitiveness of the species and thus subject to strict regulations. Interestingly, the controls of potato (Solanum tuberosum) tuber and tomato (S. lycopersicum) fruit development use common mechanisms, including the action of the BEL transcription factors (TFs). Although more than ten BEL genes have been identified in either genome, only a few of them have been characterized. The review summarizes knowledge of BEL TFs' roles in these closely related Solanaceae species, focusing on those that are essential for tuberization in potato, namely StBEL5, StBEL11 and StBEL29, and for fruit development in tomato - SlBEL11, SlBL2 and SIBL4. Comprehension of the roles of individual BEL TFs, however, is not yet sufficient. Different levels of understanding of important characteristics are described, such as BEL transcript accumulation patterns, their mobility, BEL protein interaction with KNOX partners, subcellular localisation, and their target genes during initiation and development of the organs in question. A comparison of the knowledge on BEL TFs and their mechanisms of action in potato and tomato may provide inspiration for faster progress in the study of both models through the exchange of information and ideas. Both crops are extremely important for human nutrition. In addition, their production is likely to be threatened by the upcoming climate change, so there is a particular need for breeding using a deep knowledge of control mechanisms.

Potato and sweetpotato breeding at the international potato center: approaches, outcomes and the way forward.

Root and tuber crop breeding is at the front and center of CIP's science program, which seeks to develop and disseminate sustainable agri-food technologies, information and practices to serve objectives including poverty alleviation, income generation, food security and the sustainable use of natural resources. CIP was established in 1971 in Peru, which is part of potato's center of origin and diversity, with an initial mandate on potato and expanding to include sweetpotato in 1986. Potato and sweetpotato are among the top 10 most consumed food staples globally and provide some of the most affordable sources of energy and vital nutrients. Sweetpotato plays a key role in securing food for many households in Africa and South Asia, while potato is important worldwide. Both crops grow in a range of conditions with relatively few inputs and simple agronomic techniques. Potato is adapted to the cooler environments, while sweetpotato grows well in hot climates, and hence, the two crops complement each other. Germplasm enhancement (pre-breeding), the development of new varieties and building capacity for breeding and variety testing in changing climates with emphasis on adaptation, resistance, nutritional quality and resource-use efficiency are CIP's central activities with significant benefits to the poor. Investments in potato and sweetpotato breeding and allied disciplines at CIP have resulted in the release of many varieties some of which have had documented impact in the release countries. Partnership with diverse types of organizations has been key to the centers way of working toward improving livelihoods through crop production in the global South.

Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles.

Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.

Fertilization and cultivation management promotes soil phosphorus availability by enhancing soil P-cycling enzymes and the phosphatase encoding genes in bulk and rhizosphere soil of a maize crop in sloping cropland.

Fertilization and cultivation managements exert significant effects on crop growth and soil-associated nutrients in croplands. However, there is a lack of knowledge regarding how these practices affect soil phosphorus-cycling enzymes and functional genes involved in regulating global P-cycling, especially under intense agricultural management practices in sloping croplands. A long-term field (15-year) trial was conducted in a 15° sloping field based on five treatments: no fertilizer amendments + downslope cultivation (CK); mixed treatment of mineral fertilizer and organic manure + downslope cultivation (T1); mineral fertilizer alone + downslope cultivation (T2); 1.5-fold mineral fertilizer + downslope cultivation (T3); and mineral fertilizer + contour cultivation (T4). Bulk and rhizosphere soil samples were collected after the maize crop was harvested to determine the P fraction, P-cycling enzymes, and phosphatase-encoding genes. Results indicated that fertilization management significantly increased the inorganic (Pi) and organic soil (Po) P fractions compared to CK, except for NaOH-extractable Po in T1 and T3 in bulk and rhizosphere soils, respectively. For the cultivation treatments, the content of Pi pools in the downslope cultivation of T1 and T3 was significantly larger than that in the contour cultivation of T4 in bulk and rhizosphere soils. However, the content of NaOH-extractable Po in T1 and T3 was lower compared to T4 in bulk soil and vice versa for the NaHCO3-P and HCl-Po fractions in the rhizosphere. We also found that fertilization and cultivation managements significantly increased the activity of acid phosphatase (ACP), alkaline phosphatase (ALP), phytase, phosphodiesterases (PDE), and phoC and phoD gene abundance in bulk and rhizosphere soils, with a larger effect on the activity of ALP and the phosphatase encoding phoD gene, especially in T1 and T3 in the rhizosphere. Soil organic carbon (SOC) and microbial biomass C and P (MBC and MBP) were the main predictors for regulating P-cycling enzymes and phoC- and phoD gene abundance. A strong association of P-cycling enzymes, especially ALP and phytase, and the abundance of phoD genes with the P fraction indicated that the soil P cycle was mainly mediated by microbial-related processes. Together, our results demonstrated that an adequate amount of mineral fertilizer alone or combined with organic fertilizer plus downslope cultivation is more effective in promoting soil P availability by enhancing the activity of ALP, phytase, and phoD genes. This provides valuable information for sustaining soil microbial-regulated P management practices in similar agricultural lands worldwide.

Pig manure treatment strategies for mitigating the spread of antibiotic resistance.

Due to the risk of pathogenic antibiotic-resistant bacteria and their antibiotic-resistance genes transfer from livestock feces to the soil and cultivated crops, it is imperative to find effective on-farm manure treatments to minimize that hazardous potential. An introduced worldwide policy of sustainable development, focus on ecological agricultural production, and the circular economy aimed at reducing the use of artificial fertilizers; therefore, such treatment methods should also maximize the fertilization value of animal manure. The two strategies for processing pig manure are proposed in this study-storage and composting. The present study examines the changes in the physicochemical properties of treated manure, in the microbiome, and in the resistome, compared to raw manure. This is the first such comprehensive analysis performed on the same batch of manure. Our results suggest that while none of the processes eliminates the environmental risk, composting results in a faster and more pronounced reduction of mobile genetic elements harboring antibiotic resistance genes, including those responsible for multi-drug resistance. Overall, the composting process can be an efficient strategy for mitigating the spread of antibiotic resistance in the environment and reducing the risk of its transfer to crops and the food chain while providing essential fertilizer ingredients.

Molecular genetics of cytoplasmic male sterility and restorer-of-fertility for the fine tuning of pollen production in crops.

Cytoplasmic male sterility (CMS) is an increasingly important issue within the context of hybrid seed production. Its genetic framework is simple: S-cytoplasm for male sterility induction and dominant allele of the restorer-of-fertility gene (Rf) for suppression of S. However, breeders sometimes encounter a phenotype of CMS plants too complex to be explained via this simple model. The molecular basis of CMS provides clue to the mechanisms that underlie the expression of CMS. Mitochondria have been associated with S, and several unique ORFs to S-mitochondria are thought to be responsible for the induction of male sterility in various crops. Their functions are still the subject of debate, but they have been hypothesized to emit elements that trigger sterility. Rf suppresses the action of S by various mechanisms. Some Rfs, including those that encode the pentatricopeptide repeat (PPR) protein and other proteins, are now considered members of unique gene families that are specific to certain lineages. Additionally, they are thought to be complex loci in which several genes in a haplotype simultaneously counteract an S-cytoplasm and differences in the suite of genes in a haplotype can lead to multiple allelism including strong and weak Rf at phenotypic level. The stability of CMS is influenced by factors such as the environment, cytoplasm, and genetic background; the interaction of these factors is also important. In contrast, unstable CMS becomes inducible CMS if its expression can be controlled. CMS becomes environmentally sensitive in a genotype-dependent manner, suggesting the feasibility of controlling the expression of CMS.

Genomic variation in the genus Beta based on 656 sequenced beet genomes.

Cultivated beets (Beta vulgaris ssp. vulgaris) constitute important crop plants, in particular sugar beet as an indispensable source of sucrose. Several species of wild beets of the genus Beta with distribution along the European Atlantic coast, Macaronesia, and throughout the Mediterranean area exist. Thorough characterization of beet genomes is required for straightforward access to genes promoting genetic resistance against biotic and abiotic stress. Analysing short-read data of 656 sequenced beet genomes, we identified 10 million variant positions in comparison to the sugar beet reference genome RefBeet-1.2. The main groups of species and subspecies were distinguishable based on shared variation, and the separation of sea beets (Beta vulgaris ssp. maritima) into a Mediterranean and an Atlantic subgroup as suggested by previous studies could be confirmed. Complementary approaches of variant-based clustering were employed based on PCA, genotype likelihoods, tree calculations, and admixture analysis. Outliers suggested the occurrence of inter(sub)specific hybridisation, independently confirmed by different analyses. Screens for regions under artificial selection in the sugar beet genome identified 15 Mbp of the genome as variation-poor, enriched for genes involved in shoot system development, stress response, and carbohydrate metabolism. The resources presented herein will be valuable for crop improvement and wild species monitoring and conservation efforts, and for studies on beet genealogy, population structure and population dynamics. Our study provides a wealth of data for in-depth analyses of further aspects of the beet genome towards a thorough understanding of the biology of this important complex of a crop species and its wild relatives.

Genetically modified crops do not present variations in pollen viability and morphology when compared to their conventional counterparts.

Modern agricultural biotechnologies, such as those derived from genetic modification, are solutions that can enable an increase in food production, lead to more efficient use of natural resources, and promote environmental impact reduction. Crops with altered genetic materials have been extensively subjected to safety assessments to fulfill regulatory requirements prior to commercialization. The Brazilian National Technical Biosafety Commission (CTNBio) provides provisions for commercial release of transgenic crops in Brazil, including requiring information on pollen dispersion ability as part of environmental risk assessment, which includes pollen viability and morphology studies. Here we present the pollen viability and morphology of non-transgenic conventional materials, single-event genetically modified (GM) products, and stacked GM products from soybean, maize and cotton cultivated in Brazil. Microscopical observation of stained pollen grain was conducted to determine the percentage of pollen viability as well as pollen morphology, which is assessed by measuring pollen grain diameter. The pollen viability and diameter of GM soybean, maize and cotton, evaluated across a number of GM events in each crop, were similar to the conventional non-GM counterparts. Pollen characterization data contributed to the detailed phenotypic description of GM crops, supporting the conclusion that the studied events were not fundamentally different from the conventional control.

Genome-Wide Admixture Mapping Identifies Wild Ancestry-of-Origin Segments in Cultivated Robusta Coffee.

Humans have had a major influence on the dissemination of crops beyond their native range, thereby offering new hybridization opportunities. Characterizing admixed genomes with mosaic origins generates valuable insight into the adaptive history of crops and the impact on current varietal diversity. We applied the ELAI tool-an efficient local ancestry inference method based on a two-layer hidden Markov model to track segments of wild origin in cultivated accessions in the case of multiway admixtures. Source populations-which may actually be limited and partially admixed-must be generally specified when using such inference models. We thus developed a framework to identify local ancestry with admixed source populations. Using sequencing data for wild and cultivated Coffea canephora (commonly called Robusta), our approach was found to be highly efficient and accurate on simulated hybrids. Application of the method to assess elite Robusta varieties from Vietnam led to the identification of an accession derived from a likely backcross between two genetic groups from the Congo Basin and the western coastal region of Central Africa. Admixtures resulting from crop hybridization and diffusion could thus lead to the generation of elite high-yielding varieties. Our methods should be widely applicable to gain insight into the role of hybridization during plant and animal evolutionary history.

Differential ability of three bee species to move genes via pollen.

Since the release of genetically engineered (GE) crops, there has been increased concern about the introduction of GE genes into non-GE fields of a crop and their spread to feral or wild cross-compatible relatives. More recently, attention has been given to the differential impact of distinct pollinators on gene flow, with the goal of developing isolation distances associated with specific managed pollinators. To examine the differential impact of bee species on gene movement, we quantified the relationship between the probability of getting a GE seed in a pod, and the order in which a flower was visited, or the cumulative distance traveled by a bee in a foraging bout. We refer to these relationships as 'seed curves' and compare these seeds curves among three bee species. The experiments used Medicago sativa L. plants carrying three copies of the glyphosate resistance (GR) allele as pollen donors (M. sativa is a tetraploid), such that each pollen grain carried the GR allele, and conventional plants as pollen recipients. Different foraging metrics, including the number of GR seeds produced over a foraging bout, were also quantified and contrasted among bee species. The lowest number of GR seeds set per foraging bout, and the GR seeds set at the shortest distances, were produced following leafcutting bee visits. In contrast, GR seeds were found at the longest distances following bumble bee visits. Values for honey bees were intermediate. The ranking of bee species based on seed curves correlated well with field-based gene flow estimates. Thus, differential seed curves of bee species, which describe patterns of seed production within foraging bouts, translated into distinct abilities of bee species to move genes at a landscape level. Bee behavior at a local scale (foraging bout) helps predict gene flow and the spread of GE genes at the landscape scale.

Engineering Nutritionally Improved Edible Plant Oils.

In contrast to traditional breeding, which relies on the identification of mutants, metabolic engineering provides a new platform to modify the oil composition in oil crops for improved nutrition. By altering endogenous genes involved in the biosynthesis pathways, it is possible to modify edible plant oils to increase the content of desired components or reduce the content of undesirable components. However, introduction of novel nutritional components such as omega-3 long-chain polyunsaturated fatty acids needs transgenic expression of novel genes in crops. Despite formidable challenges, significant progress in engineering nutritionally improved edible plant oils has recently been achieved, with some commercial products now on the market.

The Power and Perils of De Novo Domestication Using Genome Editing.

There is intense interest in using genome editing technologies to domesticate wild plants, or accelerate the improvement of weakly domesticated crops, in de novo domestication. Here, we discuss promising genetic strategies, with a focus on plant development. Importantly, genome editing releases us from dependence on random mutagenesis or intraspecific diversity, allowing us to draw solutions more broadly from diversity. However, sparse understanding of the complex genetics of diversity limits innovation. Beyond genetics, we urge the ethical use of indigenous knowledge, indigenous plants, and ethnobotany. De novo domestication still requires conventional breeding by phenotypic selection, especially in the development of crops for diverse environments and cultures. Indeed, uniting genome editing with selective breeding could facilitate faster and better outcomes than either technology alone. Domestication is complex and incompletely understood, involving changes to many aspects of plant biology and human culture. Success in de novo domestication requires careful attention to history and collaboration across traditional boundaries.

The Perspective of Arbuscular Mycorrhizal Symbiosis in Rice Domestication and Breeding.

In nature, symbiosis with arbuscular mycorrhizal (AM) fungi contributes to sustainable acquisition of phosphorus and other elements in over 80% of plant species; improving interactions with AM symbionts may mitigate some of the environmental problems associated with fertilizer application in grain crops such as rice. Recent developments of high-throughput genome sequencing projects of thousands of rice cultivars and the discovery of the molecular mechanisms underlying AM symbiosis suggest that interactions with AM fungi might have been an overlooked critical trait in rice domestication and breeding. In this review, we discuss genetic variation in the ability of rice to form AM symbioses and how this might have affected rice domestication. Finally, we discuss potential applications of AM symbiosis in rice breeding for more sustainable agriculture.

Cas12a-based on-site, rapid detection of genetically modified crops.

A CRISPR/LbCas12a-based nucleic acid detection method that uses crude leaf extracts as samples and is rapid (≤40 min for a full run) and highly sensitive (0.01%) can be used to monitor genetically modified organisms in the field.

Genome evolution and diversity of wild and cultivated potatoes.

Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and the vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have the potential to revolutionize future potato breeding and production1-4. So far, relatively few studies have examined the genome evolution and diversity of wild and cultivated landrace potatoes, which limits the application of their diversity in potato breeding. Here we assemble 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota, the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum. Extensive discordance of phylogenomic relationships suggests the complexity of potato evolution. We find that the potato genome substantially expanded its repertoire of disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative of the effect of tuber-based propagation strategies on the evolution of the potato genome. We discover a transcription factor that determines tuber identity and interacts with the mobile tuberization inductive signal SP6A. We also identify 561,433 high-confidence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplified by a 5.8-Mb inversion that is associated with carotenoid content in tubers. This study will accelerate hybrid potato breeding and enrich our understanding of the evolution and biology of potato as a global staple food crop.

Narrowing down molecular targets for improving phosphorus-use efficiency in maize (Zea mays L.).

Conventional agricultural practices rely heavily on chemical fertilizers to boost production. Among the fertilizers, phosphatic fertilizers are copiously used to ameliorate low-phosphate availability in the soil. However, phosphorus-use efficiency (PUE) for major cereals, including maize, is less than 30%; resulting in more than half of the applied phosphate being lost to the environment. Rock phosphate reserves are finite and predicted to exhaust in near future with the current rate of consumption. Thus, the dependence of modern agriculture on phosphatic fertilizers poses major food security and sustainability challenges. Strategies to optimize and improve PUE, like genetic interventions to develop high PUE cultivars, could have a major impact in this area. Here, we present the current understanding and recent advances in the biological phenomenon of phosphate uptake, translocation, and adaptive responses of plants under phosphate deficiency, with special reference to maize. Maize is one of the most important cereal crops that is cultivated globally under diverse agro-climatic conditions. It is an industrial, feed and food crop with multifarious uses and a fast-rising global demand and consumption. The interesting aspects of diversity in the root system architecture traits, the interplay between signaling pathways contributing to PUE, and an in-depth discussion on promising candidate genes for improving PUE in maize are elaborated.