Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Following the domestication of maize over the past ∼10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop

MiRNA Control of Vegetative Phase Change in Trees

After germination, plants enter juvenile vegetative phase and then transition to an adult vegetative phase before producing reproductive structures. The character and timing of the juvenile-to-adult transition vary widely between species. In annual plants, this transition occurs soon after germination and usually involves relatively minor morphological changes, whereas in trees and other perennial woody plants it occurs after months or years and can involve major changes in shoot architecture. Whether this transition is controlled by the same mechanism in annual and perennial plants is unknown. In the annual forb Arabidopsis thaliana and in maize (Zea mays), vegetative phase change is controlled by the sequential activity of microRNAs miR156 and miR172. miR156 is highly abundant in seedlings and decreases during the juvenile-to-adult transition, while miR172 has an opposite expression pattern. We observed similar changes in the expression of these genes in woody species with highly differentiated, well-characterized juvenile and adult phases (Acacia confusa, Acacia colei, Eucalyptus globulus, Hedera helix, Quercus acutissima), as well as in the tree Populus x canadensis, where vegetative phase change is marked by relatively minor changes in leaf morphology and internode length. Overexpression of miR156 in transgenic P. x canadensis reduced the expression of miR156-targeted SPL genes and miR172, and it drastically prolonged the juvenile phase. Our results indicate that miR156 is an evolutionarily conserved regulator of vegetative phase change in both annual herbaceous plants and perennial trees

Exploring DNA

DNA structure has been leveraged in a variety of facets that allow scientists to perform a range of assays, including ones for identification of species, establishing evolutionary relationships between taxa, or even identifying individuals. Here, we present a DNA barcoding method as practical, hands-on approach that connects several experimental techniques in one sequence to teach the principles behind DNA isolation, purification, PCR, sequencing, and phylogeny analysis. Our set of exercises is designed for a teaching university laboratory setting. The three laboratory class assignments utilize DNA from a mushroom (can be purchased at a supermarket) and provide a pipeline to guide students through the process of identifying an unknown sample, like in many research laboratories. The third assignment can be used as a stand-alone exercise on phylogeny analysis and can be taught remotely. Students explore the theory behind the standard molecular techniques and apply it in a hands-on setting that involves experimental design, sample preparation, and use of hallmark molecular instruments

Lewy body dementia: Overcoming barriers and identifying solutions

\ua9 2024 The Authors. Alzheimer\u27s & Dementia published by Wiley Periodicals LLC on behalf of Alzheimer\u27s Association.Despite its high prevalence among dementias, Lewy body dementia (LBD) remains poorly understood with a limited, albeit growing, evidence base. The public-health burden that LBD imposes is worsened by overlapping pathologies, which contribute to misdiagnosis, and lack of treatments. For this report, we gathered and analyzed public-domain information on advocacy, funding, research outputs, and the therapeutic pipeline to identify gaps in each of these key elements. To further understand the current gaps, we also conducted interviews with leading experts in regulatory/governmental agencies, LBD advocacy, academic research, and biopharmaceutical research, as well as with funding sources. We identified wide gaps across the entire landscape, the most critical being in research. Many of the experts participated in a workshop to discuss the prioritization of research areas with a view to accelerating therapeutic development and improving patient care. This white paper outlines the opportunities for bridging the major LBD gaps and creates the framework for collaboration in that endeavor. Highlights: A group representing academia, government, industry, and consulting expertise was convened to discuss current progress in Dementia with Lewy Body care and research. Consideration of expert opinion,natural language processing of the literature as well as publicly available data bases, and Delphi inspired discussion led to a proposed consensus document of priorities for the field

Genome Elimination: Translating Basic Research into a Future Tool for Plant Breeding

During the course of our history, humankind has been through different periods of agricultural improvement aimed at enhancing our food supply and the performance of food crops. In recent years, it has become apparent that future crop improvement efforts will require new approaches to address the local challenges of farmers while empowering discovery across industry and academia. New plant breeding approaches are needed to meet this challenge to help feed a growing world population. Here I discuss how a basic research discovery is being translated into a potential future tool for plant breeding, and share the story of researcher Simon Chan, who recognized the potential application of this new approach--genome elimination--for the breeding of staple food crops in Africa and South America

Adaptability and stability of corn inbred lines regarding resistance to gray leaf spot and northern leaf blight

The objectives of this study were to identify resistant and susceptible corn inbred lines based on their stability and adaptability for resistance to disease symptoms of gray leaf spot and northern leaf blight, suggest resistant inbred lines aimed at producing synthetics, and identify the sowing dates with higher occurrence of diseases to use these dates for identification of genetic resistance. We evaluated 41 corn inbred lines in randomized block designs with three replications and 11 sowing dates. Evaluations were performed 30 days after silking. Stability and adaptability analyses were performed by the regression method. The highest severities of disease occurred in sowing from June to September. On average, all the inbred lines were classified as resistant; however, considering adaptability and stability, five inbred lines were found suitable to produce dent synthetics resistant to both diseases. For flint synthetics resistant to both diseases, inbred lines IVF1-7,IVF1-10, 2F, 9F, and 10F are most suitable

Improving the efficiency of soybean breeding with high-throughput canopy phenotyping

Background: In the early stages of plant breeding programs high-quality phenotypes are still a constraint to improve genetic gain. New field-based high-throughput phenotyping (HTP) platforms have the capacity to rapidly assess thousands of plots in a field with high spatial and temporal resolution, with the potential to measure secondary traits correlated to yield throughout the growing season. These secondary traits may be key to select more time and most efficiently soybean lines with high yield potential. Soybean average canopy coverage (ACC), measured by unmanned aerial systems (UAS), is highly heritable, with a high genetic correlation with yield. The objective of this study was to compare the direct selection for yield with indirect selection using ACC and using ACC as a covariate in the yield prediction model (Yield|ACC) in early stages of soybean breeding. In 2015 and 2016 we grew progeny rows (PR) and collected yield and days to maturity (R8) in a typical way and canopy coverage using a UAS carrying an RGB camera. The best soybean lines were then selected with three parameters, Yield, ACC and Yield|ACC, and advanced to preliminary yield trials (PYT). Results: We found that for the PYT in 2016, after adjusting yield for R8, there was no significant difference among the mean performances of the lines selected based on ACC and Yield. In the PYT in 2017 we found that the highest yield mean was from the lines directly selected for yield, but it may be due to environmental constraints in the canopy growth. Our results indicated that PR selection using Yield|ACC selected the most top-ranking lines in advanced yield trials. Conclusions: Our findings emphasize the value of aerial HTP platforms for early stages of plant breeding. Though ACC selection did not result in the best performance lines in the second year of selections, our results indicate that ACC has a role in the effective selection of high-yielding soybean lines

The Inheritance Pattern of 24 nt siRNA Clusters in Arabidopsis Hybrids Is Influenced by Proximity to Transposable Elements

Hybrids often display increased size and growth, and thus are widely cultivated in agriculture and horticulture. Recent discoveries demonstrating the important regulatory roles of small RNAs have greatly improved our understanding of many basic biological questions, and could illuminate the molecular basis for the enhanced growth and size of hybrid plants. We profiled small RNAs by deep sequencing to characterize the inheritance patterns of small RNA levels in reciprocal hybrids of two Arabidopsis thaliana accessions, Columbia and Landsberg erecta. We find 24-nt siRNAs predominate among those small RNAs that are differentially expressed between the parents. Following hybridization, the transposable element (TE)-derived siRNAs are often inherited in an additive manner, whereas siRNAs associated with protein-coding genes are often down-regulated in hybrids to the levels observed for the parent with lower relative siRNA levels. Among the protein-coding genes that exhibit this pattern, genes that function in pathogen defense, abiotic stress tolerance, and secondary metabolism are significantly enriched. Small RNA clusters from protein-coding genes where a TE is present within one kilobase show a different predominant inheritance pattern (additive) from those that do not (low-parent dominance). Thus, down-regulation in the form of low-parent dominance is likely the default pattern of inheritance for genic siRNA, and a different inheritance mechanism for TE siRNA is suggested