First, the epigenomic datasets were used to infer a small set of chromatin states. Then, in a second step, these states were intersected with transcriptomic and annotation data to generate a more nuanced global classification. The first step employed a hidden Markov modeller ChromHMM to binarize chromatin signals and produce alow-resolution map of chromatin states across the rice genome . The selection of the number of states was informed by the ChromHMM option CompareModels to determine the correlation between the emissions of models having different numbers of states. Selecting a 50-state model as an over parameterized reference, we observed a rapid convergence towards this model’s outputs after 15 states were incorporated, and the mean state correlation with the closest state in the 50-state model exceeded 0.9 once 20 states were included . We therefore selected a 20-state ChromHMM model . This number is higher than early estimates of the number of chromatin states in plants but fewer than the 38 states previously inferred in rice from a broader set of histone marks. The inferred number of chromatin states is anticipated to vary to some degree with the type of chromatin marks used as input,livestock fodder system and to this end we selected marks based on testing for high levels of intra-replicate correlation but low levels of correlation between marks in A. thaliana public datasets. In a second step, we intersected these chromatin states with further binarized annotation data and evidence for roles in transcription or transcription initiation. These data included reference genome annotation , phastCons scores, and RNA-Seq and PRO-Seq alignments .

The intersection of the 20 states with these data generated a more ontologically complete and higher-resolution set of 640 possible genome classes, of which 246 were identified with an appreciable coverage of the rice genome of total sequence.With the rice genome partitioned into 246 genomic classes , we estimated ρ for each class using greenINSIGHT, as previously described. The 246 class ρ scores were then distributed back to each nucleotide in each class, giving each nucleotide in the genome a fitCons score . A simple validation of class coherence was performed to ensure that the distribution of ρ as a function of class size was different from that expected under a random sampling model .Among the 246 fitCons classes, we further defined three categories of potentially functional noncoding regions by considering their functional and epigenomic characteristics, as well as their ρ scores. The first category, termed conserved classes, includes 46 noncoding element classes with evidence of sequence conservation among Oryza species . Conserved classes have high ρ and are prevalent in the promoter regions of a subset of protein-coding genes where they probably act as cis-regulatory elements. Gene Ontology enrichment analysis suggests that these are predominantly associated with transcription factor and developmental genes . The density of upstream conserved classes was strongly linked to genes with the highest fold change in expression between tissues , again suggesting tissue-specific or developmental roles. De novo motif analysis using Homer of these 46 classes revealed generally complex motifs , including well-characterized transcription factor-binding sites. The second category comprises 17 classes, termed open chromatin classes, which have a broader range of ρ but have ATAC-Seq signals that are at greater than or equal to tenfold above background . While their ρ tends to be similar to ρ for UTRs and promoters , this ranges from ρ=0.013 to ρ=0.946 . These open chromatin classes are associated with stable gene expression profiles across multiple tissues and are often enriched for simple tandem repeat motifs .The third category includes 11 classes enriched for intergenic bidirectional divergent PRO-Seq signals .

These signals are often characteristic of mammalian enhancer RNA, but were also recently suggested in plants. Using dREG to identify enhancer RNA signals from PRO-Seq data, we found 1,000 high-scoring dREG sites in regions >1 kb from genes, suggesting that these sites form a set of putative rice enhancer elements . The INSIGHT and fitCons approaches provide a set of potentially powerful methods for identifying selective constraint on a genome-wide scale. INSIGHT has been used to identify different types of enhancers, such as exonic splicing enhancers in humans, shadow enhancers in Drosophila and novel motifs such as the Coordinator motif found within human cranial neural crest cellspecific enhancers. In the human genome, fitCons maps were revealed to have higher sensitivity than other methods for locating multiple types of functional noncoding elements with putative roles in transcriptional regulation. Our fitCons map for rice provides a catalogue of putative functional sites that can allow patterns of selection between different genes, genomic regions and genetic pathways to be explored. The map we have developed has limitations; for example, since every base within a fitCons class will receive the same fitCons score , we cannot determine which specific bases within a class are under selection. The validation of fitCons scores relative to the actual fitness impacts of mutations remains to be tested. Subsequent experimental analyses will help shed light on the function of the candidate noncoding regulatory elements that we have described in this study. Nevertheless, some of the broad features of the distribution of ρ in the rice genome confirm what we know about the biology of specific genome elements, suggesting that the inferred ρ values are related to underlying biological features. Integrating evolutionary information with functional genomic and epigenomic data permits identification of important regulatory components of crop genomes, improving genome annotation and helping to guide molecular genetic studies. fitCons maps can also help in genetic mapping and crop breeding efforts, including the identification of candidate deleterious mutations that can be targeted for removal in next-generation breeding efforts. As more such maps are produced, it will be possible to undertake comparative analyses of genomic selection across species and help develop more precise genomic breeding programs.Humanity is in a historical moment in which the capacity to live without irreversibly compromising the environmental and biophysical conditions on which it depends is dramatically questioned .

Anthropogenic pressure on the Earth system has reached a point where abrupt environmental change is feared with global sustainability becoming a mere utopia. Despite the adoption of governance initiatives, such as the 2030 Agenda for Sustainable Development and the related 17 Sustainable Development Goals , there are significant challenges and intrinsic trade-offs that arise from the interaction of social and environmental systems . In particular, the interdependencies among the food, energy, and water systems are central to the global sustainability question . During the second half of the twentieth century, unprecedented growth in global crop production fueled in part by the recent availability of nitrogen fertilizers occurred side by side with unprecedented population growth. Because of their reliance on trade, some countries have sustained high rates of demographic growth despite their low agricultural yields ; however, globally, both crop production and population have dramatically increased in the last century. The degree to which humanity is susceptible to a severe global food crisis in the 21st century is a matter of much debate and growing uncertainty. Global population is projected to continue to rise this century, with median estimates from the UN of 9.6 billion people by 2050 and 10.9 billion by 2100 . At the same time,fodder system trays the consumption of animal products and other resource-intensive foods is likely to grow . Water is a vital part of this story, as an important limiting factor controlling food production . The ability to maintain adequate food supplies with limited water resources has therefore become a pressing concern . In fact, despite the development of new technology , the human pressure on global water resources has been increasing at alarming rates in response to population growth and changes in diet, raising new concerns about the planet’s ability to feed humanity within the limited renewable freshwater resources . An often overlooked aspect of the water crisis is the emergent competition for water resources between the food and energy industries, which is expected to dominate the water security debate in the next few decades . Until recently, most of the energy needs of industrial societies have been met with the use of conventional fossil fuels that require relatively low water costs for their extraction. In addition to renewable energy, such as hydro power, the near future will see an increasing reliance on unconventional fossil fuel deposits, such as oil sands, shale oil, and shale gas, which require greater amounts of water . These deposits account for most of the proven fossil fuels on Earth, and their extraction might be limited by water availability, especially in arid and semiarid regions where stronger competition is expected to emerge between water uses for food and energy . The growth in demand for renewable energy is also likely to substantially increase dam development, which can have numerous social and environmental consequences in river basins; for example, Zarfl et al. recently estimated that about 3,700 large hydropower dams were planned or under construction globally. At the same time, recent bioenergy policies Parliament, 2009; U.S. Congress, 2007 have mandated a certain degree of reliance on renewable energy, stimulating the development of the bio-fuel industry with a direct competition between food and energy uses of crops and embodied water .

Competition in water use for food and energy security constitutes the core of an emerging debate on the food energy-water nexus: the growing societal needs for food and energy rely on the same pool of limited freshwater resources, a situation that is generating new questions on the environmental, ethical, economics, and policy implications of human appropriation of water resources. The FEW nexus is an emerging research focus for natural and social scientists who are exploring the impact of water limitations on the production of energy and food , and the extent to which the human pressure on the global freshwater system is expected to increase in response to the growing demand for food and energy . Although advancements have been made in terms of understanding linkages among FEW systems and working toward integrated modeling , the highly interdisciplinary nature of FEW research has resulted in somewhat disparate clusters of FEW studies. This article seeks to review and synthesize a broad set of issues related to each FEW system individually , then outline a range of intersections among each system—“nexus” points— relevant to scholars in environmental sciences, engineering, economics, political ecology, and other social sciences and analyze their pairwise interactions . We extend the FEW nexus concepts to consider linkages between biophysical and social impacts , governance, globalization, and resilience and look toward the future to ask what issues are on the horizon for each FEW system and their intersection in terms of food, energy, and water security. We also discuss the challenges emerging from the analysis of FEW dynamics and the associated “trilemma” of using natural resources, such as water for food, energy, or environmental needs. This review provides a global perspective on FEW trade-offs through an analysis of globalization of patterns, international investments, and global resilience. The article ends with a review of possible new approaches to a more sustainable management of the FEW system through new advanced technologies, low technological methods, and reduced consumption.Food systems encompass the different production, distribution, and consumption activities that link people to the food they eat, as well as the system outcomes for society and the environment . Food system activities include the use of natural resources and labor in the production, processing, and transport of food, as well as individual food consumption decisions . Food systems are therefore shaped by policies related to agriculture, trade, and food, as well as other institutional arrangements, alongside the cultural, educational, and economic dimensions of food consumers .Global crop supply has more than tripled, and animal production has increased 2.5-fold over the past 50 years , 2013 and by 50% since the mid-1980s . Currently, only five countries―Brazil, China, India, Indonesia, and the United States―produce more than one half of the world’s crops. In addition, just four crops―wheat, rice, maize, and soybeans―constitute more than one half of current food production. Food systems have become increasingly globalized; 23% of food calories currently are traded internationally, and about 85% of countries rely on food imports to meet domestic demand .