Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops

Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics.     

Genetic Diversity and Population Structure of Broomcorn Millet (Panicum miliaceum L.) Cultivars and Landraces in China Based on Microsatellite Markers

Broomcorn millet (Panicum miliaceum L.), one of the first domesticated crops, has been grown in Northern China for at least 10,000 years. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, we analyzed the genetic diversity of 88 accessions of broomcorn millet collected from various provinces of China. Amplification with 67 simple sequence repeat (SSR) primers revealed moderate levels of diversity in the investigated accessions. A total of 179 alleles were detected, with an average of 2.7 alleles per locus. Polymorphism information content and expected heterozygosity ranged from 0.043 to 0.729 (mean = 0.376) and 0.045 to 0.771 (mean = 0.445), respectively. Cluster analysis based on the unweighted pair group method of mathematical averages separated the 88 accessions into four groups at a genetic similarity level of 0.633. A genetic structure assay indicated a close correlation between geographical regions and genetic diversity. The uncovered information will be valuable for defining gene pools and developing breeding programs for broomcorn millet. Furthermore, the millet-specific SSR markers developed in this study should serve as useful tools for assessment of genetic diversity and elucidation of population structure in broomcorn millet.     

Root-derived nitrous oxide emissions from an Upper Midwest agricultural ecosystem

Agroecosystems are the dominant source of anthropogenic nitrous oxide (N₂O) emissions globally, yet the partitioning of nitrogen sources supporting N₂O emissions is not well understood. Fertilizer-derived N₂O emissions receive significant attention, while N₂O emissions from organic nitrogen sources, particularly belowground sources, are rarely studied. Here, in situ corn roots (Zea mays L.) were isotopically-labeled with nitrogen (N) and carbon (C) to examine effects of different long-term management systems on root-derived N₂O emissions measured during the following soybean crop in southwest Minnesota, USA. Systems differed in management intensity (tillage and fertilization), crop rotation diversity (two or four crops), and fertilizer type (inorganic or organic). The average contribution of root-derived nitrogen to cumulative N₂O–N emitted over the growing season was 8%, and was higher in 2-year (11%) than 4-year rotations (6%). The fractional loss of root-derived N as N₂O, which is an estimate of the annual emission factor for root-derived N₂O, was small (0.07–0.52%). Management intensity effects on root-derived N₂O emissions and on the root-derived fraction of N₂O emitted differed between two growing seasons as did the effects of fertilizer type on root-derived N cycling rates. Overall, rotation diversity (2 vs. 4-year rotations) exhibited the strongest management effect on root-derived N₂O emissions, suggesting that root-derived N₂O emissions could be mitigated by greater crop rotation diversity.     

Application of CRISPR/Cas9 in Crop Quality Improvement

The various crop species are major agricultural products and play an indispensable role in sustaining human life. Over a long period, breeders strove to increase crop yield and improve quality through traditional breeding strategies. Today, many breeders have achieved remarkable results using modern molecular technologies. Recently, a new gene-editing system, named the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, has also succeeded in improving crop quality. It has become the most popular tool for crop improvement due to its versatility. It has accelerated crop breeding progress by virtue of its precision in specific gene editing. This review summarizes the current application of CRISPR/Cas9 technology in crop quality improvement. It includes the modulation in appearance, palatability, nutritional components and other preferred traits of various crops. In addition, the challenge in its future application is also discussed.     

Recent Developments in Breeding Soybeans for Improved Oil Quality

Soybean breeding has traditionally focused on improving crop productivity. While this is still the main objective of soybean breeding programs, there is increased emphasis on improving the intrinsic characteristics of the seeds. Breeding goals with respect to oil quality improvement have been threefold: (1) reducing lipoxygenase activity, (2) decreasing linolenic acid concentrations in soybean oil and more recently (3) reducing the saturated fatty acid, palmitate, in soybean oil. The first two are aimed at improving oil flavor and shelf life. The third has been added as a result of medical concerns about excess saturated fats in the human diet. Considerable progress has been made toward achieving all three objectives. Improved soybean germplasm has been released and is being used to develop high yielding cultivars improved oil quality. Null alleles for three lipoxygenase isozymes have been transferred into the cultivar ‘Century’ through backcrossing. Three different germplasm sources have been developed through mutagenesis and selection with low concentrations of linolenic acid (3.0 to 3.5%). This material has been released and is being widely used by public and private breeders to incorporate the low linolenic acid trait into high yielding cultivars. Cultivars with 2% germplasm with lower concentrations of palmitic acid in soybean oil by as much as 50%. In the U.S., soybean oil accounts for about 50% of the palmitic acid in diets. Therefore, reducing palmitic acid in soybean oil could significantly decrease saturated fat consumption without dietary change. Other research in progress includes studies of the genetic inheritance and control oil quality traits and efforts to use molecular genetics to improve oil quality.     

Entwicklungstendenzen bei der Züchtung von Ölfrüchten anhand der Anmeldungen beim Bundessortenamt

Trends in the Breeding of Oilseeds on the Basis of Registrations in ?Bundessortenamt”? Trends in the breeding of oilseeds can be well assessed on the basis of registrations for the protection of varieties filed at the ?Bundessortenamt”?. Rapeseed, the most important oilseed in our climatic region, has undergone considerable progress since 1970 as the first registrations of the zero-erucic varieties were made. Differentiation is made between two different types of rape, i. e. those grown for producing oilseed and those grown as intermediate crop for the production of feedstuff. In the production of rape as oilseed, which was switched over in 1974 to zero-erucic varieties, the yield is now higher than the former varieties containing erucic acid. Registrations of the double-low varieties, i. e. zero-erucic and lowglucosinolate, are often being made mainly for use as intermediate crop.     

Plant Glandular Trichomes as Targets for Breeding or Engineering of Resistance to Herbivores

Glandular trichomes are specialized hairs found on the surface of about 30% of all vascular plants and are responsible for a significant portion of a plant’s secondary chemistry. Glandular trichomes are an important source of essential oils, i.e., natural fragrances or products that can be used by the pharmaceutical industry, although many of these substances have evolved to provide the plant with protection against herbivores and pathogens. The storage compartment of glandular trichomes usually is located on the tip of the hair and is part of the glandular cell, or cells, which are metabolically active. Trichomes and their exudates can be harvested relatively easily, and this has permitted a detailed study of their metabolites, as well as the genes and proteins responsible for them. This knowledge now assists classical breeding programs, as well as targeted genetic engineering, aimed to optimize trichome density and physiology to facilitate customization of essential oil production or to tune biocide activity to enhance crop protection. We will provide an overview of the metabolic diversity found within plant glandular trichomes, with the emphasis on those of the Solanaceae, and of the tools available to manipulate their activities for enhancing the plant’s resistance to pests.     

Frontiers in Dissecting and Managing Brassica Diseases: From Reference-Based RGA Candidate Identification to Building Pan-RGAomes

The Brassica genus contains abundant economically important vegetable and oilseed crops, which are under threat of diseases caused by fungal, bacterial and viral pathogens. Resistance gene analogues (RGAs) are associated with quantitative and qualitative disease resistance and the identification of candidate RGAs associated with disease resistance is crucial for understanding the mechanism and management of diseases through breeding. The availability of Brassica genome assemblies has greatly facilitated reference-based quantitative trait loci (QTL) mapping for disease resistance. In addition, pangenomes, which characterise both core and variable genes, have been constructed for B. rapa, B. oleracea and B. napus. Genome-wide characterisation of RGAs using conserved domains and motifs in reference genomes and pangenomes reveals their clustered arrangements and presence of structural variations. Here, we comprehensively review RGA identification in important Brassica genome and pangenome assemblies. Comparison of the RGAs in QTL between resistant and susceptible individuals allows for efficient identification of candidate disease resistance genes. However, the reference-based QTL mapping and RGA candidate identification approach is restricted by the under-represented RGA diversity characterised in the limited number of Brassica assemblies. The species-wide repertoire of RGAs make up the pan-resistance gene analogue genome (pan-RGAome). Building a pan-RGAome, through either whole genome resequencing or resistance gene enrichment sequencing, would effectively capture RGA diversity, greatly expanding breeding resources that can be utilised for crop improvement.     

Bedeutung der Ertragsphysiologie für die Züchtung von Raps

The Importance of Crop Physiology for the Breeding of Oilseed Rape Crop physiology describes processes, which directly or indirectly control crop yield. Usually these processes and the resulting traits interact in a complex manner and are highly sensitive to environmental conditions, so that a direct influence of these processes on yield is seldom determined. However, the knowledge of crop physiology helps to find critical phases in yield formation and to use these information in plant breeding procedures. In this study the application of the knowledge of crop physiology by plant breeders is described for some source (e. g. genotypic variability of leaf and pod areas) and sink traits (especially No. of seeds per pod) for oilseed rape. Furthermore, examples are given to improve nitrogen uptake rate and nitrogen use efficiency by means of plant breeding.     

Outlook for high‐oleic peanuts and peanut products in 21st century markets

The global oilseed market is dominated by and steadily is becoming more dependent on palm and soybean as major commodity sources to meet growing demand for edible vegetable oil and protein. However, the loss of GRAS status for hydrogenated oils in the U.S., concern for sustainable production practices, debate on dietary saturated fats, and other constraints signal the need for economic alternatives in the oilseed commodity market. Recent technological advances elevate the position of oilseed peanut in such consideration [1]. For example, analysis of the peanut genome sequence has: 1) revealed the chromosomal location of genes that can protect the crop against major diseases (thus reducing need for multiple applications of fungicides), and genes that mediate high‐oleic acid concentration (thus enhancing health benefits, longer product shelf‐life, and improved flavor); 2) generated DNA markers that help breeders track and stack desired genes in hybrid lines; and 3) enabled modern DNA‐sequence driven breeding methods that cut years off the timeline for developing varieties. These capabilities will help reduce cost of production, lead industry transition to high‐oleic products, and ensure an adequate supply of safe, nutritious and healthy peanuts and peanut products.     

Some Experiences of Using Different Analytical Methods in Screening for Oil and Protein Content in Rapeseed

In this study some analytical methods, which have been used in oil crop breeding, are compared from the point of view of plant breeding. For oil content determination a gravimetric method, NMR and NIR have been used. Protein content has been determined by the classical Kjeldahl technique, by the Biuret method and by NIR. The results indicate that the NIR spectroscopy is specially useful in screening breeding materials. This method enables the breeder to select for several quality characters simultaneously at a high speed and at a low cost. Since NIR spectroscopy is nondestructive, the same seed lot can be used for analysis and planting. Thus it is possible to select on a large scale for single plants.     

Effects of input level and crop diversity on soil nitrate-N,extractable P,aggregation, organic C and N,and nutrient balance in the Canadian Prairie

A field experiment was conducted from 1995 to 2006 on a Dark Brown Chernozem (Typic Boroll) loam soil at Scott, Saskatchewan, Canada to determine the influence of input level and crop diversity on accumulation and distribution of nitrate-N and extractable P in the soil profile, and soil pH, dry aggregation, organic C and N, and nutrient balance sheets in the second 6-year rotation cycle (2001–2006). Treatments were combinations of three input levels (organic input under conventional tillage—ORG; reduced input under no-till—RED; and high input under conventional tillage—HIGH), three crop diversities (fallow-based rotations with low crop diversity—LOW; diversified rotations using annual cereal, oilseed and pulse grain crops—DAG; and diversified rotations using annual grain and perennial forage crops—DAP), and six crop phases including green manure (GM), chem-fallow or tilled-fallow (F). Amount of nitrate-N in 0-240 cm soil was usually highest under the HIGH input-LOW crop diversity treatment and lowest under the ORG input-DAP crop diversity treatment. The distribution of nitrate-N in various soil depths suggested downward movement of nitrate-N up to 240 cm depth, especially with LOW crop diversity compared to DAP crop diversity, and with HIGH input. In some years, the ORG input systems had higher nitrate-N than the RED or HIGH input systems, which was attributed to low extractable P in soil for optimum crop growth and reduced nutrient uptake with ORG input management. Extractable P in soil was higher by a small margin for HIGH or RED input relative to ORG input in the 0–15 cm layer, suggesting little downward movement of P. Crop diversity did not affect extractable soil P due to the low baseline levels of P in this soil. The proportion of fine dry aggregates (<1.3 mm, erodible fraction) in 0–5 cm soil was highest with LOW crop diversity-HIGH input system, and lowest with DAG diversity-RED input system. The opposite was true for large aggregates (>12.7 mm). Wet aggregate stability was higher for RED input compared to ORG and HIGH input, which was attributed to the increase in the concentration of organic C in aggregates in the RED input system. Amount of light fraction organic matter (LFOM), light fraction organic C (LFOC) and light fraction organic N (LFON) in 0–15 cm soil was higher for RED input compared to ORG and HIGH inputs, and higher for DAG and DAP crop diversities than for LOW crop diversity. Soil N and P were usually deficient under ORG input management, but large amounts of N and P were unaccounted for, or in surplus, under RED and HIGH inputs, despite a marked increase in plant N and P uptake and crop yield compared to ORG input. Overall, our findings suggest that soil quality can be improved and nutrient accumulation in the soil profile can be minimized by increasing cropping frequency, reducing/eliminating tillage, and using appropriate combinations of fertilizer input and diversified cropping.     

Factors affecting the agronomic effectiveness of phosphate rock for direct application

Phosphorus (P) is critically needed to improve soil fertility for sustainable crop production in large areas of developing countries. In recent years, phosphate rock (PR) for direct application has been tested in tropical acid soils as a potential alternative to conventional water-soluble P fertilizers like single superphosphate (SSP) and triple superphosphate (TSP). Some developing countries have PR deposits which, if used to supplement other imported P fertilizers, would allow a saving of much needed foreign exchange. Solubility of P fertilizers is not the only criterion in selection of the most suitable P fertilizer. This paper discusses the results of experiments to compare the relative agronomic effectiveness (RAE) of various PR sources with respect to SSP or TSP as influenced by four important factors: PR sources, soil properties, management practices, and crop species. Under certain conditions, PRs can be agronomically effective.     

Epigenetic Mechanisms in Penile Carcinoma

Penile carcinoma (PeCa) represents an important public health problem in poor and developing countries. Despite its unpredictable behavior and aggressive treatment, there have only been a few reports regarding its molecular data, especially epigenetic mechanisms. The functional diversity in different cell types is acquired by chromatin modifications, which are established by epigenetic regulatory mechanisms involving DNA methylation, histone acetylation, and miRNAs. Recent evidence indicates that the dysregulation in these processes can result in the development of several diseases, including cancer. Epigenetic alterations, such as the methylation of CpGs islands, may reveal candidates for the development of specific markers for cancer detection, diagnosis and prognosis. There are a few reports on the epigenetic alterations in PeCa, and most of these studies have only focused on alterations in specific genes in a limited number of cases. This review aims to provide an overview of the current knowledge of the epigenetic alterations in PeCa and the promising results in this field. The identification of epigenetically altered genes in PeCa is an important step in understanding the mechanisms involved in this unexplored disease.     

Transposable Elements and Stress in Vertebrates: An Overview

Since their identification as genomic regulatory elements, Transposable Elements (TEs) were considered, at first, molecular parasites and later as an important source of genetic diversity and regulatory innovations. In vertebrates in particular, TEs have been recognized as playing an important role in major evolutionary transitions and biodiversity. Moreover, in the last decade, a significant number of papers has been published highlighting a correlation between TE activity and exposition to environmental stresses and dietary factors. In this review we present an overview of the impact of TEs in vertebrate genomes, report the silencing mechanisms adopted by host genomes to regulate TE activity, and finally we explore the effects of environmental and dietary factor exposures on TE activity in mammals, which is the most studied group among vertebrates. The studies here reported evidence that several factors can induce changes in the epigenetic status of TEs and silencing mechanisms leading to their activation with consequent effects on the host genome. The study of TE can represent a future challenge for research for developing effective markers able to detect precocious epigenetic changes and prevent human diseases.     

Epigenetic Regulation of Cardiomyocyte Differentiation from Embryonic and Induced Pluripotent Stem Cells

With the intent to achieve the best modalities for myocardial cell therapy, different cell types are being evaluated as potent sources for differentiation into cardiomyocytes. Embryonic stem cells and induced pluripotent stem cells have great potential for future progress in the treatment of myocardial diseases. We reviewed aspects of epigenetic mechanisms that play a role in the differentiation of these cells into cardiomyocytes. Cardiomyocytes proliferate during fetal life, and after birth, they undergo permanent terminal differentiation. Upregulation of cardiac-specific genes in adults induces hypertrophy due to terminal differentiation. The repression or expression of these genes is controlled by chromatin structural and epigenetic changes. However, few studies have reviewed and analyzed the epigenetic aspects of the differentiation of embryonic stem cells and induced pluripotent stem cells into cardiac lineage cells. In this review, we focus on the current knowledge of epigenetic regulation of cardiomyocyte proliferation and differentiation from embryonic and induced pluripotent stem cells through histone modification and microRNAs, the maintenance of pluripotency, and its alteration during cardiac lineage differentiation.