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Genetic variation

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https://www.readbyqxmd.com/read/28822173/-breakthrough-in-key-science-and-technologies-in-dendrobium-catenatum-industry
#1
Ji-Ping Si, Qi Wang, Zhong-Jian Liu, Jing-Jing Liu, Yi-Bo Luo
In view of the significant difficulties of propagation, planting and simple product in Dendrobium catenatum(D. officinale)industry development, a series of research were carried out. Genome study showed that D. catenatum is a specie of diploid with 38 chromosomes and 28 910 protein-coding genes. It was identified that specific genes accumulated in different organs at the transcriptome level. We got an insight into the gene regulation mechanism of the loss of the endospermous seed, the wide ecological adaptability and the synthesis of polysaccharides, which provided a theoretical basis for genetic engineering breeding and development and utilization of active pharmaceutical ingredients...
June 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28822130/exploiting-natural-variation-to-discover-candidate-genes-involved-in-photosynthesis-related-traits
#2
Franklin Magnum de Oliveira Silva, Lucas de Ávila Silva, Wagner L Araújo, Agustin Zsögön, Adriano Nunes-Nesi
Naturally occurring genetic variation in plants can be very useful to dissect the complex regulation of primary metabolism as well as of physiological traits such as photosynthesis and photorespiration. The physiological and genetic mechanisms underlying natural variation in closely related species or accessions may provide important information that can be used to improve crop yield. In this chapter we describe in detail the use of a population of introgression lines (ILs), with the Solanum pennellii IL population as a study case, as a tool for the identification of genomic regions involved in the control of photosynthetic efficiency...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28822116/interactions-between-variation-in-candidate-genes-and-environmental-factors-in-the-etiology-of-schizophrenia-and-bipolar-disorder-a-systematic-review
#3
REVIEW
Błażej Misiak, Filip Stramecki, Łukasz Gawęda, Katarzyna Prochwicz, Maria M Sąsiadek, Ahmed A Moustafa, Dorota Frydecka
Schizophrenia and bipolar disorder (BD) are complex and multidimensional disorders with high heritability rates. The contribution of genetic factors to the etiology of these disorders is increasingly being recognized as the action of multiple risk variants with small effect sizes, which might explain only a minor part of susceptibility. On the other site, numerous environmental factors have been found to play an important role in their causality. Therefore, in recent years, several studies focused on gene × environment interactions that are believed to bridge the gap between genetic underpinnings and environmental insults...
August 18, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28821934/whole-exome-sequencing-to-identify-the-cause-of-congenital-sensorineural-hearing-loss-in-carriers-of-a-heterozygous-gjb2-mutation
#4
Thomas Parzefall, Alexandra Frohne, Martin Koenighofer, Andreas Kirchnawy, Berthold Streubel, Christian Schoefer, Klemens Frei, Trevor Lucas
Bi-allelic variations in the gap junction protein beta-2 (GJB2) gene cause up to 50% of cases of newborn hearing loss. Heterozygous pathogenic GJB2 variations are also fivefold overrepresented in idiopathic patient groups compared to the normal-hearing population. Whether hearing loss in this group is due to unidentified additional variations within GJB2 or variations in other deafness genes is unknown in most cases. Whole-exome sequencing offers an effective approach in the search for causative variations in patients with Mendelian diseases...
August 18, 2017: European Archives of Oto-rhino-laryngology
https://www.readbyqxmd.com/read/28821914/breeding-progress-genotypic-and-environmental-variation-and-correlation-of-quality-traits-in-malting-barley-in-german-official-variety-trials-between-1983-and-2015
#5
Friedrich Laidig, Hans-Peter Piepho, Dirk Rentel, Thomas Drobek, Uwe Meyer
Evaluation of breeding progress for spring barley varieties in Germany showed that both grain yield and malting quality were considerably improved during the last 33 years, and that genetic effects of protein concentration and malting traits were not associated. Based on historical data, this study aimed to investigate yield potential and malting quality of 187 varieties tested and released in German registration trials to evaluate the value for cultivation and use (VCU) during 1983-2015, and to quantify the environmental variability and the association among traits...
August 18, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28821787/analysis-of-spatial-genetic-variation-reveals-genetic-divergence-among-populations-of-primula-veris-associated-to-contrasting-habitats
#6
Pablo Deschepper, Rein Brys, Miguel A Fortuna, Hans Jacquemyn
Genetic divergence by environment is a process whereby selection causes the formation of gene flow barriers between populations adapting to contrasting environments and is often considered to be the onset of speciation. Nevertheless, the extent to which genetic differentiation by environment on small spatial scales can be detected by means of neutral markers is still subject to debate. Previous research on the perennial herb Primula veris has shown that plants from grassland and forest habitats showed pronounced differences in phenology and flower morphology, suggesting limited gene flow between habitats...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821769/patterns-of-transcriptional-parallelism-and-variation-in-the-developing-olfactory-system-of-drosophila-species
#7
Jia Wern Pan, Qingyun Li, Scott Barish, Sumie Okuwa, Songhui Zhao, Charles Soeder, Matthew Kanke, Corbin D Jones, Pelin Cayirlioglu Volkan
Organisms have evolved strikingly parallel phenotypes in response to similar selection pressures suggesting that there may be shared constraints limiting the possible evolutionary trajectories. For example, the behavioral adaptation of specialist Drosophila species to specific host plants can exhibit parallel changes in their adult olfactory neuroanatomy. We investigated the genetic basis of these parallel changes by comparing gene expression during the development of the olfactory system of two specialist Drosophila species to that of four other generalist species...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821546/a-supervised-statistical-learning-approach-for-accurate-legionella-pneumophila-source-attribution-during-outbreaks
#8
Andrew H Buultjens, Kyra Y L Chua, Sarah L Baines, Jason Kwong, Wei Gao, Zoe Cutcher, Stuart Adcock, Susan Ballard, Mark B Schultz, Takehiro Tomita, Nela Subasinghe, Glen P Carter, Sacha J Pidot, Lucinda Franklin, Torsten Seemann, Anders Gonçalves Da Silva, Benjamin P Howden, Timothy P Stinear
Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium (Legionella pneumophila) has an unusual population structure with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused by multiple L. pneumophila genotypes in a single source. These factors can confound cluster identification using standard phylogenomic methods. Here, we show that a statistical learning approach based onL...
August 18, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28821186/molecular-population-genetics-of-the-northern-elephant-seal-mirounga-angustirostris
#9
Alicia Abadía-Cardoso, Nelson B Freimer, Kristy Deiner, John Carlos Garza
The northern elephant seal, Mirounga angustirostris, was heavily hunted and declared extinct in the 19th century. However, a colony remained on remote Guadalupe Island, Mexico and the species has since repopulated most of its historical distribution. Here, we present a comprehensive evaluation of genetic variation in the species. First, we assess the effect of the demographic bottleneck on microsatellite variability and compare it with that found in other pinnipeds, demonstrating levels of variation similar to that in species that continue to be threatened with extinction...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28821185/phylogeography-and-ecological-niche-modeling-of-the-desert-iguana-dipsosaurus-dorsalis-baird-girard-1852-in-the-baja-california-peninsula
#10
Tania Valdivia-Carrillo, Francisco J García-De León, Ma Carmen Blázquez, Carina Gutiérrez-Flores, Patricia González Zamorano
Understanding the factors that explain the patterns of genetic structure or phylogeographic breaks at an intraspecific level is key to inferring the mechanisms of population differentiation in its early stages. These topics have been well studied in the Baja California region, with vicariance and the dispersal ability of individuals being the prevailing hypothesis for phylogeographic breaks. In this study, we evaluated the phylogeographic patterns in the desert iguana (Dipsosaurus dorsalis), a species with a recent history in the region and spatial variation in life history traits...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28821183/improvement-of-the-threespine-stickleback-genome-using-a-hi-c-based-proximity-guided-assembly
#11
Catherine L Peichel, Shawn T Sullivan, Ivan Liachko, Michael A White
Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28821014/efficient-and-accurate-causal-inference-with-hidden-confounders-from-genome-transcriptome-variation-data
#12
Lingfei Wang, Tom Michoel
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for higly accurate causal inference between gene expression traits using cis-regulatory DNA variations as causal anchors, which improves current methods by taking into consideration hidden confounders and weak regulations. Findr outperformed existing methods on the DREAM5 Systems Genetics challenge and on the prediction of microRNA and transcription factor targets in human lymphoblastoid cells, while being nearly a million times faster...
August 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28820946/proteogenomic-investigation-of-strain-variation-in-clinical-mycobacterium-tuberculosis-isolates
#13
Tiaan Heunis, Anzaan Dippenaar, Robin M Warren, Paul D van Helden, Ruben G van der Merwe, Nicolaas C Gey van Pittius, Arnab Pain, Samantha L Sampson, David L Tabb
Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M...
August 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28820491/mapping-of-qtls-for-seed-phorbol-esters-a-toxic-chemical-in-jatropha-curcas-l
#14
Kitiya Amkul, Kularb Laosatit, Prakit Somta, Sangrea Shim, Suk-Ha Lee, Patcharin Tanya, Peerasak Srinives
Jatropha (Jatropha curcas L.) is an oil-bearing plant that has potential to be cultivated as a biodiesel crop. The seed cake after oil extraction has 40-50% protein that can be used in animal feeds. A major limitation in utilizing the cake is the presence of phorbol esters (PE), a heat-tolerant toxic chemical. To identify the quantitative trait loci (QTLs) for PE, we constructed a genetic linkage map from an F₂ population of 95 individuals from a cross "Chai Nat" × "M10" using 143 simple sequence repeat (SSR) markers...
August 18, 2017: Genes
https://www.readbyqxmd.com/read/28820331/polo-like-kinase-1-plk1-dependent-phosphorylation-of-methylenetetrahydrofolate-reductase-mthfr-regulates-replication-via-histone-methylation
#15
Xueyan Li, Shanshan Nai, Yuehe Ding, Qizhi Geng, Bingtao Zhu, Kai Yu, Wei-Guo Zhu, Meng-Qiu Dong, Xiao-Dong Su, Xingzhi Xu, Jing Li
Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme regulating the folate cycle and its genetic variations have been associated with various human diseases. Previously we identified that MTHFR is phosphorylated by cyclin-dependent kinase 1 (CDK1) at T34 and MTHFR underlies heterochromatin maintenance marked by H3K9me3 levels. Herein we demonstrate that pT34 creates a binding motif that docks MTHFR to the polo-binding domain (PBD) of polo-like kinase 1 (PLK1), a fundamental kinase that orchestrates many cell cycle events...
August 18, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28819774/whole-exome-sequencing-of-wild-derived-inbred-strains-of-mice-improves-power-to-link-phenotype-and-genotype
#16
Peter L Chang, Emily Kopania, Sara Keeble, Brice A J Sarver, Erica Larson, Annie Orth, Khalid Belkhir, Pierre Boursot, François Bonhomme, Jeffrey M Good, Matthew D Dean
The house mouse is a powerful model to dissect the genetic basis of phenotypic variation, and serves as a model to study human diseases. Despite a wealth of discoveries, most classical laboratory strains have captured only a small fraction of genetic variation known to segregate in their wild progenitors, and existing strains are often related to each other in complex ways. Inbred strains of mice independently derived from natural populations have the potential to increase power in genetic studies with the addition of novel genetic variation...
August 17, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28819563/novel-clcn7-compound-heterozygous-mutations-in-intermediate-autosomal-recessive-osteopetrosis
#17
Nana Okamoto, Tomohiro Kohmoto, Takuya Naruto, Kiyoshi Masuda, Takahide Komori, Issei Imoto
Osteopetrosis is a heritable disorder of the skeleton that is characterized by increased bone density on radiographs caused by defects in osteoclast formation and function. Mutations in >10 genes are identified as causative for this clinically and genetically heterogeneous disease in humans. We report two novel missense variations in a compound heterozygous state in the CLCN7 gene, detected through targeted exome sequencing, in a 15-year-old Japanese female with intermediate autosomal recessive osteopetrosis...
2017: Human Genome Variation
https://www.readbyqxmd.com/read/28819256/fbn30-in-wild%C3%A2-anopheles-gambiae-functions-as-a-pathogen-recognition-molecule-against-clinically-circulating-plasmodium-falciparum-in-malaria-endemic-areas-in-kenya
#18
Guodong Niu, Genwei Zhang, Caio Franca, Yingjun Cui, Stephen Munga, Yaw Afrane, Jun Li
Malaria is a worldwide health problem that affects two-thirds of the world population. Plasmodium invasion of anopheline mosquitoes is an obligatory step for malaria transmission. However, mosquito-malaria molecular interactions in nature are not clear. A genetic variation within mosquito fibrinogen related-protein 30 (FBN30) was previously identified to be associated with Plasmodium falciparum infection in natural Anopheles gambiae populations at malaria endemic areas in Kenya, and reducing FBN30 expression by RNAi makes mosquitoes more susceptible to P...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819253/majority-of-human-traits-do-not-show-evidence-for-sex-specific-genetic-and-environmental-effects
#19
Sven Stringer, Tinca Polderman, Danielle Posthuma
Sex differences in the etiology of human trait variation are a major topic of interest in the social and medical sciences given its far-reaching implications. For example, in genetic research, the presence of sex-specific effects would require sex-stratified analysis, and in clinical practice sex-specific treatments would be warranted. Here, we present a study of 2,335,920 twin pairs, in which we tested sex differences in genetic and environmental contributions to variation in 2,608 reported human traits, clustered in 50 trait categories...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819228/convergent-and-divergent-genetic-changes-in-the-genome-of-chinese-and-european-pigs
#20
Jing Wang, Huiying Zou, Lei Chen, Xi Long, Jing Lan, Wenjie Liu, Li Ma, Chao Wang, Xinyu Xu, Liming Ren, Zhenglong Gu, Ning Li, Xiaoxiang Hu, Yaofeng Zhao, Yiqiang Zhao
Since 10,000 BC, continuous human selection has led to intense genetic and phenotypic changes in pig (Sus scrofa) domestication. Through whole genome analysis of 257 individuals, we demonstrated artificial unidirectional and bidirectional selection as the primary force to shape the convergent and divergent changes between Chinese domestic pigs (CHD) and European domestic pigs (EUD). We identified 31 genes in unidirectional selection regions that might be related to fundamental domestication requirements in pigs...
August 17, 2017: Scientific Reports
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