Σάββατο, 23 Μαρτίου 2019

Genes, Genomes, Genetics Mission

Noncanonical Contributions of MutL{gamma} to VDE-Initiated Crossovers During Saccharomyces cerevisiae Meiosis
In Saccharomyces cerevisiae, the meiosis-specific axis proteins Hop1 and Red1 are present nonuniformly across the genome. In a previous study, the meiosis-specific VMA1-derived endonuclease (VDE) was used to examine Spo11-independent recombination in a recombination reporter inserted in a Hop1/Red1-enriched region (HIS4) and in a Hop1/Red1-poor region (URA3). VDE-initiated crossovers at HIS4 were mostly dependent on Mlh3, a component of the MutL meiotic recombination intermediate resolvase, while...
G3: .Genes, Genomes, Genetics Mission - Online First Articles
00:33
Realized Genome Sharing in Heritability Estimation Using Random Effects Models
For heritability estimation using a two-component random effects model, we provided formulas for the limiting distribution of the maximum likelihood estimate. These formulas are applicable even when the wrong measure of kinship is used to capture additive genetic correlation. When the model is correctly specified, we showed that the asymptotic sampling variance of heritability estimate is determined by both the study design and the extent of variation in the kinship measure that constitutes the additive...
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00:33
Genetic Dissection of Resistance to the Three Fungal Plant Pathogens Blumeria graminis, Zymoseptoria tritici, and Pyrenophora tritici-repentis Using a Multiparental Winter Wheat Population
Bread wheat (Triticum aestivum L.) is one of the world's most important crop species. The development of new varieties resistant to multiple pathogens is an ongoing task in wheat breeding, especially in times of increasing demand for sustainable agricultural practices. Despite this, little is known about the relations between various fungal disease resistances at the genetic level, and the possible consequences for wheat breeding strategies. As a first step to fill this gap, we analyzed the genetic...
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00:33
{-}{-}{-}{-}An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)
Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (~20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (www.congenie.org),...
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Thu Mar 21, 2019 23:22
Long-Term Combinatorial Exposure to Trichloroethylene and Inorganic Arsenic in Genetically Heterogeneous Mice Results in Renal Tubular Damage and Cancer-Associated Molecular Changes
Trichloroethylene (TCE) and inorganic arsenic (iAs) are environmental contaminants that can target the kidney. Chronic exposure to TCE is associated with increased incidence of renal cell carcinoma, while co-exposure to TCE and iAs likely occurs in exposed human populations, such as those near Superfund sites. In order to better understand the kidney health consequences of TCE and/or iAs exposure, a genetically heterogeneous mouse population derived from FVB/NJ and CAST/EiJ mouse strains and deficient...
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Thu Mar 21, 2019 23:22
BGData - A Suite of R Packages for Genomic Analysis with Big Data
We created a suite of packages to enable analysis of extremely large genomic data sets (potentially millions of individuals and millions of molecular markers) within the R environment. The package offers: a matrix-like interface for .bed files (PLINK's binary format for genotype data), a novel class of linked arrays that allows linking data stored in multiple files to form a single array accessible from the R computing environment, methods for parallel computing capabilities that can carry out computations...
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Wed Mar 20, 2019 23:47
Genetic Properties Responsible for the Transgressive Segregation of Days to Heading in Rice
Transgressive segregation produces hybrid progeny phenotypes that exceed the parental phenotypes. Unlike heterosis, extreme phenotypes caused by transgressive segregation are heritably stable. We examined transgressive phenotypes of flowering time in rice, and revealed transgressive segregation in F2 populations derived from a cross between parents with similar (proximal) days to heading (DTH). The DTH phenotypes of the A58 x Kitaake F2 progenies were frequently more extreme than those of either...
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Wed Mar 20, 2019 23:47
HSB-1 Inhibition and HSF-1 Overexpression Trigger Overlapping Transcriptional Changes to Promote Longevity in Caenorhabditis elegans
Heat shock factor 1 (HSF-1) is a component of the heat shock response pathway that is induced by cytoplasmic proteotoxic stress. In addition to its role in stress response, HSF-1 also acts as a key regulator of the rate of organismal aging. Overexpression of HSF-1 promotes longevity in C. elegans via mechanisms that remain less understood. Moreover, genetic ablation of a negative regulator of HSF-1, termed as heat shock factor binding protein 1 (HSB-1), results in hsf-1-dependent life span extension...
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Wed Mar 20, 2019 23:47
Novel exc Genes Involved in Formation of the Tubular Excretory Canals of Caenorhabditis elegans
Regulation of luminal diameter is critical to the function of small single-celled tubes, of which the seamless tubular excretory canals of Caenorhabditis elegans provide a tractable genetic model. Mutations in several sets of genes exhibit the Exc phenotype, in which canal luminal growth is visibly altered. Here, a focused reverse genomic screen of genes highly expressed in the canals found 18 genes that significantly affect luminal outgrowth or diameter. These genes encode novel proteins as well...
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Mon Mar 18, 2019 23:41
Early Developmental Stress Affects Subsequent Gene Expression Response to an Acute Stress in Atlantic Salmon: An Approach for Creating Robust Fish for Aquaculture?
Stress during early life has potential to program and alter the response to stressful events and metabolism in later life. Repeated short exposure of Atlantic salmon to cold water and air during embryonic (E), post-hatch (PH) or both phases of development (EPH) has been shown to alter the methylome and transcriptome and to affect growth performance during later life compared to untreated controls (CO). The aim of this study was to investigate how the transcriptome of these fish responds to subsequent...
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Mon Mar 18, 2019 23:41
Imperfect Linkage Disequilibrium Generates Phantom Epistasis (& Perils of Big Data)
The genetic architecture of complex human traits and diseases is affected by large number of possibly interacting genes, but detecting epistatic interactions can be challenging. In the last decade, several studies have alluded to problems that linkage disequilibrium can create when testing for epistatic interactions between DNA markers. However, these problems have not been formalized nor have their consequences been quantified in a precise manner. Here we use a conceptually simple three locus model...
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Sat Mar 16, 2019 00:00
Integrating Molecular Markers and Environmental Covariates To Interpret Genotype by Environment Interaction in Rice (Oryza sativa L.) Grown in Subtropical Areas
Understanding the genetic and environmental basis of genotype x environment interaction (GxE) is of fundamental importance in plant breeding. If we consider GxE in the context of genotype x year interactions (GxY), predicting which lines will have stable and superior performance across years is an important challenge for breeders. A better understanding of the factors that contribute to the overall grain yield and quality of rice (Oryza sativa L.) will lay the foundation for developing new breeding...
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Sat Mar 16, 2019 00:00
A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain-Specific Maternal Effects on Litter Size
Reproductive success in the eight founder strains of the Collaborative Cross (CC) was measured using a diallel-mating scheme. Over a 48-month period we generated 4,448 litters, and provided 24,782 weaned pups for use in 16 different published experiments. We identified factors that affect the average litter size in a cross by estimating the overall contribution of parent-of-origin, heterosis, inbred, and epistatic effects using a Bayesian zero-truncated overdispersed Poisson mixed model. The phenotypic...
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Sat Mar 16, 2019 00:00
Cleaning Genotype Data from Diversity Outbred Mice
Data cleaning is an important first step in most statistical analyses, including efforts to map the genetic loci that contribute to variation in quantitative traits. Here we illustrate approaches to quality control and cleaning of array-based genotyping data for multiparent populations (experimental crosses derived from more than two founder strains), using MegaMUGA array data from a set of 291 from Diversity Outbred (DO) mice. Our approach employs data visualizations that can reveal problems at...
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Sat Mar 16, 2019 00:00
Full-Length Transcriptome Sequencing and the Discovery of New Transcripts in the Unfertilized Eggs of Zebrafish (Danio rerio)
Understanding early gene expression in zebrafish embryos is a prerequisite for developmental biology research. In this study, 1,629,447 polymerase reads were obtained from the unfertilized eggs of zebrafish via full-length transcriptome sequencing using the PacBio RS II platform firstly. Then, 102,920 unique isoforms were obtained by correction, clustering and comparison with the zebrafish genome. 12,782 genes in the genome were captured, accounting for 39.71% of the all annotated genes. Approximately...
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Thu Mar 14, 2019 21:50
Use of F2 Bulks in Training Sets for Genomic Prediction of Combining Ability and Hybrid Performance
Developing training sets for genomic prediction in hybrid crops requires producing hybrid seed for a large number of entries. In autogamous crop species (e.g., wheat, rice, rapeseed, cotton) this requires elaborate hybridization systems to prevent self-pollination and presents a significant impediment to the implementation of hybrid breeding in general and genomic selection in particular. An alternative to F1 hybrids are bulks of F2 seed from selfed F1 plants (F1:2). Seed production for F1:2 bulks...
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Tue Mar 12, 2019 22:45
Variation in Filamentous Growth and Response to Quorum-Sensing Compounds in Environmental Isolates of Saccharomyces cerevisiae
In fungi, filamentous growth is a major developmental transition that occurs in response to environmental cues. In diploid Saccharomyces cerevisiae, it is known as pseudohyphal growth and presumed to be a foraging mechanism. Rather than unicellular growth, multicellular filaments composed of elongated, attached cells spread over and into surfaces. This morphogenetic switch can be induced through quorum sensing with the aromatic alcohols phenylethanol and tryptophol. Most research investigating pseudohyphal...
G3: .Genes, Genomes, Genetics Mission - Online First Articles
Tue Mar 12, 2019 22:45
Whole Genome Sequencing and Progress Towards Full Inbreeding of the Mouse Collaborative Cross Population
Two key features of recombinant inbred panels are well-characterized genomes and reproducibility. Here we report on the sequenced genomes of six additional Collaborative Cross (CC) strains and on inbreeding progress of 72 CC strains. We have previously reported on the sequences of 69 CC strains that were publicly available, bringing the total of CC strains with whole genome sequence up to 75. The sequencing of these six CC strains updates the efforts towards inbreeding undertaken by the UNC Systems...
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Mon Mar 11, 2019 23:53
New Deep Learning Genomic-Based Prediction Model for Multiple Traits with Binary, Ordinal, and Continuous Phenotypes
Multiple-trait experiments with mixed phenotypes (binary, ordinal and continuous) are not rare in animal and plant breeding programs. However, there is a lack of statistical models that can exploit the correlation between traits with mixed phenotypes in order to improve prediction accuracy in the context of genomic selection (GS). For this reason, when breeders have mixed phenotypes, they usually analyze them using univariate models, and thus are not able to exploit the correlation between traits,...
G3: .Genes, Genomes, Genetics Mission - Online First Articles
Mon Mar 11, 2019 23:53
Assessment of Genetic Differentiation and Linkage Disequilibrium in Solanum pimpinellifolium Using Genome-Wide High-Density SNP Markers
To mine new favorable alleles for tomato breeding, we investigated the feasibility of utilizing Solanum pimpinellifolium as a diverse panel of genome-wide association study through the restriction site-associated DNA sequencing technique. Previous attempts to conduct genome-wide association studies using S. pimpinellifolium were impeded by an inability to correct for population stratification and by lack of high-density markers to address the issue of rapid linkage disequilibrium decay. In the current...
G3: .Genes, Genomes, Genetics Mission - Online First Articles
Mon Mar 11, 2019 23:53
TSD: A Computational Tool To Study the Complex Structural Variants Using PacBio Targeted Sequencing Data
PacBio sequencing is a powerful approach to study DNA or RNA sequences in a longer scope. It is especially useful in exploring the complex structural variants generated by random integration or multiple rearrangement of endogenous or exogenous sequences. Here, we present a tool, TSD, for complex structural variant discovery using PacBio targeted sequencing data. It allows researchers to identify and visualize the genomic structures of targeted sequences by unlimited splitting, alignment and assembly...
G3: .Genes, Genomes, Genetics Mission - Online First Articles
Sat Mar 09, 2019 00:10
Small RNA-Seq Analysis Reveals miRNA Expression Dynamics Across Tissues in the Malaria Vector, Anopheles gambiae
Malaria continues to be a major global health problem, where disease transmission is deeply linked to the repeated blood feeding nature of the anautogenous mosquito. Given the tight link between blood feeding and disease transmission, understanding basic biology behind mosquito physiology is a requirement for developing effective vector-borne disease control strategies. In the mosquito, numerous loss of function studies with notable phenotypes demonstrate microRNAs (miRNAs) play significant roles...
G3: .Genes, Genomes, Genetics Mission - Online First Articles
Thu Mar 07, 2019 23:23
The Neurospora crassa Standard Oak Ridge Background Exhibits Atypically Efficient Meiotic Silencing by Unpaired DNA
Meiotic silencing by unpaired DNA (MSUD), an RNAi-mediated gene silencing process, is efficient in crosses made in the Neurospora crassa standard Oak Ridge (OR) genetic background. However, MSUD was decidedly less efficient when the OR-derived MSUD testers were crossed with many wild-isolated strains (W), suggesting that either sequence heterozygosity in tester x W crosses suppresses MSUD, or that OR represents the MSUD-conducive extreme in the range of genetic variation in MSUD efficiency. Our results...
G3: .Genes, Genomes, Genetics Mission - Online First Articles
Thu Mar 07, 2019 00:43

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