Systematic Screen for Drosophila Transcriptional Regulators Phosphorylated in Response to Insulin/mTOR Pathway
Insulin/insulin-like growth factor signaling (IIS) is a conserved mechanism to regulate animal physiology in response to nutrition. IIS activity controls gene expression, but only a subset of transcriptional regulators (TRs) targeted by the IIS pathway is currently known. Here we report the results of an unbiased screen for Drosophila TRs phosphorylated in an IIS-dependent manner. To conduct the screen, we built a library of 857 V5/Strep-tagged TRs under the control of Copper-inducible metallothionein promoter (pMt). The insulin-induced phosphorylation changes were detected by using Phos-tag SDS-PAGE and Western blotting. ...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Liu, Y., Mattila, J., Hietakangas, V. Tags: Investigations Source Type: research
Purebred and Crossbred Genomic Evaluation and Mate Allocation Strategies To Exploit Dominance in Pig Crossbreeding Schemes
We investigated the effectiveness of mate allocation strategies accounting for non-additive genetic effects to improve crossbred performance in a two-way crossbreeding scheme. We did this by computer simulation of 10 generations of evaluation and selection. QTL effects were simulated as correlated across purebreds and crossbreds, and (positive) heterosis was simulated as directional dominance. The purebred-crossbred correlation was 0.30 or 0.68 depending on the genetic variance component used. Dominance and additive marker effects were estimated simultaneously for purebreds and crossbreds by multiple trait genomic BLUP. Fo...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Gonzalez-Dieguez, D., Tusell, L., Bouquet, A., Legarra, A., Vitezica, Z. G. Tags: Genomic Prediction Source Type: research
Identification of Loci That Confer Resistance to Bacterial and Fungal Diseases of Maize
In this study, we evaluated a disease resistance introgression line (DRIL) population for the foliar disease Goss’s bacterial wilt and blight (GW) and conducted quantitative trait locus (QTL) mapping. We identified a total of ten QTL across multiple environments. We then combined our GW data with data on four additional foliar diseases (northern corn leaf blight, southern corn leaf blight, gray leaf spot, and bacterial leaf streak) and conducted multivariate analysis to identify regions conferring resistance to multiple diseases. We identified 20 chromosomal bins with putative multiple disease effects. We examined th...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Qiu, Y., Cooper, J., Kaiser, C., Wisser, R., Mideros, S. X., Jamann, T. M. Tags: Genetics of Immunity Source Type: research
C-Terminal HA Tags Compromise Function and Exacerbate Phenotypes of Saccharomyces cerevisiae Blooms Helicase Homolog Sgs1 SUMOylation-Associated Mutants
The Sgs1 helicase and Top3-Rmi1 decatenase form a complex that affects homologous recombination outcomes during the mitotic cell cycle and during meiosis. Previous studies have reported that Sgs1-Top3-Rmi1 function is regulated by SUMOylation that is catalyzed by the Smc5-Smc6-Mms21 complex. These studies used strains in which SGS1 was C-terminally tagged with three or six copies of a human influenza hemagglutinin-derived epitope tag (3HA and 6HA). They identified SGS1 mutants that affect its SUMOylation, which we will refer to as SGS1 SUMO-site mutants. In previous work, these mutants showed phenotypes consistent with sub...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Cohen, M., Lichten, M. Tags: Investigations Source Type: research
Closing Human Reference Genome Gaps: Identifying and Characterizing Gap-Closing Sequences
Despite continuous updates of the human reference genome, there are still hundreds of unresolved gaps which account for about 5% of the total sequence length. Given the availability of whole genome de novo assemblies, especially those derived from long-read sequencing data, gap-closing sequences can be determined. By comparing 17 de novo long-read sequencing assemblies with the human reference genome, we identified a total of 1,125 gap-closing sequences for 132 (16.9% of 783) gaps and added up to 2.2 Mb novel sequences to the human reference genome. More than 90% of the non-redundant sequences could be verified by unmapped...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Zhao, T., Duan, Z., Genchev, G. Z., Lu, H. Tags: Investigations Source Type: research
An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony
High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (Arctocephalus gazella). SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria. Out of a total of 85,359 SNPs tiled on the array, 75,601 (...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Humble, E., Paijmans, A. J., Forcada, J., Hoffman, J. I. Tags: Investigations Source Type: research
Development and Validation of an Open Access SNP Array for Nile Tilapia (Oreochromis niloticus)
Tilapia are among the most important farmed fish species worldwide, and are fundamental for the food security of many developing countries. Several genetically improved Nile tilapia (Oreochromis niloticus) strains exist, such as the iconic Genetically Improved Farmed Tilapia (GIFT), and breeding programs typically follow classical pedigree-based selection. The use of genome-wide single-nucleotide polymorphism (SNP) data can enable an understanding of the genetic architecture of economically important traits and the acceleration of genetic gain via genomic selection. Due to the global importance and diversity of Nile tilapi...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Penaloza, C., Robledo, D., Barria, A., Trinh, T. Q., Mahmuddin, M., Wiener, P., Benzie, J. A. H., Houston, R. D. Tags: Investigations Source Type: research
Taro Genome Assembly and Linkage Map Reveal QTLs for Resistance to Taro Leaf Blight
Taro (Colocasia esculenta) is a food staple widely cultivated in the humid tropics of Asia, Africa, Pacific and the Caribbean. One of the greatest threats to taro production is Taro Leaf Blight caused by the oomycete pathogen Phytophthora colocasiae. Here we describe a de novo taro genome assembly and use it to analyze sequence data from a Taro Leaf Blight resistant mapping population. The genome was assembled from linked-read sequences (10x Genomics; ~60x coverage) and gap-filled and scaffolded with contigs assembled from Oxford Nanopore Technology long-reads and linkage map results. The haploid assembly was 2.45 Gb total...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Bellinger, M. R., Paudel, R., Starnes, S., Kambic, L., Kantar, M. B., Wolfgruber, T., Lamour, K., Geib, S., Sim, S., Miyasaka, S. C., Helmkampf, M., Shintaku, M. Tags: Investigations Source Type: research
Preservation of Genetic Variation in a Breeding Population for Long-Term Genetic Gain
Genomic selection has been successfully implemented in plant and animal breeding. The transition of parental selection based on phenotypic characteristics to genomic selection (GS) has reduced breeding time and cost while accelerating the rate of genetic progression. Although breeding methods have been adapted to include genomic selection, parental selection often involves truncation selection, selecting the individuals with the highest genomic estimated breeding values (GEBVs) in the hope that favorable properties will be passed to their offspring. This ensures genetic progression and delivers offspring with high genetic ...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Vanavermaete, D., Fostier, J., Maenhout, S., De Baets, B. Tags: Genomic Prediction Source Type: research
Neuronal Ceroid Lipofuscinosis in a Domestic Cat Associated with a DNA Sequence Variant That Creates a Premature Stop Codon in CLN6
This study is only the second to identify the molecular genetic basis of a feline NCL. Other cats exhibiting similar signs can now be screened for the CLN6 variant. This could lead to establishment of a feline model of CLN6 disease that could be used in therapeutic intervention studies. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Katz, M. L., Buckley, R. M., Biegen, V., OBrien, D. P., Johnson, G. C., Warren, W. C., Lyons, L. A. Tags: Investigations Source Type: research
Genomic Prediction Enhanced Sparse Testing for Multi-environment Trials
"Sparse testing" refers to reduced multi-environment breeding trials in which not all genotypes of interest are grown in each environment. Using genomic-enabled prediction and a model embracing genotype x environment interaction (GE), the non-observed genotype-in-environment combinations can be predicted. Consequently, the overall costs can be reduced and the testing capacities can be increased. The accuracy of predicting the unobserved data depends on different factors including (1) how many genotypes overlap between environments, (2) in how many environments each genotype is grown, and (3) which prediction method is used...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Jarquin, D., Howard, R., Crossa, J., Beyene, Y., Gowda, M., Martini, J. W. R., Covarrubias Pazaran, G., Burgueno, J., Pacheco, A., Grondona, M., Wimmer, V., Prasanna, B. M. Tags: Genomic Prediction Source Type: research
Alternative Splicing Regulation of Anthocyanin Biosynthesis in Camellia sinensis var. assamica Unveiled by PacBio Iso-Seq
Although the pathway and transcription factor regulation of anthocyanin biosynthesis in tea plants [Camellia sinensis (L.) O. Ktze] are known, post-transcriptional regulation mechanisms involved in anthocyanin accumulation have not been comprehensively studied. We obtained the full-length transcriptome of a purple cultivar (‘Zijuan’) and a normal green cultivar (‘Yunkang 10#) of C. sinensis var. asssamica (Masters) showing different accumulation of anthocyanins and catechins through PacBio isoform sequencing (Iso-Seq). In total, 577,557 mapped full-length cDNAs were obtained, and 2,600 average-length gene...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Chen, L., Shi, X., Nian, B., Duan, S., Jiang, B., Wang, X., Lv, C., Zhang, G., Ma, Y., Zhao, M. Tags: Investigations Source Type: research
Asymmetric Fitness of Second-Generation Interspecific Hybrids Between Ciona robusta and Ciona intestinalis
Reproductive isolation is central to speciation, but interspecific crosses between two closely related species can produce viable and fertile hybrids. Two different species of tunicates in the same ascidian genus, Ciona robusta and Ciona intestinalis, can produce hybrids. However, wild sympatric populations display limited gene flow, suggesting the existence of obstacles to interspecific reproduction that remain unknown. Here, we took advantage of a closed culture system to cross C. robusta with C. intestinalis and established F1 and F2 hybrids. We monitored post-embryonic development, survival, and sexual maturation to ch...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Ohta, N., Kaplan, N., Ng, J. T., Gravez, B. J., Christiaen, L. Tags: Investigations Source Type: research
Genomics of Clinal Local Adaptation in Pinus sylvestris Under Continuous Environmental and Spatial Genetic Setting
We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically ext...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Tyrmi, J. S., Vuosku, J., Acosta, J. J., Li, Z., Sterck, L., Cervera, M. T., Savolainen, O., Pyhäjärvi, T. Tags: Investigations Source Type: research
Escherichia coli with a Tunable Point Mutation Rate for Evolution Experiments
The mutation rate and mutations’ effects on fitness are crucial to evolution. Mutation rates are under selection due to linkage between mutation rate modifiers and mutations’ effects on fitness. The linkage between a higher mutation rate and more beneficial mutations selects for higher mutation rates, while the linkage between a higher mutation rate and more deleterious mutations selects for lower mutation rates. The net direction of selection on mutations rates depends on the fitness landscape, and a great deal of work has elucidated the fitness landscapes of mutations. However, tests of the effect of varying ...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Sherer, N. A., Kuhlman, T. E. Tags: Investigations Source Type: research
