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G3: Genes—Genomes—Genetics

Zijing Zhang, Amber R Krauchunas, Stephanie Huang, Mariana F Wolfner
Egg activation is essential for the successful transition from a mature oocyte to a developmentally competent egg. It consists of a series of events including the resumption and completion of meiosis, initiation of translation of some maternal mRNAs and destruction of others, and changes to the vitelline envelope. This major change of cell state is accompanied by large scale alteration in the oocyte's phosphoproteome. We hypothesize that the cohort of proteins that are subject to phosphoregulation during egg activation are functionally important for processes before, during, or soon after this transition, potentially uniquely or as proteins carrying out essential cellular functions like those they do in other (somatic) cells...
July 16, 2018: G3: Genes—Genomes—Genetics
Nancy L Tran, Samuel L Goldsmith, Agapi Dimitriadou, Norma T Takaesu, Christos Consoulas, Stuart J Newfeld
CORL proteins (known as SKOR in mice, Fussel in humans and fussel in Flybase) are a family of CNS specific proteins related to Sno/Ski oncogenes. Their developmental and adult roles are largely unknown. A Drosophila CORL (dCORL) reporter gene is expressed in all Drosophila insulin-like peptide 2 (dILP2) neurons of the pars intercerebralis (PI) of the larval and adult brain. The transcription factor Drifter is also expressed in the PI in a subset of dCORL and dILP2 expressing neurons and in several non-dILP2 neurons...
July 13, 2018: G3: Genes—Genomes—Genetics
Xiexiong Deng, Min-Hao Kuo
The spindle assembly checkpoint (SAC) is key to faithful segregation of chromosomes. One requirement that satisfies SAC is appropriate tension between sister chromatids at the metaphase-anaphase juncture. Proper tension generated by poleward pulling of mitotic spindles signals biorientation of the underlying chromosome. In the budding yeast, the tension status is monitored by the conserved Shugoshin protein, Sgo1p, and the tension sensing motif (TSM) of histone H3. ChIP-seq reveals a unique TSM-dependent, tripartite domain of Sgo1p in each mitotic chromosome...
July 12, 2018: G3: Genes—Genomes—Genetics
Natasha A M Jackson, Angelina M Flores, Elizabeth D Eldon, Lisa S Klig
Inositol is a precursor for the phospholipid membrane component phosphatidylinositol (PI), involved in signal transduction pathways, endoplasmic reticulum stress, and osmoregulation. Alterations of inositol metabolism have been implicated in human reproductive issues, the therapeutic effects of drugs used to treat epilepsy and bipolar disorder, spinal cord defects, and diseases including diabetes and Alzheimer's. The sole known inositol synthetic enzyme is myo -inositol synthase (MIPS), and the homologue in D...
July 10, 2018: G3: Genes—Genomes—Genetics
Yazmin L Serrano Negron, Nancy F Hansen, Susan T Harbison
Understanding how genomic variation causes differences in observable phenotypes remains a major challenge in biology. Specifically, tracing the sequence of events originating from genomic variants of interest, from changes in transcriptional responses to protein modifications, is difficult. Ideally, one would conduct experiments with individuals that are at either extreme of the trait of interest, but such resources are often not available. Additionally, advances in genome editing will enable testing of candidate polymorphisms individually and in combination...
July 10, 2018: G3: Genes—Genomes—Genetics
Adam Norman, Julian Taylor, James Edwards, Haydn Kuchel
Genomic selection applied to plant breeding enables earlier estimates of a line's performance and significant reductions in generation interval. Several factors affecting prediction accuracy should be well understood if breeders are to harness genomic selection to its full potential. We used a panel of 10,375 bread wheat ( Triticum aestivum ) lines genotyped with 18,101 SNP markers to investigate the effect and interaction of training set size, population structure and marker density on genomic prediction accuracy...
July 3, 2018: G3: Genes—Genomes—Genetics
Rafael T Resende, Marcos Deon V de Resende, Camila F Azevedo, Fabyano Fonseca E Silva, Leonardo C Melo, Helton S Pereira, Thiago Lívio P O Souza, Paula Arielle M R Valdisser, Claudio Brondani, Rosana Pereira Vianello
The availability of high-density molecular markers in common bean has allowed to explore the genetic basis of important complex agronomic traits with increased resolution. Genome-Wide Association Studies (GWAS) and Regional Heritability Mapping (RHM) are two analytical approaches for the detection of genetic variants. We carried out GWAS and RHM for plant architecture, lodging and productivity across two important growing environments in Brazil in a germplasm of 188 common bean varieties using DArTseq genotyping strategies...
July 2, 2018: G3: Genes—Genomes—Genetics
Ying-Peng Hua, Ting Zhou, Qiong Liao, Hai-Xing Song, Chun-Yun Guan, Zhen-Hua Zhang
Nitrogen (N) is a non-mineral macronutrient essential for plant growth and development. Oilseed rape (An An Cn Cn , 2 n =4 x =38) has a high requirement for N nutrients whereas showing the lowest N use efficiency (NUE) among crops. The mechanisms underlying NUE regulation in Brassica napus remain unclear because of genome complexity. In this study, we performed high-depth and -coverage whole-genome re-sequencing (WGS) of an N-efficient (higher NUE) genotype "XY15" and an N-inefficient (lower NUE) genotype "814" of rapeseed...
July 2, 2018: G3: Genes—Genomes—Genetics
Emily Humble, Kanchon K Dasmahapatra, Alvaro Martinez-Barrio, Inês Gregório, Jaume Forcada, Ann-Christin Polikeit, Simon D Goldsworthy, Michael E Goebel, Jörn Kalinowski, Jochen B W Wolf, Joseph I Hoffman
Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal ( Arctocephalus gazella ) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing...
June 28, 2018: G3: Genes—Genomes—Genetics
Peter Scharff-Poulsen, Hisao Moriya, Mark Johnston
The yeast S. cerevisiae senses glucose through Snf3 and Rgt2, transmembrane proteins that generate an intracellular signal in response to glucose that leads to inhibition of the Rgt1 transcriptional repressor and consequently to derepression of HXT genes encoding glucose transporters. Snf3 and Rgt2 are thought to be glucose receptors because they are similar to glucose transporters. In contrast to glucose transporters, they have unusually long C-terminal tails that bind to Mth1 and Std1, paralogous proteins that regulate function of the Rgt1 transcription factor...
June 28, 2018: G3: Genes—Genomes—Genetics
Yuanyuan Xu, Yong Wang, Yuning Song, Jichao Deng, Mao Chen, Hongsheng Ouyang, Liangxue Lai, Zhanjun Li
Paired-homeodomain transcription factor 4 ( PAX4 ) gene encodes a transcription factor which plays an important role in the generation, differentiation, development, and survival of insulin-producing β-cells during mammalian pancreas development. PAX4 is a key diabetes mellitus (DM) susceptibility gene, which is associated with many different types of DM, including T1DM, T2DM, maturity onset diabetes of the young 9 (MODY9), and ketosis prone diabetes. In this study, a novel PAX4 gene knockout (KO) model was generated through co-injection of clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) mRNA/sgRNA into rabbit zygotes...
June 27, 2018: G3: Genes—Genomes—Genetics
Xiangyang Chen, Shimiao Liao, Xinya Huang, Ting Xu, Xuezhu Feng, Shouhong Guang
Rearranged chromosomes have been applied to construct genetic balancers to manipulate essential genes in C. elegans Although much effort has been put into constructing balancer chromosomes, approximately 6% (map units) of the C. elegans genome has not been covered, and this area lies mostly in pairing centers (PCs). Here, we developed a method for conditional chromosomal engineering through combinatorial use of the CRISPR/Cas9 and Cre/ LoxP technologies. Functional DNA fragments containing LoxP sequences were inserted into designated genomic loci using a modified counterselection (cs)-CRISPR method...
June 27, 2018: G3: Genes—Genomes—Genetics
Sandrine Picq, Lisa Lumley, Jindra Šíchová, Jérôme Laroche, Esther Pouliot, Bryan Brunet, Roger C Levesque, Felix A H Sperling, František Marec, Michel Cusson
Genome structure characterization can contribute to a better understanding of processes such as adaptation, speciation, and karyotype evolution, and can provide useful information for refining genome assemblies. We studied the genome of an important North American boreal forest pest, the spruce budworm, Choristoneura fumiferana, through a combination of molecular cytogenetic analyses and construction of a high-density linkage map based on single nucleotide polymorphism (SNP) markers obtained through a genotyping-by-sequencing (GBS) approach...
June 27, 2018: G3: Genes—Genomes—Genetics
Débora Y C Brandt, Jônatas César, Jérôme Goudet, Diogo Meyer
Balancing selection is defined as a class of selective regimes that maintain polymorphism above what is expected under neutrality. Theory predicts that balancing selection reduces population differentiation, as measured by FST. However, balancing selection regimes in which different sets of alleles are maintained in different populations could increase population differentiation. To tackle the connection between balancing selection and population differentiation, we investigated population differentiation at the HLA genes, which constitute the most striking example of balancing selection in humans...
June 27, 2018: G3: Genes—Genomes—Genetics
Altar Sorkaç, Michael A DiIorio, Patrick J O'Hern, Saba N Baskoylu, Hannah K Graham, Anne C Hart
The role of Notch signaling in cell-fate decisions has been studied extensively; however, this pathway is also active in adult tissues, including the nervous system. Notch signaling modulates a wide range of behaviors and processes of the nervous system in the nematode Caenorhabditis elegans , but there is no evidence for Notch signaling directly altering synaptic strength. Here, we demonstrate Notch-mediated regulation of synaptic activity at the C. elegans neuromuscular junction (NMJ). For this, we used aldicarb, an inhibitor of the enzyme acetylcholinesterase, and assessed paralysis rates of animals with altered Notch signaling...
June 27, 2018: G3: Genes—Genomes—Genetics
Katherine L Lucot, Peter J Dickinson, Carrie J Finno, Tamer A Mansour, Anna Letko, Katherine M Minor, James R Mickelson, Cord Drögemüller, C Titus Brown, Danika L Bannasch
Canine neuroaxonal dystrophy (NAD) is a recessive, degenerative neurological disease of young adult Rottweiler dogs ( Canis lupus familiaris ) characterized pathologically by axonal spheroids primarily targeting sensory axon terminals. A genome-wide association study of seven Rottweilers affected with NAD and 42 controls revealed a significantly associated region on canine chromosome 5 (CFA 5). Homozygosity within the associated region narrowed the critical interval to a 4.46 Mb haplotype (CFA5:11.28 Mb - 15...
June 26, 2018: G3: Genes—Genomes—Genetics
Yanjun Zan, Simon K G Forsberg, Örjan Carlborg
A plausible explanation for statistical epistasis revealed in genome wide association analyses is the presence of high order linkage disequilibrium (LD) between the genotyped markers tested for interactions and unobserved functional polymorphisms. Based on findings in experimental data, it has been suggested that high order LD might be a common explanation for statistical epistasis inferred between local polymorphisms in the same genomic region. Here, we empirically evaluate how prevalent high order LD is between local, as well as distal, polymorphisms in the genome...
June 26, 2018: G3: Genes—Genomes—Genetics
Vikas Belamkar, Mary J Guttieri, Waseem Hussain, Diego Jarquín, Ibrahim El-Basyoni, Jesse Poland, Aaron J Lorenz, P Stephen Baenziger
Genomic prediction (GP) is now routinely performed in crop plants to predict unobserved phenotypes. The use of predicted phenotypes to make selections is an active area of research. Here, we evaluate GP for predicting grain yield and compare genomic and phenotypic selection by tracking lines advanced. We examined four independent nurseries of F3:6 and F3:7 lines trialed at 6 to 10 locations each year. Yield was analyzed using mixed models that accounted for experimental design and spatial variations. Genotype-by-sequencing provided nearly 27,000 high-quality SNPs...
June 26, 2018: G3: Genes—Genomes—Genetics
Richard Odongo Magwanga, Pu Lu, Joy Nyangasi Kirungu, Qi Dong, Yangguang Hu, Zhongli Zhou, Xiaoyan Cai, Xingxing Wang, Yuqing Hou, Kunbo Wang, Fang Liu
Late embryogenesis abundant (LEA) proteins play key roles in plant drought tolerance. In this study, 157, 85 and 89 candidate LEA2 proteins were identified in G. hirsutum , G. arboreum and G. raimondii respectively. LEA2 genes were classified into 6 groups, designated as group 1 to 6. Phylogenetic tree analysis revealed orthologous gene pairs within the cotton genome. The cotton specific LEA2 motifs identified were E, R and D in addition to Y, K and S motifs. The genes were distributed on all chromosomes. LEA2s were found to be highly enriched in non-polar, aliphatic amino acid residues, with leucine being the highest, 9...
June 22, 2018: G3: Genes—Genomes—Genetics
Ben Ewen-Campen, Norbert Perrimon
Screening for successful CRISPR/Cas9 editing events remains a time consuming technical bottleneck in the field of Drosophila genome editing. This step can be particularly laborious for events that do not cause a visible phenotype, or those which occur at relatively low frequency. A promising strategy to enrich for desired CRISPR events is to co-select for an independent CRISPR event that produces an easily detectable phenotype. Here, we describe a simple negative co-selection strategy involving CRISPR-editing of a dominant female sterile allele, ovoD1 In this system (" ovoD co-selection"), the only functional germ cells in injected females are those that have been edited at the ovoD1 locus, and thus all offspring of these flies have undergone editing of at least one locus...
June 22, 2018: G3: Genes—Genomes—Genetics
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