RSU-1 Maintains Integrity of Caenorhabditis elegans Vulval Muscles by Regulating {alpha}-Actinin
Egg-laying behavior in Caenorhabditis elegans is a well-known model for investigating fundamental cellular processes. In egg-laying, muscle contraction is the relaxation of the vulval muscle to extrude eggs from the vulva. Unlike skeletal muscle, vulval muscle lacks visible striations of the sarcomere. Therefore, vulval muscle must counteract the mechanical stress, caused by egg extrusion and body movement, from inducing cell-shape distortion by maintaining its cytoskeletal integrity. However, the underlying mechanisms that regulate the cellular integrity in vulval muscles remain unclear. Here, we demonstrate that C. elega...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Wang, X., Huang, S., Zheng, C., Ge, W., Wu, C., Tse, Y. C. Tags: Investigations Source Type: research
Selective Loss of Diversity in Doubled-Haploid Lines from European Maize Landraces
Maize landraces are well adapted to their local environments and present valuable sources of genetic diversity for breeding and conservation. But the maintenance of open-pollinated landraces in ex-situ programs is challenging, as regeneration of seed can often lead to inbreeding depression and the loss of diversity due to genetic drift. Recent reports suggest that the production of doubled-haploid (DH) lines from landraces may serve as a convenient means to preserve genetic diversity in a homozygous form that is immediately useful for modern breeding. The production of doubled-haploid (DH) lines presents an extreme case of...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Zeitler, L., Ross-Ibarra, J., Stetter, M. G. Tags: Investigations Source Type: research
Evidence That Runt Acts as a Counter-Repressor of Groucho During Drosophila melanogaster Primary Sex Determination
Runx proteins are bifunctional transcription factors that both repress and activate transcription in animal cells. Typically, Runx proteins work in concert with other transcriptional regulators, including co-activators and co-repressors to mediate their biological effects. In Drosophila melanogaster the archetypal Runx protein, Runt, functions in numerous processes including segmentation, neurogenesis and sex determination. During primary sex determination Runt acts as one of four X-linked signal element (XSE) proteins that direct female-specific activation of the establishment promoter (Pe) of the master regulatory gene S...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Mahadeveraju, S., Jung, Y.-H., Erickson, J. W. Tags: Genetics of Sex Source Type: research
An Unusual Amino Acid Substitution Within Hummingbird Cytochrome c Oxidase Alters a Key Proton-Conducting Channel
Hummingbirds in flight exhibit the highest mass-specific metabolic rate of all vertebrates. The bioenergetic requirements associated with sustained hovering flight raise the possibility of unique amino acid substitutions that would enhance aerobic metabolism. Here, we have identified a non-conservative substitution within the mitochondria-encoded cytochrome c oxidase subunit I (COI) that is fixed within hummingbirds, but not among other vertebrates. This unusual change is also rare among metazoans, but can be identified in several clades with diverse life histories. We performed atomistic molecular dynamics simulations usi...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Dunn, C. D., Akpınar, B. A., Sharma, V. Tags: Investigations Source Type: research
Training Population Optimization for Genomic Selection in Miscanthus
Miscanthus is a perennial grass with potential for lignocellulosic ethanol production. To ensure its utility for this purpose, breeding efforts should focus on increasing genetic diversity of the nothospecies Miscanthus x giganteus (Mxg) beyond the single clone used in many programs. Germplasm from the corresponding parental species M. sinensis (Msi) and M. sacchariflorus (Msa) could theoretically be used as training sets for genomic prediction of Mxg clones with optimal genomic estimated breeding values for biofuel traits. To this end, we first showed that subpopulation structure makes a substantial contribution to the ge...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Olatoye, M. O., Clark, L. V., Labonte, N. R., Dong, H., Dwiyanti, M. S., Anzoua, K. G., Brummer, J. E., Ghimire, B. K., Dzyubenko, E., Dzyubenko, N., Bagmet, L., Sabitov, A., Chebukin, P., Głowacka, K., Heo, K., Jin, X., Nagano, H., Peng, J., Yu, C Tags: Genomic Prediction Source Type: research
qRf8-1, a Novel QTL for the Fertility Restoration of Maize CMS-C Identified by QTL-seq
This study not only expands the original fertility restoration system but also provides valuable insights into the complex genetic mechanisms underlying the fertility restoration of CMS-C. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Zheng, M., Yang, T., Liu, X., Lü, G., Zhang, P., Jiang, B., Zhou, S., Lu, Y., Lan, H., Zhang, S., Li, C., Rong, T., Cao, M. Tags: Investigations Source Type: research
Origin Specific Genomic Selection: A Simple Process To Optimize the Favorable Contribution of Parents to Progeny
Modern crop breeding is in constant demand for new genetic diversity as part of the arms race with genetic gain. The elite gene pool has limited genetic variation and breeders are trying to introduce novelty from unadapted germplasm, landraces and wild relatives. For polygenic traits, currently available approaches to introgression are not ideal, as there is a demonstrable bias against exotic alleles during selection. Here, we propose a partitioned form of genomic selection, called Origin Specific Genomic Selection (OSGS), where we identify and target selection on favorable exotic alleles. Briefly, within a population deri...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Yang, C. J., Sharma, R., Gorjanc, G., Hearne, S., Powell, W., Mackay, I. Tags: Genomic Prediction Source Type: research
Low Additive Genetic Variation in a Trait Under Selection in Domesticated Rice
Quantitative traits are important targets of both natural and artificial selection. The genetic architecture of these traits and its change during the adaptive process is thus of fundamental interest. The fate of the additive effects of variants underlying a trait receives particular attention because they constitute the genetic variation component that is transferred from parents to offspring and thus governs the response to selection. While estimation of this component of phenotypic variation is challenging, the increasing availability of dense molecular markers puts it within reach. Inbred plant species offer an additio...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Karavolias, N. G., Greenberg, A. J., Barrero, L. S., Maron, L. G., Shi, Y., Monteverde, E., Pineros, M. A., McCouch, S. R. Tags: Investigations Source Type: research
Support Vector Machine for Lung Adenocarcinoma Staging Through Variant Pathways
Lung adenocarcinoma (LUAD) is one of the most common malignant tumors. How to effectively diagnose LUAD at an early stage and make an accurate judgement of the occurrence and progression of LUAD are still the focus of current research. Support vector machine (SVM) is one of the most effective methods for diagnosing LUAD of different stages. The study aimed to explore the dynamic change of differentially expressed genes (DEGs) in different stages of LUAD, and to assess the risk of LUAD through DEGs enriched pathways and establish a diagnostic model based on SVM method. Based on TMN stages and gene expression profiles of 517...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Di, F., He, C., Pu, G., Zhang, C. Tags: Investigations Source Type: research
QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants
Linkage mapping has been widely used to identify quantitative trait loci (QTL) in many plants and usually requires a time-consuming and labor-intensive fine mapping process to find the causal gene underlying the QTL. Previously, we described QTG-Finder, a machine-learning algorithm to rationally prioritize candidate causal genes in QTLs. While it showed good performance, QTG-Finder could only be used in Arabidopsis and rice because of the limited number of known causal genes in other species. Here we tested the feasibility of enabling QTG-Finder to work on species that have few or no known causal genes by using orthologs o...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Lin, F., Lazarus, E. Z., Rhee, S. Y. Tags: Investigations Source Type: research
Systematic Identification and Analysis of Light-Responsive Circular RNA and Co-expression Networks in Lettuce (Lactuca sativa)
Circular RNA (circRNA) is a covalently-closed single-stranded RNA molecule that plays an important role in transcriptional regulation of gene expression in a variety of species. Light intensity is a pivotal environmental factor affecting plant growth and development. However, little is known regarding photoresponsive plant circRNAs. Here, we aimed to investigate the expression and function of circRNAs in lettuce leaves in response to different light intensity treatments. We performed RNA sequencing (RNA-Seq) on leaves of lettuce (Lactuca sativa) to determine circRNA expression profiles and reverse-transcription polymerase ...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Yang, Z., Yang, Z., Xie, Y., Liu, Q., Mei, Y., Wu, Y. Tags: Investigations Source Type: research
The Ancestral Caenorhabditis elegans Cuticle Suppresses rol-1
Genetic background commonly modifies the effects of mutations. We discovered that worms mutant for the canonical rol-1 gene, identified by Brenner in 1974, do not roll in the genetic background of the wild strain CB4856. Using linkage mapping, association analysis and gene editing, we determined that N2 carries an insertion in the collagen gene col-182 that acts as a recessive enhancer of rol-1 rolling. From population and comparative genomics, we infer the insertion is derived in N2 and related laboratory lines, likely arising during the domestication of Caenorhabditis elegans, and breaking a conserved protein. The ancest...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Noble, L. M., Miah, A., Kaur, T., Rockman, M. V. Tags: Investigations Source Type: research
Validation of QTLs for Fiber Quality Introgressed from Gossypium mustelinum by Selective Genotyping
Gene introgression from wild species has been shown to be a feasible approach for fiber quality improvement in Upland cotton. Previously, we developed an interspecific G. mustelinum x G. hirsutum advanced-backcross population and mapped over one hundred QTL for fiber quality traits. In the current study, a trait-based selective genotyping approach was utilized to prioritize a small subset of introgression lines with high phenotypic values for different fiber quality traits, to simultaneously validate multiple fiber quality QTL in a single experiment. A total of 75 QTL were detected by CIM and/or single-marker analysis, inc...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Chen, Q., Wang, W., Wang, C., Zhang, M., Yu, J., Zhang, Y., Yuan, B., Ding, Y., Jones, D. C., Paterson, A. H., Chee, P. W., Wang, B. Tags: Investigations Source Type: research
The Predicted RNA-Binding Protein ETR-1/CELF1 Acts in Muscles To Regulate Neuroblast Migration in Caenorhabditis elegans
Neuroblast migration is a critical aspect of nervous system development (e.g., neural crest migration). In an unbiased forward genetic screen, we identified a novel player in neuroblast migration, the ETR-1/CELF1 RNA binding protein. CELF1 RNA binding proteins are involved in multiple aspects of RNA processing including alternative splicing, stability, and translation. We find that a specific mutation in alternatively-spliced exon 8 results in migration defects of the AQR and PQR neurons, and not the embryonic lethality and body wall muscle defects of complete knockdown of the locus. Surprisingly, ETR-1 was required in bod...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Ochs, M. E., Josephson, M. P., Lundquist, E. A. Tags: Investigations Source Type: research
The Gene scb-1 Underlies Variation in Caenorhabditis elegans Chemotherapeutic Responses
Pleiotropy, the concept that a single gene controls multiple distinct traits, is prevalent in most organisms and has broad implications for medicine and agriculture. The identification of the molecular mechanisms underlying pleiotropy has the power to reveal previously unknown biological connections between seemingly unrelated traits. Additionally, the discovery of pleiotropic genes increases our understanding of both genetic and phenotypic complexity by characterizing novel gene functions. Quantitative trait locus (QTL) mapping has been used to identify several pleiotropic regions in many organisms. However, gene knockout...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Evans, K. S., Andersen, E. C. Tags: Investigations Source Type: research
