G3 Reviewer Index 2020
(Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Tags: Reviewer Index Source Type: research
Corrigendum
(Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Tags: Corrigendum Source Type: research
Widely Used Mutants of eiger, Encoding the Drosophila Tumor Necrosis Factor, Carry Additional Mutations in the NimrodC1 Phagocytosis Receptor
The process of apoptosis in epithelia involves activation of caspases, delamination of cells, and degradation of cellular components. Corpses and cellular debris are then rapidly cleared from the tissue by phagocytic blood cells. In studies of the Drosophila TNF, Eiger (Egr) and cell death in wing imaginal discs, the epithelial primordia of fly wings, we noticed that dying cells appeared to transiently accumulate in egr3 mutant wing discs, raising the possibility that their phagocytic engulfment by hemocytes was impaired. Further investigation revealed that lymph glands and circulating hemocytes from egr3 mutant larvae wer...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Kodra, A., de la Cova, C., Gerhold, A. R., Johnston, L. A. Tags: Investigations Source Type: research
High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas
Studies of linkage and linkage mapping have advanced genetic and biological knowledge for over 100 years. In addition to their growing role, today, in mapping phenotypes to genotypes, dense linkage maps can help to validate genome assemblies. Previously, we showed that 40% of scaffolds in the first genome assembly for the Pacific oyster Crassostrea gigas were chimeric, containing single nucleotide polymorphisms (SNPs) mapping to different linkage groups. Here, we merge 14 linkage maps constructed of SNPs generated from genotyping-by-sequencing (GBS) methods with five, previously constructed linkage maps, to create a compen...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Yin, X., Arias-Perez, A., Kitapci, T. H., Hedgecock, D. Tags: Investigations Source Type: research
Regional Variation in Genetic Control of Atherosclerosis in Hyperlipidemic Mice
Atherosclerosis is a polygenic disorder that often affects multiple arteries. Carotid arteries are common sites for evaluating subclinical atherosclerosis, and aortic root is the standard site for quantifying atherosclerosis in mice. We compared genetic control of atherosclerosis between the two sites in the same cohort derived from two phenotypically divergent Apoe-null (Apoe–/–) mouse strains. Female F2 mice were generated from C57BL/6 (B6) and C3H/He (C3H) Apoe–/– mice and fed 12 weeks of Western diet. Atherosclerotic lesions in carotid bifurcation and aortic root and plasma levels of fasting lip...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Jones, M. B., An, A., Shi, L. J., Shi, W. Tags: Investigations Source Type: research
Oxidative Stress Responses and Nutrient Starvation in MCHM Treated Saccharomyces cerevisiae
In 2014, the coal cleaning chemical 4-methylcyclohexane methanol (MCHM) spilled into the water supply for 300,000 West Virginians. Initial toxicology tests showed relatively mild results, but the underlying effects on cellular biology were underexplored. Treated wildtype yeast cells grew poorly, but there was only a small decrease in cell viability. Cell cycle analysis revealed an absence of cells in S phase within thirty minutes of treatment. Cells accumulated in G1 over a six-hour time course, indicating arrest instead of death. A genetic screen of the haploid knockout collection revealed 329 high confidence genes requir...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Ayers, M. C., Sherman, Z. N., Gallagher, J. E. G. Tags: Investigations Source Type: research
High-Throughput Identification of Nuclear Envelope Protein Interactions in Schizosaccharomyces pombe Using an Arrayed Membrane Yeast-Two Hybrid Library
The nuclear envelope (NE) contains a specialized set of integral membrane proteins that maintain nuclear shape and integrity and influence chromatin organization and gene expression. Advances in proteomics techniques and studies in model organisms have identified hundreds of proteins that localize to the NE. However, the function of many of these proteins at the NE remains unclear, in part due to a lack of understanding of the interactions that these proteins participate in at the NE membrane. To assist in the characterization of NE transmembrane protein interactions we developed an arrayed library of integral and peripher...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Varberg, J. M., Gardner, J. M., McCroskey, S., Saravanan, S., Bradford, W. D., Jaspersen, S. L. Tags: Investigations Source Type: research
Slow Growth and Increased Spontaneous Mutation Frequency in Respiratory Deficient afo1- Yeast Suppressed by a Dominant Mutation in ATP3
A yeast deletion mutation in the nuclear-encoded gene, AFO1, which codes for a mitochondrial ribosomal protein, led to slow growth on glucose, the inability to grow on glycerol or ethanol, and loss of mitochondrial DNA and respiration. We noticed that afo1- yeast readily obtains secondary mutations that suppress aspects of this phenotype, including its growth defect. We characterized and identified a dominant missense suppressor mutation in the ATP3 gene. Comparing isogenic slowly growing rho-zero and rapidly growing suppressed afo1- strains under carefully controlled fermentation conditions showed that energy charge was n...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Li, J., Rinnerthaler, M., Hartl, J., Weber, M., Karl, T., Breitenbach-Koller, H., Mülleder, M., Vowinckel, J., Marx, H., Sauer, M., Mattanovich, D., Ata, O., De, S., Greslehner, G. P., Geltinger, F., Burhans, B., Grant, C., Doronina, V., Ralser, M Tags: Investigations Source Type: research
The Nuclear Receptor Seven Up Regulates Genes Involved in Immunity and Xenobiotic Response in the Adult Drosophila Female Fat Body
The physiology of organisms depends on inter-organ communication in response to changes in the environment. Nuclear receptors are broadly expressed transcription factors that respond to circulating molecules to control many biological processes, including immunity, detoxification, and reproduction. Although the tissue-intrinsic roles of nuclear receptors in reproduction have been extensively studied, there is increasing evidence that nuclear receptor signaling in peripheral tissues can also influence oogenesis. We previously showed that the Drosophila nuclear receptor Seven up (Svp) is required in the adult fat body to reg...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Weaver, L. N., Drummond-Barbosa, D. Tags: Investigations Source Type: research
Runs of Homozygosity in Modern Chicken Revealed by Sequence Data
This study aimed to systematically compare the genomic distribution of the ROH islands among five populations of wild vs. commercial chickens of both layer and broiler type. To this end, we analyzed whole genome sequences of 115 birds including white layer (WL, n = 25), brown layer (BL, n = 25), broiler line A (BRA, n = 20), broiler line B (BRB, n = 20) and Red Junglefowl (RJF, n = 25). The ROH segments varied in size markedly among populations, ranging from 0.3 to 21.83 Mb reflecting their past genealogy. White layers contained the largest portion of the genome in homozygous state with an average ROH length of 432.1 Mb (&...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Talebi, R., Szmatoła, T., Meszaros, G., Qanbari, S. Tags: Investigations Source Type: research
Leveraging Multiple Layers of Data To Predict Drosophila Complex Traits
The ability to accurately predict complex trait phenotypes from genetic and genomic data are critical for the implementation of personalized medicine and precision agriculture; however, prediction accuracy for most complex traits is currently low. Here, we used data on whole genome sequences, deep RNA sequencing, and high quality phenotypes for three quantitative traits in the ~200 inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to compare the prediction accuracies of gene expression and genotypes for three complex traits. We found that expression levels (r = 0.28 and 0.38, for females and males,...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Morgante, F., Huang, W., Sorensen, P., Maltecca, C., Mackay, T. F. C. Tags: Genomic Prediction Source Type: research
Gene Copy Number Variation Does Not Reflect Structure or Environmental Selection in Two Recently Diverged California Populations of Suillus brevipes
In this study, we report opposite results for both predictions based on the analysis of gene copy number variants (CNVs) of Suillus brevipes, a mycorrhizal fungus adapted to coastal and montane habitats in California. In order to assess whether gene copy number variation mirrored population structure and selection in this species, we investigated two previously studied locally adapted populations showing a highly differentiated genomic region encompassing a gene predicted to confer salt tolerance. In addition, we examined whether copy number in the genes related to salt homeostasis was differentiated between the two popula...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Bazzicalupo, A. L., Thomas, M., Mason, R., Munro-Ehrlich, , Branco, S. Tags: Investigations Source Type: research
Estimation of Molecular Pairwise Relatedness in Autopolyploid Crops
In this study, we provide guidelines for plant geneticists and breeders to access trustworthy pairwise relatedness estimates. To this end, we simulated populations considering different ploidy levels, meiotic pairings patterns, number of loci and alleles, and inbreeding levels. Analysis were performed to access the accuracy of distinct methods and to demonstrate the usefulness of molecular marker in practical situations. Overall, our results suggest that at least 100 effective biallelic molecular markers are required to have good pairwise relatedness estimation if methods based on correlation is used. For this number of lo...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Amadeu, R. R., Lara, L. A. C., Munoz, P., Garcia, A. A. F. Tags: Investigations Source Type: research
Dissecting the Genetic Architecture of Biofuel-Related Traits in a Sorghum Breeding Population
In this study, we analyzed a breeding population for bioenergy sorghum, which was previously developed based on testcross performance, to compare genomic selection models both trained on and evaluated for the per se performance of the 3rd generation S0 individuals. Of over 200 ancestral inbred accessions in the base population, only 13 founders contributed to the 3rd generation as progenitors. Compared to the founders, the performances of the population per se were improved for target traits. The total genetic variance within the S0 generation progenies themselves for all traits was mainly additive, although non-additive v...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Ishimori, M., Takanashi, H., Hamazaki, K., Atagi, Y., Kajiya-Kanegae, H., Fujimoto, M., Yoneda, J., Tokunaga, T., Tsutsumi, N., Iwata, H. Tags: Genomic Prediction Source Type: research
A Novel Mapping Strategy Utilizing Mouse Chromosome Substitution Strains Identifies Multiple Epistatic Interactions That Regulate Complex Traits
The genetic contribution of additive vs. non-additive (epistatic) effects in the regulation of complex traits is unclear. While genome-wide association studies typically ignore gene-gene interactions, in part because of the lack of statistical power for detecting them, mouse chromosome substitution strains (CSSs) represent an alternate approach for detecting epistasis given their limited allelic variation. Therefore, we utilized CSSs to identify and map both additive and epistatic loci that regulate a range of hematologic- and metabolism-related traits, as well as hepatic gene expression. Quantitative trait loci (QTL) were...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Miller, A. K., Chen, A., Bartlett, J., Wang, L., Williams, S. M., Buchner, D. A. Tags: Investigations Source Type: research
