Unique and conserved MicroRNAs in wheat chromosome 5D revealed by next-generation sequencing

MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. In silico and structural analyses revealed a total of 55 miRNAs; 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. In total, 14 of the predicted miRNAs were identified in wheat for the first time. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat

Conservation and Use of the North American Plant Cornucopia: The Way Forward

The pages of this extensive book document the potential of a great many North American plants to enhance the productivity, sustainability, and nutritional quality of crops or to be further developed into important cultivated species in their own right. But this potential can only be realized if the plants are adequately conserved to ensure their survival and availability for research, invested in to promote their development, and marketed so as to be attractive to producers and consumers. We outline some of the key steps needed to boost the conservation and use of our regional cornucopia. In situ and ex situ conservation of North America’s useful plants are being accomplished by a variety of institutions with different mandates, but habitat destruction and other threats to wild populations continue to negatively impact many species. Information sharing, coordinating efforts, filling research gaps for wild plants, and increasing support for conservation will be necessary to more comprehensively safeguard these plants and to make them available for use. Technologies enabling more efficient exploration of the diversity within these species are rapidly advancing and offer the potential to contribute to quick advances in improvement of cultivars, but considerable further research and partnerships are needed to generate and share the results widely. Marketing of new crops can take advantage of the increasing public interest in diverse and nutritious foods, learning from successful collaborations between producers, researchers, and consumers. As a whole, North America already possesses a strong foundation from which the conservation and use of its flora can be enhanced. This includes many protected areas, strong conservation institutions, innovative research, and the willingness to collaborate across fields, institutions, and borders. There are still many silos that need to be broken down and reorganized through innovative partnerships to better conserve and benefit from the North American cornucopia. But given the incredible diversity of interesting and useful plants in the region, the remarkable efforts for many decades by many organizations to care for these plants and share them with humanity, and the increasing public interest in more diverse, healthy, and resilient food and agricultural systems, there is reason for hope

Dissecting the Genetic Basis of Local Adaptation in Soybean

Soybean (Glycine max) is the most widely grown oilseed in the world and is an important source of protein for both humans and livestock. Soybean is widely adapted to both temperate and tropical regions, but a changing climate demands a better understanding of adaptation to specific environmental conditions. Here, we explore genetic variation in a collection of 3,012 georeferenced, locally adapted landraces from a broad geographical range to help elucidate the genetic basis of local adaptation. We used geographic origin, environmental data and dense genome-wide SNP data to perform an environmental association analysis and discover loci displaying steep gradients in allele frequency across geographical distance and between landrace and modern cultivars. Our combined application of methods in environmental association mapping and detection of selection targets provide a better understanding of how geography and selection may have shaped genetic variation among soybean landraces. Moreover, we identified several important candidate genes related to drought and heat stress, and revealed important genomic regions possibly involved in the geographic divergence of soybean

History Taking as a Diagnostic Tool in Children With Chronic Cough

Chronic cough is a common symptom of many underlying respiratory and non-respiratory disorders and may be associated with less serious causes, such as gastroesophageal reflux and nasal diseases. Chronic cough in children differs from that in adults with respect to its etiologies and management since it can indicate a symptom of an underlying disease in children. Guidelines for managing chronic cough in children are based on recording the history, followed by physical examination, chest radiography, and spirometry. Thus, taking accurate respiratory history for coughing helps delineate the pathophysiological basis of the cause of chronic cough. Detailed history taking enhances the evaluation and treatment, and facilitates a tailored diagnostic identification of likely diagnoses. While studies have described evidence-based red flags in children with chronic cough, the value of skilled physicians regarding history taking has received less attention for the best patient care. In the present article, we outline the major questions comprising a detailed history taking for chronic cough in children

The hidden land use cost of upscaling cover crops

Cover cropping is considered a cornerstone practice in sustainable agriculture; however, little attention has been paid to the cover crop production supply chain. In this Perspective, we estimate land use requirements to supply the United States maize production area with cover crop seed, finding that across 18 cover crops, on average 3.8% (median 2.0%) of current production area would be required, with the popular cover crops rye and hairy vetch requiring as much as 4.5% and 11.9%, respectively. The latter land requirement is comparable to the annual amount of maize grain lost to disease in the U.S. We highlight avenues for reducing these high land use costs

A Roadmap for Functional Structural Variants in the Soybean Genome

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits

A Roadmap for Functional Structural Variants in the Soybean Genome

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits

Multi-Species Genomics-Enabled Selection for Improving Agroecosystems Across Space and Time

Plant breeding has been central to global increases in crop yields. Breeding deserves praise for helping to establish better food security, but also shares the responsibility of unintended consequences. Much work has been done describing alternative agricultural systems that seek to alleviate these externalities, however, breeding methods and breeding programs have largely not focused on these systems. Here we explore breeding and selection strategies that better align with these more diverse spatial and temporal agricultural systems

Wild relatives of potato may bolster its adaptation to new niches under future climate scenarios

Food production strategies and patterns are being altered in response to climate change. Enhancing the adaptation of important food crops to novel climate regimes will be critical to maintaining world food supplies. Climate change is altering the suitability of production areas for crops such as potato (Solanum tuberosum L.) making future productivity, resilience, and sustainability of this crop dependent on breeding for climate adaptation, including through the introgression of novel traits from its wild relatives. To better understand the future production climate envelopes of potatoes, and the potential of its wild relatives to contribute to adaptation to these environments, we estimated the climate of potato in four future climate scenarios and overlapped the current climate of 72 wild relative species and potato with these future climates. We discovered a shift of up to 12.5% by potato from current to novel climate by 2070 and varying magnitudes of overlap by different wild relatives with potato, primarily driven by the extent of endemism. To address the threat of novel climate on potato production and with the wealth of data available for the agrobiodiversity in potato wild relatives, we systematically developed a prioritization value inspired by the logic of the breeder's equation for locating potentially beneficial species possessing local adaptability, climatic plasticity, and interspecific crossability. In doing so, 26 unique species by discrete climate combinations are found, highlighting the presence of unique species to use in adapting potato to changing local climates. Further, the 20 highest prioritized values belong to diploid species, enforcing the drive to shift into diploid breeding by the potato research community, where introgression of the local climate adaptability traits may be more streamlined

Effects of relaxed lockdown on pediatric er visits during sars-cov-2 pandemic in Italy

Previously, we demonstrated an 81% reduction in pediatric Emergency Room (ER) visits in Italy during the strict lockdown due to the SARS-CoV-2 pandemic. Since May 2020, lockdown measures were relaxed until 6 November 2020, when a strict lockdown was patchily reintroduced. Our aim was to evaluate the impact of the relaxed lockdown on pediatric ER visits in Italy. We performed a retrospective multicenter study involving 14 Italian pediatric ERs. We compared total ER visits from 24 September 2020 to 6 November 2020 with those during the corresponding timeframe in 2019. We evaluated 17 ER specific diagnoses grouped in air communicable and non-air communicable diseases. We recognized four different triage categories: white, green, yellow and red. In 2020 total ER visits were reduced by 51% compared to 2019 (16,088 vs. 32,568, respectively). The decrease in air communicable diseases was significantly higher if compared to non-air communicable diseases (−64% vs. −42%, respectively). ER visits in each triage category decreased in 2020 compared to 2019, but in percentage, white and red codes remained stable, while yellow codes slightly increased and green codes slightly decreased. Our results suggest that preventive measures drastically reduced the circulation of air communicable diseases even during the reopening of social activities but to a lesser extent with regard to the strict lockdown period (March–May 2020)