Genotypic Characterization of the U.S. Peanut Core Collection
Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the entire available core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of 253 accessions was replicated, using between two and five seeds per accession, to assess heterogeneity with...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Otyama, P. I., Kulkarni, R., Chamberlin, K., Ozias-Akins, P., Chu, Y., Lincoln, L. M., MacDonald, G. E., Anglin, N. L., Dash, S., Bertioli, D. J., Fernandez-Baca, D., Graham, M. A., Cannon, S. B., Cannon, E. K. S. Tags: Investigations Source Type: research
Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding
In this study, we first investigated how mutations at conserved nucleotide sites normally viewed as deleterious, such as nonsynonymous sites, accumulated in a wheat, Triticum aestivum, breeding lineage. By comparing a 150 year old ancestral and modern cultivar, we found recent nucleotide polymorphisms altered amino acids and occurred within conserved genes at frequencies expected in the absence of purifying selection. Mutations that are deleterious in other contexts likely had very small or no effects on target traits within the breeding lineage. Second, we investigated if breeders selected alleles with favorable effects o...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Raherison, E., Majidi, M. M., Goessen, R., Hughes, N., Cuthbert, R., Knox, R., Lukens, L. Tags: Investigations Source Type: research
Genetic Analysis of Stem Diameter and Water Contents To Improve Sorghum Bioenergy Efficiency
Biofuel made from agricultural products has the potential in contribute to a stable supply of fuel for growing energy demands. Some salient plant traits, such as stem diameter and water content, and their relationship to other important biomass-related traits are so far poorly understood. Here, we performed QTL mapping for three stem diameter and two water content traits in a S. bicolor BTx623 x IS3620c recombinant inbred line population of 399 genotypes, and validated the genomic regions identified using genome-wide association studies (GWAS) in a diversity panel of 354 accessions. The discovery of both co-localized and n...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Kong, W., Jin, H., Goff, V. H., Auckland, S. A., Rainville, L. K., Paterson, A. H. Tags: Investigations Source Type: research
PhenoMIP: High-Throughput Phenotyping of Diverse Caenorhabditis elegans Populations via Molecular Inversion Probes
Whether generated within a lab setting or isolated from the wild, variant alleles continue to be an important resource for decoding gene function in model organisms such as Caenorhabditis elegans. With advances in massively parallel sequencing, multiple whole-genome sequenced (WGS) strain collections are now available to the research community. The Million Mutation Project (MMP) for instance, analyzed 2007 N2-derived, mutagenized strains. Individually, each strain averages ~400 single nucleotide variants amounting to ~80 protein-coding variants. The effects of these variants, however, remain largely uncharacterized and que...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Mok, C., Belmarez, G., Edgley, M. L., Moerman, D. G., Waterston, R. H. Tags: Investigations Source Type: research
TheCellVision.org: A Database for Visualizing and Mining High-Content Cell Imaging Projects
Advances in genome engineering and high throughput imaging technologies have enabled genome-scale screens of single cells for a variety of phenotypes, including subcellular morphology and protein localization. We constructed TheCellVision.org, a freely available and web-accessible image visualization and data browsing tool that serves as a central repository for fluorescence microscopy images and associated quantitative data produced by high-content screening experiments. Currently, TheCellVision.org hosts ~575,590 images and associated analysis results from two published high-content screening (HCS) projects focused on th...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Masinas, M. P. D., Usaj, M. M., Usaj, M., Boone, C., Andrews, B. J. Tags: Software and Data Resources Source Type: research
A Faster and More Accurate Algorithm for Calculating Population Genetics Statistics Requiring Sums of Stirling Numbers of the First Kind
Ewen’s sampling formula is a foundational theoretical result that connects probability and number theory with molecular genetics and molecular evolution; it was the analytical result required for testing the neutral theory of evolution, and has since been directly or indirectly utilized in a number of population genetics statistics. Ewen’s sampling formula, in turn, is deeply connected to Stirling numbers of the first kind. Here, we explore the cumulative distribution function of these Stirling numbers, which enables a single direct estimate of the sum, using representations in terms of the incomplete beta func...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Chen, S. L., Temme, N. M. Tags: Software and Data Resources Source Type: research
Identification of Genes Involved in the Differentiation of R7y and R7p Photoreceptor Cells in Drosophila
The R7 and R8 photoreceptor cells of the Drosophila compound eye mediate color vision. Throughout the majority of the eye, these cells occur in two principal types of ommatidia. Approximately 35% of ommatidia are of the pale type and express Rh3 in R7 cells and Rh5 in R8 cells. The remaining 65% are of the yellow type and express Rh4 in R7 cells and Rh6 in R8 cells. The specification of an R8 cell in a pale or yellow ommatidium depends on the fate of the adjacent R7 cell. However, pale and yellow R7 cells are specified by a stochastic process that requires the genes spineless, tango and klumpfuss. To identify additional ge...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Earl, J. B., Vanderlinden, L. A., Jacobsen, T. L., Aldrich, J. C., Saba, L. M., Britt, S. G. Tags: Mutant Screen Report Source Type: research
Genome Profiling for Aflatoxin B1 Resistance in Saccharomyces cerevisiae Reveals a Role for the CSM2/SHU Complex in Tolerance of Aflatoxin B1-Associated DNA Damage
Exposure to the mycotoxin aflatoxin B1 (AFB1) strongly correlates with hepatocellular carcinoma (HCC). P450 enzymes convert AFB1 into a highly reactive epoxide that forms unstable 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 (AFB1-N7-Gua) DNA adducts, which convert to stable mutagenic AFB1 formamidopyrimidine (FAPY) DNA adducts. In CYP1A2-expressing budding yeast, AFB1 is a weak mutagen but a potent recombinagen. However, few genes have been identified that confer AFB1 resistance. Here, we profiled the yeast genome for AFB1 resistance. We introduced the human CYP1A2 into ~90% of the diploid deletion library, and pooled ...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: St. John, N., Freedland, J., Baldino, H., Doyle, F., Cera, C., Begley, T., Fasullo, M. Tags: Mutant Screen Report Source Type: research
Combining Auxin-Induced Degradation and RNAi Screening Identifies Novel Genes Involved in Lipid Bilayer Stress Sensing in Caenorhabditis elegans
Alteration of the lipid composition of biological membranes interferes with their function and can cause tissue damage by triggering apoptosis. Upon lipid bilayer stress, the endoplasmic reticulum mounts a stress response similar to the unfolded protein response. However, only a few genes are known to regulate lipid bilayer stress. We performed a suppressor screen that combined the auxin-inducible degradation (AID) system with conventional RNAi in C. elegans to identify members of the lipid bilayer stress response. AID-mediated degradation of the mediator MDT-15, a protein required for the upregulation of fatty acid desatu...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Venz, R., Korosteleva, A., Jongsma, E., Ewald, C. Y. Tags: Mutant Screen Report Source Type: research
A Reference Genome Sequence for Giant Sequoia
The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, was used as evidence to annotate a ...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Scott, A. D., Zimin, A. V., Puiu, D., Workman, R., Britton, M., Zaman, S., Caballero, M., Read, A. C., Bogdanove, A. J., Burns, E., Wegrzyn, J., Timp, W., Salzberg, S. L., Neale, D. B. Tags: Genome Report Source Type: research
Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing
The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis ar...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Ozerov, M. Y., Flajshans, M., Noreikiene, K., Vasemägi, A., Gross, R. Tags: Genome Report Source Type: research
A Reference Genome from the Symbiotic Hydrozoan, Hydra viridissima
Various Hydra species have been employed as model organisms since the 18th century. Introduction of transgenic and knock-down technologies made them ideal experimental systems for studying cellular and molecular mechanisms involved in regeneration, body-axis formation, senescence, symbiosis, and holobiosis. In order to provide an important reference for genetic studies, the Hydra magnipapillata genome (species name has been changed to H. vulgaris) was sequenced a decade ago (Chapman et al., 2010) and the updated genome assembly, Hydra 2.0, was made available by the National Human Genome Research Institute in 2017. While H....
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Hamada, M., Satoh, N., Khalturin, K. Tags: Genome Report Source Type: research
Joint Formal Comment for PLGE and Commentary for G3
(Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Tags: Commentary Source Type: research
Characterization of the F Locus Responsible for Floral Anthocyanin Production in Potato
Anthocyanins are pigmented secondary metabolites produced via the flavonoid biosynthetic pathway and play important roles in plant stress responses, pollinator attraction, and consumer preference. Using RNA-sequencing analysis of a cross between diploid potato (Solanum tuberosum L.) lines segregating for flower color, we identified a homolog of the ANTHOCYANIN 2 (AN2) gene family that encodes a MYB transcription factor, herein termed StFlAN2, as the regulator of anthocyanin production in potato corollas. Transgenic introduction of StFlAN2 in white-flowered homozygous doubled-monoploid plants resulted in a recovery of purpl...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Laimbeer, F. P. E., Bargmann, B. O. R., Holt, S. H., Pratt, T., Peterson, B., Doulis, A. G., Buell, C. R., Veilleux, R. E. Tags: Investigations Source Type: research
Identification of Essential Genes and Fluconazole Susceptibility Genes in Candida glabrata by Profiling Hermes Transposon Insertions
Within the budding yeasts, the opportunistic pathogen Candida glabrata and other members of the Nakaseomyces clade have developed virulence traits independently from C. albicans and C. auris. To begin exploring the genetic basis of C. glabrata virulence and its innate resistance to antifungals, we launched the Hermes transposon from a plasmid and sequenced more than 500,000 different semi-random insertions throughout the genome. With machine learning, we identified 1278 protein-encoding genes (25% of total) that could not tolerate transposon insertions and are likely essential for C. glabrata fitness in vitro. Interestingl...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Gale, A. N., Sakhawala, R. M., Levitan, A., Sharan, R., Berman, J., Timp, W., Cunningham, K. W. Tags: Investigations Source Type: research
