Abstract to come

C. Nathan Hancock, Tetandianocee Germany,  Sam Burns, Priscilla S. Redd, Jeffery Lipford,  Sergio Alan Cervantes-Perez, Marc Libault, Lisa Kanizay, Melinda Yerka, and Wayne Parrott
1Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, 2University of Nebraska Lincoln, Lincoln, NE, 3Center for Applied Genetic Technology, University of Georgia, Athens, GA

Introduction/Background. Connecting phenotypes to the underlying changes in the genome is the key to understanding gene function. Screening a transposon-mutagenized soybean population allowed for the discovery of a recessively inherited chlorotic phenotype. This “Yellow Leaf” phenotype results in smaller stature, weaker stems, and smaller root system with smaller nodules.

Hypothesis/Goal of Study. The goal of this project was to identify the mutation responsible for the “Yellow Leaf” phenotype.

Methods and Results. Genome sequencing identified 15 candidate genes with mutations likely to result in loss of function. Amplicon sequencing of a segregating population was then used to narrow the list to a single candidate, a two-base pair change in Glyma.07G102300. Single cell expression analysis indicates that this gene is expressed primarily in mesophyll cells and the mutation disrupts the second intron splice site, resulting in an early frame shift. Previous studies have shown that mutations to TCD5 (Os05g34040), the rice homolog of Glyma.07G102300, produced a chlorotic phenotype that was more pronounced in cool temperatures. Growing the soybean “Yellow Leaf” mutant at lower temperatures also resulted in a more severe phenotype.

Discussion/Conclusions. Our results indicate that that the mutation in Glyma.07G102300 is causal of the “Yellow Leaf” phenotype. Initial analysis suggests that this gene is important for chloroplast function, but additional experiments are needed to understand its enzymatic role.

Grant/Funding Support. National Institutes of Health National Institute of General Medical Sciences (P20GM13499-20); National Science Foundation.

Nancy Meyer, Claudia Lopez, and Craig Yoshioka
Pacific Northwest Cryo-EM Center, Oregon Health and Science University, Portland, Oregon

Introduction/Background. Cryo-Electron microscopy (CryoEM) is a method used to image biological molecules in native-like states, allowing researchers to computationally reveal the 3D molecular structures critical to uncovering both mechanistic insights and driving therapuetic development. Recent advances in cryo-EM technology enable users to determine protein structure at unprecedented detail. However, many labs have limited expertise and lack access to the necessary high-end microscopes, slowing adoption of these powerful cryoEM technologies and progress in a range of biomedical fields.

Hypothesis/Goal of Study. To address this issue, the NIH Common Fund, which supports trans-NIH programs that focus on major biomedical challenges and emerging opportunities, is seeking to improve the availability and utility of cryo-EM by establishing three National Service Centers (as well as curriculum development) through the Transformative High-Resolution Cryo-Electron Microscopy program. The Centers’ mission is to make cryo-EM accessible by offering access to instrumentation and training to increase the number of independent cryo-EM laboratories. Of particular interest is to offer accessibility to IDeA states across the country.

Methods and Results. The three national cryoEM centers are: the National Center for Cryo-EM Access and Training (NCCAT), Stanford-Slac Cryo-EM Center (S2C2), and the Pacific Northwest Cryo-EM Center (PNCC). In addition to no-charge, state-of-the-art instrumentation and training, the centers offer onsite guidance with sample preparation. IDeA state institutions are encourage to apply and prioritized.

Discussion/Conclusions. By investing in instrumentation and expert staffing at these national cryo-EM “hubs,” the NIH Common Fund hopes to facilitate more efficient data collection and further democratize entry into the ever-growing cryo-EM field.

Grant/Funding Support. U24 GM129547

Alejandro Q. Nato, Jr.1, Vinícius Magalhães Borges1,2, Natália Fagundes Borges Teruel3, Lilian Kimura2,  Andréa Roseli Vancan Russo Horimoto4,5, Ellen M. Wijsman5,6, and Regina Célia Mingroni-Netto2
1Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, 2Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil, 3Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada, 4Division of Aging, Brigham and Women’s Hospital, Boston, MA, 5Department of Biostatistics, University of Washington, Seattle, WA, 6Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA

Introduction/Background. Essential hypertension (EH) is a cardiovascular risk factor, featuring heightened systolic (SBP) and/or diastolic (DBP) blood pressure. In Brazil, hypertension is indicated by SBP ≥ 140 and/or DBP ≥ 90 mmHg, affecting 24.3% of the population. Global EH heritability spans 15-60%. Among African Brazilian ancestry Quilombo populations, estimated heritabilities are 36.1% (SBP) and 42.9% (DBP).

Hypothesis/Goal of Study. To pinpoint genetic contributors fostering EH susceptibility within Quilombo populations, we conducted whole exome sequencing (WES) analysis on 26 samples from 3 extended pedigrees (167 affected, 261 unaffected, 3 unknown).

Methods and Results. Utilizing IDT xGen Exome Hyb Panel v2, Illumina TruSeq Exome Kit, and Illumina Nextera DNA Exome protocols, we curated WES data from distinct panels to retain common variants. We focused on the top 5 chromosomal regions of interest (ROIs) identified via admixture-adjusted genome-wide linkage analyses. We present findings from our WES analysis underpinning the “common disease-common variant” hypothesis. We used four criteria for variant filtration in annotated VCF files: (1) autosomal, (2) has alternate allele, (3) within exonic/splice site, and (4) allele frequency (AF) ≤ 0.2. Variant AFs were drawn from gnomAD, ExAC, ESP6500, and ABraOM datasets. Synonymous variants were excluded. Our scrutiny unearthed 57 missense variants across 30 genes within the identified ROIs: 82.1% marker completion rate in ROI1, 90.4% (ROI2), 27.5% (ROI3), 69.2% (ROI4), and 55% (ROI5). Subsequently, we are investigating the top variants to explore potential interactions of the translated proteins and associated mutations with certain ligands.

Discussion/Conclusions. Our strategy captures and evaluates exonic genome portions, potentially unveiling insights into genetic components underlying EH. These discoveries underscore genetic intricacies within these regions and their plausible involvement in EH susceptibility. By elucidating the interplay between genetic variants and their translated proteins, our study deepens understanding of the underlying mechanisms involved in the etiology of EH.

Grant/Funding Support. P20GM103434

Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY

Bioinformatics Core Director and Assistant Director, Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE)

The University of Louisville Genome Technologies Centers (GTC) consists of three highly collaborative branches: the Sequencing Technology Center (STC), the Bioinformatics Core, and the Genome Technology Education Center (GTEC).  Each of these interact to bring high throughput sequencing capabilities to researchers throughout Kentucky as well as national and international collaborations.  In addition to short-read sequencing applications (i.e. Illumina-based), the STC is a licensed PacBio service provider, making available to researchers typical and novel long-read sequencing applications such as whole genome sequencing, DNA methylation, IsoSeq for alternative isoform analysis, FLAIRR-Seq for understanding immune cell expression diversity, and capture-based methods for identifying non-host insertions (such as retroviruses). In addition, the STC utilizes direct Oxford Nanopore long-read sequencing for RNA events such as 5mC methylation.  The STC is a fee-based service provider with both internal and external fee structures available to University of Louisville and KY INBRE researchers, as well as national and international collaborators.