Brown-top millet: an overview of breeding, genetic, and genomic resources development for crop improvement.

MAIN CONCLUSION: Brown-top millet is a lesser-known millet with a high grain nutrient value, early maturation, and drought tolerance that needs basic research to understand and conserve food security. Brown-top millet [Urochloa ramosa (L.)] is currently cultivated in some developing countries (especially in India) for food and fodder, although it is less known among the small millets. Like other millets, it contains macro- and micronutrients, vitamins, minerals, proteins, and fiber, all of which have rich health benefits. The nutritional importance and health benefits of brown-top millet are still unknown to many people due to a lack of awareness, wide cultivation, and research. Hence, this millet is currently overshadowed by other major cereals. This review article aims to present the nutritional, breeding, genetic, and genomic resources of brown-top millet to inform millet and other plant researchers. It is important to note that genetic and genomic resources have not yet been created for this millet. To date, there are no genomic and transcriptomic resources for brown-top millet to develop single nucleotide polymorphisms (SNP) and insertion/Deletions (InDels) for breeding studies. Furthermore, studies regarding nutritional significance and health benefits are required to investigate the exact nutritional contents and health benefits of the brown-top millet. The present review delves into the nutritional value and health advantages of brown-top millet, as supported by the available literature. The limitations of producing brown-top millet have been enumerated. We also cover the status of marker-assisted breeding and functional genomics research on closely related species. Lastly, we draw insights for further research such as developing omics resources and applying genome editing to study and improve brown-top millet. This review will help to start breeding and other molecular studies to increase the growth and development of this cereal.

The Era of Plant Breeding: Conventional Breeding to Genomics-assisted Breeding for Crop Improvement.

Plant breeding has made a significant contribution to increasing agricultural production. Conventional breeding based on phenotypic selection is not effective for crop improvement. Because phenotype is considerably influenced by environmental factors, which will affect the selection of breeding materials for crop improvement. The past two decades have seen tremendous progress in plant breeding research. Especially the availability of high-throughput molecular markers followed by genomic-assisted approaches significantly contributed to advancing plant breeding. Integration of speed breeding with genomic and phenomic facilities allowed rapid quantitative trait loci (QTL)/gene identifications and ultimately accelerated crop improvement programs. The advances in sequencing technology helps to understand the genome organization of many crops and helped with genomic selection in crop breeding. Plant breeding has gradually changed from phenotype-to-genotype-based to genotype-to-phenotype-based selection. High-throughput phenomic platforms have played a significant role in the modern breeding program and are considered an essential part of precision breeding. In this review, we discuss the rapid advance in plant breeding technology for efficient crop improvements and provide details on various approaches/platforms that are helpful for crop improvement. This review will help researchers understand the recent developments in crop breeding and improvements.

Epigenetic modifications and miRNAs determine the transition of somatic cells into somatic embryos.

KEY MESSAGE: This review discusses the epigenetic changes during somatic embryo (SE) development, highlights the genes and miRNAs involved in the transition of somatic cells into SEs as a result of epigenetic changes, and draws insights on biotechnological opportunities to study SE development. Somatic embryogenesis from somatic cells occurs in a series of steps. The transition of somatic cells into somatic embryos (SEs) is the most critical step under genetic and epigenetic regulations. Major regulatory genes such as SERK, WUS, BBM, FUS3/FUSA3, AGL15, and PKL, control SE steps and development by turning on and off other regulatory genes. Gene transcription profiles of somatic cells during SE development is the result of epigenetic changes, such as DNA and histone protein modifications, that control and decide the fate of SE formation. Depending on the type of somatic cells and the treatment with plant growth regulators, epigenetic changes take place dynamically. Either hypermethylation or hypomethylation of SE-related genes promotes the transition of somatic cells. For example, the reduced levels of DNA methylation of SERK and WUS promotes SE initiation. Histone modifications also promote SE induction by regulating SE-related genes in somatic cells. In addition, miRNAs contribute to the various stages of SE by regulating the expression of auxin signaling pathway genes (TIR1, AFB2, ARF6, and ARF8), transcription factors (CUC1 and CUC2), and growth-regulating factors (GRFs) involved in SE formation. These epigenetic and miRNA functions are unique and have the potential to regenerate bipolar structures from somatic cells when a pluripotent state is induced. However, an integrated overview of the key regulators involved in SE development and downstream processes is lacking. Therefore, this review discusses epigenetic modifications involved in SE development, SE-related genes and miRNAs associated with epigenetics, and common cis-regulatory elements in the promoters of SE-related genes. Finally, we highlight future biotechnological opportunities to alter epigenetic pathways using the genome editing tool and to study the transition mechanism of somatic cells.

Effects of Individual or Combined Deficiency of Phosphorous and Zinc on Phenotypic, Nutrient Uptake, and Molecular Responses of Finger Millet (Eleusine coracana): A Nutri-Rich Cereal Crop.

Deficiencies of either phosphorus (P) or zinc (Zn) or both are one of the major abiotic constraints influencing agricultural production. Research on the effects of individual or combined P and Zn deficiency is limited in cereals. This study reports the effects of the individual or combined deficiency of inorganic phosphate (Pi) and Zn on the phenotypic, root hair modification, nutrient uptake, and molecular responses of finger millet (Eleusine coracana), a nutri-rich cereal crop. Finger millet seedlings were grown hydroponically under control (+Pi+Zn), individual Pi deficiency (-Pi), individual Zn deficiency (-Zn), and combined Pi and Zn deficiency (-Pi-Zn) conditions for 30 days to find the phenotypic, root hair modification, nutrient uptake, and molecular responses. Compared to the individual -Zn condition, the individual -Pi condition had more of an effect in terms of biomass reduction. The combined -Pi-Zn condition increased the root hair length and density compared to the other three conditions. The individual -Zn condition increased the Pi uptake, while the individual -Pi condition favored the Zn uptake. EcZIP2 was highly upregulated in shoot tissues under the individual -Zn condition, and EcPHT1;2 was highly expressed in root tissues under the individual -Pi condition. This is the first study to report the effects of the individual or combined deficiency of Pi and Zn in finger millet and may lead to future studies to better manage P and Zn deficiency.

Strigolactone Mediates Moso Bamboo Root Response to Phosphate Stress.

Both phosphate (Pi) deficiency and high Pi significantly affect moso bamboo growth and degrade bamboo forests. A novel plant hormone, strigolactone (SL), plays a crucial role in root growth under low Pi, but the SL regulatory mechanism has not been systematically reported in moso bamboo. In our study, we investigated the SL-mediated root growth mechanism in response to Pi stress in moso bamboo. With the decrease of the Pi level, 5-deoxystrigol and strigol significantly increased in the root exudates. Transcriptome sequencing of the primary root tip and lateral root primordium zone (LRP) under low, sufficient, and high Pi indicated that SL-biosynthesis and -signaling changes are part of the early root responses. The effects of the SL analogue (rac-GR24) and SL inhibitor (TIS108) on the root architecture under low and high Pi revealed that SL mediates bamboo root responses by regulating its biosynthesis and signal transduction and influencing other hormone pathways.

Significance and genetic control of membrane transporters to improve phytoremediation and biofortification processes.

Humans frequently consume plant-based foods in their daily life. Contamination of agricultural soils by heavy metals (HMs) is a major food and nutritional security issue. The crop plants grown in HM-contaminated agricultural soil may accumulate more HMs in their edible part, further transferring into the food chain. Consumption of HM-rich crops can cause severe health issues in humans. On the other hand, the low content of the essential HM in the edible part of the crop also causes health problems. Therefore, researchers must try to reduce the non-essential HM in the edible part of the crop plants and improve the essential HMs. Phytoremediation and biofortification are the two strategies for resolving this problem. The genetic component helps to improve the efficiency of phytoremediation and biofortification processes in plants. They help eliminate HMs from soil and improve essential HM content in crop plants. The membrane transporter genes (genetic components) are critical in these two strategies. Therefore, engineering membrane transporter genes may help reduce the non-essential HM content in the edible part of crop plants. Targeted gene editing by genome editing tools like CRISPR could help plants achieve efficient phytoremediation and biofortification. This article covers gene editing's scope, application, and implication to improve the phytoremediation and biofortification processes in non-crop and crop plants.

Biofortification of Crops to Fight Anemia: Role of Vacuolar Iron Transporters.

Plant-based foods provide all the crucial nutrients for human health. Among these, iron (Fe) is one of the essential micronutrients for plants and humans. A lack of Fe is a major limiting factor affecting crop quality, production, and human health. There are people who suffer from various health problems due to the low intake of Fe in their plant-based foods. Anemia has become a serious public health issue due to Fe deficiency. Enhancing Fe content in the edible part of food crops is a major thrust area for scientists worldwide. Recent progress in nutrient transporters has provided an opportunity to resolve Fe deficiency or nutritional problems in plants and humans. Understanding the structure, function, and regulation of Fe transporters is essential to address Fe deficiency in plants and to improve Fe content in staple food crops. In this review, we summarized the role of Fe transporter family members in the uptake, cellular and intercellular movement, and long-distance transport of Fe in plants. We draw insights into the role of vacuolar membrane transporters in the crop for Fe biofortification. We also provide structural and functional insights into cereal crops' vacuolar iron transporters (VITs). This review will help highlight the importance of VITs for improving the Fe biofortification of crops and alleviating Fe deficiency in humans.

Zinc supply influenced the growth, yield, zinc content, and expression of ZIP family transporters in sorghum.

MAIN CONCLUSION: Zinc deficiency altered shoot and root growth, plant biomass, yield, and ZIP family transporter gene expression in sorghum. Zinc (Zn) deficiency affects several crop plants' growth and yield, including sorghum. We have evaluated the sorghum under various concentrations of Zn supply for phenotypic changes, Zn content, and expression of Zn-regulated, iron-regulated transporter-like proteins (ZIP) family genes. Zn deficiency reduced the shoot and root growth, plant biomass, and yield by > 50%. The length and number of lateral roots were increased by more than 50% under deficient Zn compared to sufficient Zn. Ten SbZIP family transporter genes showed dynamic expression in shoot and root tissues of sorghum under deficient and sufficient Zn. SbZIP2, 5, 6, 7, and 8 were expressed in all tissues under deficient and sufficient Zn. SbZIP2, 4, 5, 6, 7, 8, and 10 were highly induced in shoot tissues by deficient Zn. The expression level of SbZIP6, 7, 8, and 9 was higher in root tissues under deficient Zn. The phylogenetic analysis revealed that most SbZIP family proteins are closely associated with the ZmZIP family of maize. The functional residues His177 and Gly182 are fully conserved in all SbZIP family transporters, as revealed by homology modeling and multiple sequence alignment. This study may provide a foundation for improving the Zn-use efficiency of sorghum.

The role of metal transporters in phytoremediation: A closer look at Arabidopsis.

Pollution of the environment by heavy metals (HMs) has recently become a global issue, affecting the health of all living organisms. Continuous human activities (industrialization and urbanization) are the major causes of HM release into the environment. Over the years, two methods (physical and chemical) have been widely used to reduce HMs in polluted environment. However, these two methods are inefficient and very expensive to reduce the HMs released into the atmosphere. Alternatively, researchers are trying to remove the HMs by employing hyper-accumulator plants. This method, referred to phytoremediation, is highly efficient, cost-effective, and eco-friendly. Phytoremediation can be divided into five types: phytostabilization, phytodegradation, rhizofiltration, phytoextraction, and phytovolatilization, all of which contribute to HMs removal from the polluted environment. Brassicaceae family members (particularly Arabidopsis thaliana) can accumulate more HMs from the contaminated environment than those of other plants. This comprehensive review focuses on how HMs pollute the environment and discusses the phytoremediation measures required to reduce the impact of HMs on the environment. We discuss the role of metal transporters in phytoremediation with a focus on Arabidopsis. Then draw insights into the role of genome editing tools in enhancing phytoremediation efficiency. This review is expected to initiate further research to improve phytoremediation by biotechnological approaches to conserve the environment from pollution.

Application of CRISPR/Cas system in cereal improvement for biotic and abiotic stress tolerance.

MAIN CONCLUSION: Application of the recently developed CRISPR/Cas tools might help enhance cereals' growth and yield under biotic and abiotic stresses. Cereals are the most important food crops for human life and an essential source of nutrients for people in developed and developing countries. The growth and yield of all major cereals are affected by both biotic and abiotic stresses. To date, molecular breeding and functional genomic studies have contributed to the understanding and improving cereals' growth and yield under biotic and abiotic stresses. Clustered, regularly inter-spaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been predicted to play a major role in precision plant breeding and developing non-transgenic cereals that can tolerate adverse effects of climate change. Variants of next-generation CRISPR/Cas tools, such as prime editor, base editor, CRISPR activator and repressor, chromatin imager, Cas12a, and Cas12b, are currently used in various fields, including plant science. However, few studies have been reported on applying the CRISPR/Cas system to understand the mechanism of biotic and abiotic stress tolerance in cereals. Rice is the only plant used frequently for such studies. Genes responsible for biotic and abiotic stress tolerance have not yet been studied by CRISPR/Cas system in other major cereals (sorghum, barley, maize and small millets). Examining the role of genes that respond to biotic and abiotic stresses using the CRISPR/Cas system may help enhance cereals' growth and yield under biotic and abiotic stresses. It will help to develop new and improved cultivars with biotic- and abiotic-tolerant traits for better yields to strengthen food security. This review provides information for cereal researchers on the current status of the CRISPR/Cas system for improving biotic and abiotic stress tolerance in cereals.

Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops-An Updated Overview.

Cereals have evolved various tolerance mechanisms to cope with abiotic stress. Understanding the abiotic stress response mechanism of cereal crops at the molecular level offers a path to high-yielding and stress-tolerant cultivars to sustain food and nutritional security. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. Omics approaches generate a massive amount of data, and adequate advancements in computational tools have been achieved for effective analysis. The combination of integrated omics and bioinformatics approaches has been recognized as vital to generating insights into genome-wide stress-regulation mechanisms. In this review, we have described the self-driven drought, heat, and salt stress-responsive mechanisms that are highlighted by the integration of stress-manipulating components, including transcription factors, co-expressed genes, proteins, etc. This review also provides a comprehensive catalog of available online omics resources for cereal crops and their effective utilization. Thus, the details provided in the review will enable us to choose the appropriate tools and techniques to reduce the negative impacts and limit the failures in the intensive crop improvement study.

Insights to improve the plant nutrient transport by CRISPR/Cas system.

We need to improve food production to feed the ever growing world population especially in a changing climate. Nutrient deficiency in soils is one of the primary bottlenecks affecting the crop production both in developed and developing countries. Farmers are forced to apply synthetic fertilizers to improve the crop production to meet the demand. Understanding the mechanism of nutrient transport is helpful to improve the nutrient-use efficiency of crops and promote the sustainable agriculture. Many transporters involved in the acquisition, export and redistribution of nutrients in plants are characterized. In these studies, heterologous systems like yeast and Xenopus were most frequently used to study the transport function of plant nutrient transporters. CRIPSR/Cas system introduced recently has taken central stage for efficient genome editing in diverse organisms including plants. In this review, we discuss the key nutrient transporters involved in the acquisition and redistribution of nutrients from soil. We draw insights on the possible application CRISPR/Cas system for improving the nutrient transport in plants by engineering key residues of nutrient transporters, transcriptional regulation of nutrient transport signals, engineering motifs in promoters and transcription factors. CRISPR-based engineering of plant nutrient transport not only helps to study the process in native plants with conserved regulatory system but also aid to develop non-transgenic crops with better nutrient use-efficiency. This will reduce the application of synthetic fertilizers and promote the sustainable agriculture strengthening the food and nutrient security.

Remediation of microplastics using bionanomaterials: A review.

Pollution by microplastics (MPs) formed by the physicochemical breakdown of plastics are a worldwide issue with long-lasting and hazardous natural effects. The natural expulsion of MPs takes several years and can be dangerous. Several effective technological innovations have been developed over the years to remediate harmful MPs. Among them, a blend of nanotechnological techniques using bionanomaterials has been investigated to a large extent. The objective of this review is to compile the MPs found in the environment and bionanomaterial-based approaches for their removal. This information is important for researchers who are exploring the adverse consequences of MPs and their remediation and developing advanced eco-friendly strategies to control and eradicate MPs in the future. The control and eradication of MPs depend on all of us; hence, the proper awareness of MPs pollution must be provided to every individual, as all of us are a part of the environment.

Management of phosphorus nutrient amid climate change for sustainable agriculture.

Nutrients are essential for plant growth and development and influence overall agricultural production. Phosphorus (P) is a major nutrient required for many physiological and biochemical functions of a plant. Phosphate rock is the major source of phosphate fertilizer but is becoming increasingly limited in both developing and developed countries. The resources of phosphate rock need to be conserved, and import dependency on phosphate fertilizer needs to be minimized; this will help increase the availability of phosphate fertilizer over the next 300 yr. Climate change creates new challenges in the management of nutrients including P, affecting the overall production of crops. The availability, acquisition, and translocation of P are influenced by the fluctuation of temperatures, pH, drought, and elevated CO2 . Both lower and higher soil temperatures reduce uptake and translocation of P. High soil pH affects P concentration and decreases the rate of plant P uptake. Low soil pH decreases the activity of soil microorganisms, the rate of transpiration, and P uptake and utilization. Elevated CO2 decreases P uptake from soil by the plants. Future research is needed on chemical, molecular, microbiological, and physiological aspects to improve the understanding on how temperature, pH, drought, and elevated CO2 affect the availability, acquisition, and transport of P by plants. Better P management strategies are required to secure the P supply to ensure long-term protection of soil fertility and to avoid environmental impacts such as eutrophication and water pollution, ensuring sustainable food production.

Phosphate supply influenced the growth, yield and expression of PHT1 family phosphate transporters in seven millets.

MAIN CONCLUSION: Phosphate starvation altered the root morphology and phosphate uptake with the induction of PHT1 family transporter genes in root and shoot tissues of seven millets. Millets are nutrient-rich cereals majorly cultivated in Asia and Africa. Foxtail millet (FoxM), pearl millet (PeaM), finger millet (FinM), kodo millet (KodM), little millet (LitM), proso millet (ProM), and barnyard millet (BarM) were examined for the influence of external phosphorous (P) supply on phenotypic traits, P uptake, yield, and PHosphate Transporter1 (PHT1) family gene expression. Millet seedlings grown under low Pi condition (LPC) produced significantly lower mean values for all traits except for lateral root length (LRL) and lateral root number (LRN) which were increased under LPC. Under LPC, seed weight (SW) also reduced by > 75% and had significantly lower levels of total P (TP) and Pi contents in leaf and root tissues. Expression dynamics of 12 PHT1 family (PHT1;1-1;12) transporters genes were analyzed in 7 millets. PHT1;2 has been found to be a constitutive transporter gene in all millets. Under LPC, root tissues showed the overexpression of PHT1;2, 1;3, 1;4 and 1;9 in FoxM, PHT1;1, 1;2, 1;3, 1;4, 1;8 and 1;10 in PeaM, PHT1;2 and 1;3 in FinM and ProM and PHT1;3, 1;6 and 1;11 in BarM. In leaf, LPC induced the expression of PHT1;3, 1;4 and 1;6 in FoxM, PHT1;2, 1;3, 1;4 and 1;8 in PeaM, PHT1;2, 1;3 and 1;4 in FinM and KodM, PHT1;2 in LitM and PHT1;4 in ProM and BarnM. This comprehensive study on the influence of P in phenotype, physiology, and molecular responses may help to improve the P uptake and its use efficiency of millets in future.