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BMC Genetics

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https://www.readbyqxmd.com/read/28716086/dynamics-in-multiplicity-of-plasmodium-falciparum-infection-among-children-with-asymptomatic-malaria-in-central-ghana
#1
Akua Kyerewaa Botwe, Kwaku Poku Asante, George Adjei, Samuel Assafuah, David Dosoo, Seth Owusu-Agyei
BACKGROUND: The determinants of malaria parasite virulence is not entirely known, but the outcome of malaria infection (asymptomatic or symptomatic) has been associated with carriage of distinct parasite genotypes. Alleles considered important for erythrocyte invasion and selected as candidate targets for malaria vaccine development are increasingly being shown to have distinct characteristics in infection outcomes. Any unique/distinct patterns or alleles linked to infection outcome should be reproducible for a given malaria-cohort regardless of location, time or intervention...
July 17, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28709395/karyotype-differentiation-in-tellin-shells-bivalvia-tellinidae
#2
Daniel García-Souto, Gonzalo Ríos, Juan J Pasantes
BACKGROUND: Although Tellinidae is one of the largest and most diverse families of bivalves, its taxonomy is utterly chaotic. This is mainly due to the morphological diversity and homoplasy displayed by their shells and to the scarcity of the molecular phylogenetic studies performed on them. A molecular cytogenetic analysis of four tellin shell species, Bosemprella incarnata, Macomangulus tenuis, Moerella donacina and Serratina serrata, was performed. To molecularly characterize the analyzed specimens, the sequence of a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) was also studied...
July 14, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28693419/de-novo-transcriptomic-analysis-of-cowpea-vigna-unguiculata-l-walp-for-genic-ssr-marker-development
#3
Honglin Chen, Lixia Wang, Xiaoyan Liu, Liangliang Hu, Suhua Wang, Xuzhen Cheng
BACKGROUND: Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding of cowpea. The objectives of this study were to analyse the cowpea transcriptome and develop genic molecular markers for future genetic studies of this genus. RESULTS: Approximately 54 million high-quality cDNA sequence reads were obtained from cowpea based on Illumina paired-end sequencing technology and were de novo assembled to generate 47,899 unigenes with an N50 length of 1534 bp...
July 11, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28679362/genome-wide-association-study-identifies-candidate-genes-for-piglet-splay-leg-syndrome-in-different-populations
#4
Xingjie Hao, Graham Plastow, Chunyan Zhang, Sutong Xu, Zhiqiu Hu, Tianfu Yang, Kai Wang, Huawei Yang, Xiaoxue Yin, Shili Liu, Zhenghua Wang, Zhiquan Wang, Shujun Zhang
BACKGROUND: Piglet splay leg syndrome (PSL) is one of the most frequent genetic defects, and can cause considerable economic loss in pig production. The present understanding of etiology and pathogenesis of PSL is poor. The current study focused on identifying loci associated with PSL through a genome-wide association study (GWAS) performed with the Illumina Porcine60 SNP Beadchip v2.0. The study was a case/control design with four pig populations (Duroc, Landrace, Yorkshire and one crossbred of Landrace × Yorkshire)...
July 5, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28673260/gene-expression-variations-in-high-altitude-adaptation-a-case-study-of-the-asiatic-toad-bufo-gargarizans
#5
Weizhao Yang, Yin Qi, Bin Lu, Liang Qiao, Yayong Wu, Jinzhong Fu
BACKGROUND: Genome-wide investigation of molecular mechanisms for high-altitude adaptation has attracted great attention in the last few years. In order to understand the contribution of gene expression level variations to high-altitude adaptation in Asiatic toads (Bufo gargarizans), we implemented a reciprocal transplant experiment between low- and high-altitude sites and sequenced 12 transcriptomes from brain, heart, and liver tissues. RESULTS: A large number of genes with expression differences (DEGs) between high- and low-altitude individuals (193 fixed and 844 plastic) were identified, and the majority of them were tissue specific...
July 3, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28673243/genetic-effects-of-pdgfrb-and-march1-identified-in-gwas-revealing-strong-associations-with-semen-production-traits-in-chinese-holstein-bulls
#6
Shuli Liu, Hongwei Yin, Cong Li, Chunhua Qin, Wentao Cai, Mingyue Cao, Shengli Zhang
BACKGROUND: Using a genome-wide association study strategy, our previous study discovered 19 significant single-nucleotide polymorphisms (SNPs) related to semen production traits in Chinese Holstein bulls. Among them, three SNPs were within or close to the phosphodiesterase 3A (PDE3A), membrane associated ring-CH-type finger 1 (MARCH1) and platelet derived growth factor receptor beta (PDGFRB) genes. The present study was designed with the objectives of identifying genetic polymorphism of the PDE3A, PDGFRB and MARCH1 genes and their effects on semen production traits in a Holstein bull population...
July 3, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28673234/genomic-variability-in-mexican-chicken-population-using-copy-number-variants
#7
E Gorla, M C Cozzi, S I Román-Ponce, F J Ruiz López, V E Vega-Murillo, S Cerolini, A Bagnato, M G Strillacci
BACKGROUND: Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability in the Mexican Creole chicken population using CNVs. RESULTS: The Hidden Markov Model of the PennCNV software detected a total of 1924 CNVs in the genome of the 256 samples processed with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix)...
July 3, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28651548/canis-mtdna-hv1-database-a-web-based-tool-for-collecting-and-surveying-canis-mtdna-hv1-haplotype-in-public-database
#8
Quan Ke Thai, Dung Anh Chung, Hoang-Dung Tran
BACKGROUND: Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database...
June 26, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28651540/cattle-phenotypes-can-disguise-their-maternal-ancestry
#9
Kanokwan Srirattana, Kieren McCosker, Tim Schatz, Justin C St John
BACKGROUND: Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (VIC), southern Australia, which is a temperate climate, and the Northern Territory (NT), the northern part of Australia, which has a tropical climate, to determine if the mtDNA profiles of these cattle are indicative of breed and phenotype, and whether these profiles are appropriate for their environments...
June 26, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28645331/circadian-clock-gene-polymorphisms-in-relation-to-sleep-patterns-and-obesity-in-african-americans-findings-from-the-jackson-heart-study
#10
Pia Riestra, Samson Y Gebreab, Ruihua Xu, Rumana J Khan, Amadou Gaye, Adolfo Correa, Nancy Min, Mario Sims, Sharon K Davis
BACKGROUND: Circadian rhythms regulate key biological processes and the dysregulation of the intrinsic clock mechanism affects sleep patterns and obesity onset. The CLOCK (circadian locomotor output cycles protein kaput) gene encodes a core transcription factor of the molecular circadian clock influencing diverse metabolic pathways, including glucose and lipid homeostasis. The primary objective of this study was to evaluate the associations between CLOCK single nucleotide polymorphisms (SNPs) and body mass index (BMI)...
June 23, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28637429/effects-of-selection-for-fast-growth-on-survival-rate-during-grow-out-phase-in-giant-freshwater-prawn-macrobrachium-rosenbergii
#11
Nguyen Thanh Vu, Trinh Quoc Trong, Nguyen Hong Nguyen
BACKGROUND: Correlated genetic response in survival to selection for high growth has not been reported in giant freshwater prawn (GFP) (Macrobrachium rosenbergii). The main aim of this study was to measure genetic changes and estimate heritability for this character (survival rate) and its genetic associations with body traits in a GFP population selected over eight generations from 2008 to 2015. Statistical analyses were conducted on 106,696 data records, using threshold logistic mixed model...
June 21, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28637423/the-relation-between-dna-methylation-patterns-and-serum-cytokine-levels-in-community-dwelling-adults-a-preliminary-study
#12
Chris P Verschoor, Lisa M McEwen, Vikas Kohli, Christina Wolfson, Dawn Me Bowdish, Parminder Raina, Michael S Kobor, Cynthia Balion
BACKGROUND: The levels of circulating cytokines fluctuate with age, acute illness, and chronic disease, and are predictive of mortality; this is also true for patterns of DNA (CpG) methylation. Given that immune cells are particularly sensitive to changes in the concentration of cytokines in their microenvironment, we hypothesized that serum levels of TNF, IL-6, IL-8 and IL-10 would correlate with genome-wide alterations in the DNA methylation levels of blood leukocytes. To test this, we evaluated community-dwelling adults (n = 14; 48-78 years old) recruited to a pilot study for the Canadian Longitudinal Study on Aging (CLSA), examining DNA methylation patterns in peripheral blood mononuclear cells using the Illumina HumanMethylation 450 K BeadChip...
June 21, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28606108/detection-of-gene-environment-interactions-in-the-presence-of-linkage-disequilibrium-and-noise-by-using-genetic-risk-scores-with-internal-weights-from-elastic-net-regression
#13
Anke Hüls, Katja Ickstadt, Tamara Schikowski, Ursula Krämer
BACKGROUND: For the analysis of gene-environment (GxE) interactions commonly single nucleotide polymorphisms (SNPs) are used to characterize genetic susceptibility, an approach that mostly lacks power and has poor reproducibility. One promising approach to overcome this problem might be the use of weighted genetic risk scores (GRS), which are defined as weighted sums of risk alleles of gene variants. The gold-standard is to use external weights from published meta-analyses. METHODS: In this study, we used internal weights from the marginal genetic effects of the SNPs estimated by a multivariate elastic net regression and thereby provided a method that can be used if there are no external weights available...
June 12, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28606097/genome-wide-identification-and-characterization-of-snrk2-gene-family-in-cotton-gossypium-hirsutum-l
#14
Zhao Liu, Xiaoyang Ge, Zuoren Yang, Chaojun Zhang, Ge Zhao, Eryong Chen, Ji Liu, Xueyan Zhang, Fuguang Li
BACKGROUND: Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) is a plant-specific serine/threonine kinase family involved in the abscisic acid (ABA) signaling pathway and responds to osmotic stress. A genome-wide analysis of this protein family has been conducted previously in some plant species, but little is known about SnRK2 genes in upland cotton (Gossypium hirsutum L.). The recent release of the G. hirsutum genome sequence provides an opportunity to identify and characterize the SnRK2 kinase family in upland cotton...
June 12, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28578657/in-vivo-screening-reveals-interactions-between-drosophila-manf-and-genes-involved-in-the-mitochondria-and-the-ubiquinone-synthesis-pathway
#15
Riitta Lindström, Päivi Lindholm, Mari Palgi, Mart Saarma, Tapio I Heino
BACKGROUND: Mesencephalic Astrocyte-derived Neurotrophic Factor (MANF) and Cerebral Dopamine Neurotrophic Factor (CDNF) form an evolutionarily conserved family of neurotrophic factors. Orthologues for MANF/CDNF are the only neurotrophic factors as yet identified in invertebrates with conserved amino acid sequence. Previous studies indicate that mammalian MANF and CDNF support and protect brain dopaminergic system in non-cell-autonomous manner. However, MANF has also been shown to function intracellularly in the endoplasmic reticulum...
June 2, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28577537/large-scale-mitochondrial-dna-analysis-of-native-honey-bee-apis-mellifera-populations-reveals-a-new-african-subgroup-private-to-the-south-west-indian-ocean-islands
#16
Maéva Angélique Techer, Johanna Clémencet, Christophe Simiand, Sookar Preeaduth, Hamza Abdou Azali, Bernard Reynaud, Delatte Hélène
BACKGROUND: The South West Indian Ocean (SWIO) archipelagos and Madagascar constitute a hotspot of biodiversity with a high rate of endemism. In this area, the endemic subspecies A. m. unicolor has been described in Madagascar. It belongs to the African lineage, one of the four described evolutionary lineages in honey bees. Despite a long beekeeping tradition and several recorded European introductions, few studies have been carried out on the diversity and proportion of honey bee subspecies...
June 2, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28569139/genomic-prediction-in-early-selection-stages-using-multi-year-data-in-a-hybrid-rye-breeding-program
#17
Angela-Maria Bernal-Vasquez, Andres Gordillo, Malthe Schmidt, Hans-Peter Piepho
BACKGROUND: The use of multiple genetic backgrounds across years is appealing for genomic prediction (GP) because past years' data provide valuable information on marker effects. Nonetheless, single-year GP models are less complex and computationally less demanding than multi-year GP models. In devising a suitable analysis strategy for multi-year data, we may exploit the fact that even if there is no replication of genotypes across years, there is plenty of replication at the level of marker loci...
May 31, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28549462/development-of-a-snp-panel-dedicated-to-parentage-assignment-in-french-sheep-populations
#18
F Tortereau, C R Moreno, G Tosser-Klopp, B Servin, J Raoul
BACKGROUND: The efficiency of breeding programs partly relies on the accuracy of the estimated breeding values which decreases when pedigrees are incomplete. Two reproduction techniques are mainly used by sheep breeders to identify the sires of lambs: animal insemination and natural matings with a single ram per group of ewes. Both methods have major drawbacks, notably time-consuming tasks for breeders, and are thus used at varying levels in breeding programs. As a consequence, the percentage of known sires can be very low in some breeds and results in less accurate estimated breeding values...
May 26, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525989/determination-of-genetic-effects-of-atf3-and-cdkn1a-genes-on-milk-yield-and-compositions-in-chinese-holstein-population
#19
REVIEW
Bo Han, Weijun Liang, Lin Liu, Yanhua Li, Dongxiao Sun
BACKGROUND: Our previous RNA-sequencing study revealed that the ATF3 and CDKN1A genes were remarkably differentially expressed between the mammary glands of lactating Holstein cows with extremely high and low milk protein and fat percentage so that both of them were considered as candidates for milk composition. Herein, we further verified whether these genes have genetic effects on milk production traits in a Chinese Holstein cow population. RESULTS: By re-sequencing the entire coding and regulatory regions, we identified four SNPs in 5'promoter region, two in exons, seven in 3' un-translated region (UTR), and six in 3'flanking region of ATF3 gene, and one SNP in exon 5, two in 3'UTR, and two in 3'flanking region of CDKN1A gene...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525987/genetic-correlation-of-the-plasma-lipidome-with-type-2-diabetes-prediabetes-and-insulin-resistance-in-mexican-american-families
#20
Hemant Kulkarni, Manju Mamtani, Gerard Wong, Jacquelyn M Weir, Christopher K Barlow, Thomas D Dyer, Laura Almasy, Michael C Mahaney, Anthony G Comuzzie, Ravindranath Duggirala, Peter J Meikle, John Blangero, Joanne E Curran
BACKGROUND: Differential plasma concentrations of circulating lipid species are associated with pathogenesis of type 2 diabetes (T2D). Whether the wide inter-individual variability in the plasma lipidome contributes to the genetic basis of T2D is unknown. Here, we investigated the potential overlap in the genetic basis of the plasma lipidome and T2D-related traits. RESULTS: We used plasma lipidomic data (1202 pedigreed individuals, 319 lipid species representing 23 lipid classes) from San Antonio Family Heart Study in Mexican Americans...
May 19, 2017: BMC Genetics
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