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    1781 results match your criteria BMC Genetics [Journal]

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    Association between ß2-adrenergic receptor gene polymorphisms and adverse events of ritodrine in the treatment of preterm labor: a prospective observational study.
    BMC Genet 2017 Nov 13;18(1):96. Epub 2017 Nov 13.
    College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea.
    Background: Ritodrine, a tocolytic β2-agonist, has been used extensively in Europe and Asia despite its safety concerns. This study was designed to identify associations between β2-adrenergic receptor (ADRB2) polymorphisms and adverse drug events (ADEs) in patients with preterm labor treated with ritodrine.

    Results: This follow-up study was prospectively conducted at Ewha Womans University Mokdong Hospital in Korea. Read More

    Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.).
    BMC Genet 2017 Nov 9;18(1):95. Epub 2017 Nov 9.
    State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, 410081, China.
    Background: Crucian carp is a popular ornamental strain in Asia with variants in body color. To further explore the genetic mechanisms underlying gray and red body color formation in crucian carp, the skin transcriptomes and partial DNA methylation sites were obtained from red crucian carp (RCC) and white crucian carp (WCC). Here, we show significant differences in mRNA expression and DNA methylation sites between skin tissues of RCC and WCC. Read More

    Detection of QTLs for seedling characteristics in barley (Hordeum vulgare L.) grown under hydroponic culture condition.
    BMC Genet 2017 Nov 7;18(1):94. Epub 2017 Nov 7.
    College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
    Background: Seedling characteristics play significant roles in the growth and development of barley (Hordeum vulgare L.), including stable stand establishment, water and nutrients uptake, biotic resistance and abiotic stresses, and can influence yield and quality. However, the genetic mechanisms underlying seedling characteristics in barley are largely unknown and little research has been done. Read More

    Network analysis for count data with excess zeros.
    BMC Genet 2017 Nov 6;18(1):93. Epub 2017 Nov 6.
    Department of Statistics, University of Seoul, Seoul, 02504, Korea.
    Background: Undirected graphical models or Markov random fields have been a popular class of models for representing conditional dependence relationships between nodes. In particular, Markov networks help us to understand complex interactions between genes in biological processes of a cell. Local Poisson models seem to be promising in modeling positive as well as negative dependencies for count data. Read More

    Genetic variability in Italian populations of Drosophila suzukii.
    BMC Genet 2017 Nov 3;18(1):87. Epub 2017 Nov 3.
    Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
    Background: Drosophila suzukii is a highly destructive pest species, causing substantial economic losses in soft fruit production. To better understand migration patterns, gene flow and adaptation in invaded regions, we studied the genetic structure of D. suzukii collected across Italy, where it was first observed in 2008. Read More

    Whole genome population genetics analysis of Sudanese goats identifies regions harboring genes associated with major traits.
    BMC Genet 2017 Oct 23;18(1):92. Epub 2017 Oct 23.
    Albrecht Daniel Thaer-Institut für Agrar- und Gartenbauwissenschaften, Humboldt-Universität zu Berlin, Invalidenstraße 42, D-10115, Berlin, Germany.
    Background: Sudan is endowed with a variety of indigenous goat breeds which are used for meat and milk production and which are well adapted to the local environment. The aim of the present study was to determine the genetic diversity and relationship within and between the four main Sudanese breeds of Nubian, Desert, Taggar and Nilotic goats. Using the 50 K SNP chip, 24 animals of each breed were genotyped. Read More

    Generalized disequilibrium test for association in qualitative traits incorporating imprinting effects based on extended pedigrees.
    BMC Genet 2017 Oct 16;18(1):90. Epub 2017 Oct 16.
    State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China.
    Background: For dichotomous traits, the generalized disequilibrium test with the moment estimate of the variance (GDT-ME) is a powerful family-based association method. Genomic imprinting is an important epigenetic phenomenon and currently, there has been increasing interest of incorporating imprinting to improve the test power of association analysis. However, GDT-ME does not take imprinting effects into account, and it has not been investigated whether it can be used for association analysis when the effects indeed exist. Read More

    Genetic evidence of multiple invasions and a small number of founders of Asian Palmyra palm (Borassus flabellifer) in Thailand.
    BMC Genet 2017 Oct 12;18(1):88. Epub 2017 Oct 12.
    Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.
    Background: Borassus flabellifer or Asian Palmyra palm is an important crop for local economies in the South and Southeast Asia for its fruit and palm sugar production. Archeological and historical evidence indicated the presence of this species in Southeast Asia dating back at least 1500 years. B. Read More

    Identification of putative markers linked to grain plumpness in rice (Oryza sativa L.) via association mapping.
    BMC Genet 2017 Oct 12;18(1):89. Epub 2017 Oct 12.
    State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
    Background: Poor grain plumpness (GP) is one of the main constraints to reaching the yield potential of hybrid rice.

    Results: In this study, the GP of 177 rice varieties was investigated in three locations across 2 years. By combining the genotype data of 261 simple sequence repeat (SSR) markers, association mapping was conducted to identify the marker-GP association loci. Read More

    Fine mapping of a QTL affecting levels of skatole on pig chromosome 7.
    BMC Genet 2017 Oct 11;18(1):85. Epub 2017 Oct 11.
    Topigs Norsvin, Storhamargata 44, 2317, Hamar, Norway.
    Background: Previous studies in the Norwegian pig breeds Landrace and Duroc have revealed a QTL for levels of skatole located in the region 74.7-80.5 Mb on SSC7. Read More

    Hox genes reveal genomic DNA variation in tetraploid hybrids derived from Carassius auratus red var. (female) × Megalobrama amblycephala (male).
    BMC Genet 2017 Oct 11;18(1):86. Epub 2017 Oct 11.
    State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
    Background: Allotetraploid F1 hybrids (4nF1) (AABB, 4n = 148) were generated from the distant hybridization of Carassius auratus red var. (RCC) (AA, 2n = 100) (♀) × Megalobrama amblycephala (BSB) (BB, 2n = 48) (♂). It has been reported that Hox gene clusters are highly conserved among plants and vertebrates. Read More

    Quantitative trait loci associated with different polar metabolites in perennial ryegrass - providing scope for breeding towards increasing certain polar metabolites.
    BMC Genet 2017 Oct 10;18(1):84. Epub 2017 Oct 10.
    Teagasc, Crops Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland.
    Background: Recent advances in the mapping of biochemical traits have been reported in Lolium perenne. Although the mapped traits, including individual sugars and fatty acids, contribute greatly towards ruminant productivity, organic acids and amino acids have been largely understudied despite their influence on the ruminal microbiome.

    Results: In this study, we used a targeted gas-chromatography mass spectrometry (GC-MS) approach to profile the levels of 25 polar metabolites from different classes (sugars, amino acids, phenolic acids, organic acids and other nitrogen-containing compounds) present in a L. Read More

    LAIT: a local ancestry inference toolkit.
    BMC Genet 2017 Sep 6;18(1):83. Epub 2017 Sep 6.
    Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
    Background: Inferring local ancestry in individuals of mixed ancestry has many applications, most notably in identifying disease-susceptible loci that vary among different ethnic groups. Many software packages are available for inferring local ancestry in admixed individuals. However, most of these existing software packages require specific formatted input files and generate output files in various types, yielding practical inconvenience. Read More

    Refining the South Asian Origin of the Romani people.
    BMC Genet 2017 Aug 31;18(1):82. Epub 2017 Aug 31.
    University of Pecs, Szentagothai Research Centre, Ifjusag Road 20, Pecs, H-7624, Hungary.
    Background:  Recent genetic studies based on genome-wide Single Nucleotide Polymorphism (SNP) data further investigated the history of Roma and suggested that the source of South Asian ancestry in Roma originates most likely from the Northwest region of India.

    Methods: In this study, based also on genome-wide SNP data, we attempted to refine these findings using significantly larger number of European Roma samples, an extended dataset of Indian groups and involving Pakistani groups into the analyses. Our Roma data contained 179 Roma samples. Read More

    The satellite DNA AflaSAT-1 in the A and B chromosomes of the grasshopper Abracris flavolineata.
    BMC Genet 2017 Aug 29;18(1):81. Epub 2017 Aug 29.
    Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo, CEP 13506-900, Brazil.
    Background: Satellite DNAs (satDNAs) are organized in repetitions directly contiguous to one another, forming long arrays and composing a large portion of eukaryote genomes. These sequences evolve according to the concerted evolution model, and homogenization of repeats is observed at the intragenomic level. Satellite DNAs are the primary component of heterochromatin, located primarily in centromeres and telomeres. Read More

    Identifying highly informative genetic markers for quantification of ancestry proportions in crossbred sheep populations: implications for choosing optimum levels of admixture.
    BMC Genet 2017 Aug 24;18(1):80. Epub 2017 Aug 24.
    Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor Mendel Straße 33, A-1180, Vienna, Austria.

    A major QTL on chromosome 7HS controls the response of barley seedling to salt stress in the Nure × Tremois population.
    BMC Genet 2017 Aug 22;18(1):79. Epub 2017 Aug 22.
    CREA, Research Centre for Genomics and Bioinformatics, 29017, Fiorenzuola d'Arda, Italy.
    Background: Seedling establishment is a crucial and vulnerable stage in the crop life cycle which determines further plant growth. While many studies are available on salt tolerance at the vegetative stage, the mechanisms and genetic bases of salt tolerance during seedling establishment have been poorly investigated. Here, a novel and accurate phenotyping protocol was applied to characterize the response of seedlings to salt stress in two barley cultivars (Nure and Tremois) and their double-haploid population. Read More

    Prenatal caloric restriction alters lipid metabolism but not hepatic Fasn gene expression and methylation profiles in rats.
    BMC Genet 2017 Aug 15;18(1):78. Epub 2017 Aug 15.
    Department of Human Nutrition and Hygiene, Poznań University of Life Sciences, Wojska Polskiego 31, 60-624, Poznan, Poland.
    Background: Undernutrition is an increasingly common problem. Insufficient calorie intake and nutrient deficiencies during pregnancy may have an impact not only on the mother, but may also alter metabolism in the infant. In this study, we have applied a calorie-restricted diet during gestation and examined its effect on hepatic Fasn mRNA and DNA methylation profiles in rats and their female progeny. Read More

    Investigating knockdown resistance (kdr) mechanism against pyrethroids/DDT in the malaria vector Anopheles funestus across Africa.
    BMC Genet 2017 Aug 9;18(1):76. Epub 2017 Aug 9.
    Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
    Background: Understanding the molecular basis of insecticide resistance is key to improve the surveillance and monitoring of malaria vector populations under control. In the major malaria vector Anopheles funestus, little is currently known about the role of the knockdown resistance (kdr) mechanism. Here, we investigated the presence and contribution of knockdown resistance (kdr) to pyrethroids/DDT resistance observed in Anopheles funestus across Africa. Read More

    Mapping of leptin and its syntenic genes to chicken chromosome 1p.
    BMC Genet 2017 Aug 9;18(1):77. Epub 2017 Aug 9.
    Department of Animal Science, Agricultural Research Organization, Volcani Center, P.O. Box 15159, 7528809, Rishon LeTsiyon, Israel.
    Background: Misidentification of the chicken leptin gene has hampered research of leptin signaling in this species for almost two decades. Recently, the genuine leptin gene with a GC-rich (~70%) repetitive-sequence content was identified in the chicken genome but without indicating its genomic position. This suggests that such GC-rich sequences are difficult to sequence and therefore substantial regions are missing from the current chicken genome assembly. Read More

    Variations in 5S rDNAs in diploid and tetraploid offspring of red crucian carp × common carp.
    BMC Genet 2017 Aug 8;18(1):75. Epub 2017 Aug 8.
    State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
    Background: The allotetraploid hybrid fish (4nAT) that was created in a previous study through an intergeneric cross between red crucian carp (Carassius auratus red var., ♀) and common carp (Cyprinus carpio L., ♂) provided an excellent platform to investigate the effect of hybridization and polyploidization on the evolution of 5S rDNA. Read More

    A de novo missense mutation of FGFR2 causes facial dysplasia syndrome in Holstein cattle.
    BMC Genet 2017 Aug 2;18(1):74. Epub 2017 Aug 2.
    Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
    Background: Surveillance for bovine genetic diseases in Denmark identified a hitherto unreported congenital syndrome occurring among progeny of a Holstein sire used for artificial breeding. A genetic aetiology due to a dominant inheritance with incomplete penetrance or a mosaic germline mutation was suspected as all recorded cases were progeny of the same sire. Detailed investigations were performed to characterize the syndrome and to reveal its cause. Read More

    Genetic structure and relationships within and between cultivated and wild korarima [Aframomum corrorima (Braun) P.C.M. Jansen] in Ethiopia as revealed by simple sequence repeat (SSR) markers.
    BMC Genet 2017 Aug 1;18(1):72. Epub 2017 Aug 1.
    Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, -23053, Alnarp, SE, Sweden.
    Background: Korarima [Aframomum corrorima (Braun) P.C.M. Read More

    Resampling-based tests for Lasso in genome-wide association studies.
    BMC Genet 2017 Jul 24;18(1):70. Epub 2017 Jul 24.
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, 55455, USA.
    Background: Genome-wide association studies involve detecting association between millions of genetic variants and a trait, which typically use univariate regression to test association between each single variant and the phenotype. Alternatively, Lasso penalized regression allows one to jointly model the relationship between all genetic variants and the phenotype. However, it is unclear how to best conduct inference on the individual Lasso coefficients, especially in high-dimensional settings. Read More

    Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion.
    BMC Genet 2017 Jul 21;18(1):69. Epub 2017 Jul 21.
    Wildlife Research Center, Kyoto University, 2-24 Tanaka-Sekiden-cho, Sakyo, Kyoto, 606-8203, Japan.
    Background: Neuregulin 3 (NRG3) plays a key role in central nervous system development and is a strong candidate for human mental disorders. Thus, genetic variation in NRG3 may have some impact on a variety of phenotypes in non-mammalian vertebrates. Recently, genome-wide screening for short insertions and deletions in chicken (Gallus gallus) genomes has provided useful information about structural variation in functionally important genes. Read More

    Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps.
    BMC Genet 2017 Jul 21;18(1):68. Epub 2017 Jul 21.
    Department of Mathematics and Statistics, University of Otago, Dunedin, 9058, New Zealand.
    Background: Investments in genetic selection have played a major role in the New Zealand sheep industry competitiveness. Selection may erode genetic diversity, which is a crucial factor for the success of breeding programs. Better understanding of linkage disequilibrium (LD) and ancestral effective population size (Ne) through quantifying this diversity and comparison between populations allows for more informed decisions with regards to selective breeding taking population genetic diversity into account. Read More

    Dynamics in multiplicity of Plasmodium falciparum infection among children with asymptomatic malaria in central Ghana.
    BMC Genet 2017 Jul 17;18(1):67. Epub 2017 Jul 17.
    Ghana Health Service. Health Research Unit, Kintampo Health Research Centre. MOH/GHS, P.O.Box 200, College of Health Street, Kintampo, Brong Ahafo, Ghana.
    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. Read More

    Karyotype differentiation in tellin shells (Bivalvia: Tellinidae).
    BMC Genet 2017 Jul 14;18(1):66. Epub 2017 Jul 14.
    Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310, Vigo, Spain.
    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. Read More

    De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development.
    BMC Genet 2017 Jul 11;18(1):65. Epub 2017 Jul 11.
    The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
    Background: Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. Read More

    Genome-wide association study identifies candidate genes for piglet splay leg syndrome in different populations.
    BMC Genet 2017 Jul 5;18(1):64. Epub 2017 Jul 5.
    Key Lab of Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
    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. Read More

    Gene expression variations in high-altitude adaptation: a case study of the Asiatic toad (Bufo gargarizans).
    BMC Genet 2017 Jul 3;18(1):62. Epub 2017 Jul 3.
    Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
    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. Read More

    Genetic effects of PDGFRB and MARCH1 identified in GWAS revealing strong associations with semen production traits in Chinese Holstein bulls.
    BMC Genet 2017 Jul 3;18(1):63. Epub 2017 Jul 3.
    Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
    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. Read More

    Genomic variability in Mexican chicken population using copy number variants.
    BMC Genet 2017 Jul 3;18(1):61. Epub 2017 Jul 3.
    Department of Veterinary Medicine, Universitá degli Studi di Milano, Via Celoria 10, 20133, Milan, Italy.
    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). Read More

    Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database.
    BMC Genet 2017 Jun 26;18(1):60. Epub 2017 Jun 26.
    Nguyen Tat Thanh University, 300A Nguyen Tat Thanh street, District 4, Ho Chi Minh city, Vietnam.
    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. Read More

    Cattle phenotypes can disguise their maternal ancestry.
    BMC Genet 2017 Jun 26;18(1):59. Epub 2017 Jun 26.
    Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.
    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. Read More

    Circadian CLOCK gene polymorphisms in relation to sleep patterns and obesity in African Americans: findings from the Jackson heart study.
    BMC Genet 2017 Jun 23;18(1):58. Epub 2017 Jun 23.
    National Human Genome Research Institute Genomics of Metabolic, Cardiovascular and Inflammatory Disease Branch Social Epidemiology Research Unit, National Institutes of Health, 10 Center Drive, Bethesda, MD, 20892, USA.
    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). Read More

    Effects of selection for fast growth on survival rate during grow-out phase in giant freshwater prawn (Macrobrachium rosenbergii).
    BMC Genet 2017 Jun 21;18(1):56. Epub 2017 Jun 21.
    Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD, 4558, Australia.
    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. Read More

    The relation between DNA methylation patterns and serum cytokine levels in community-dwelling adults: a preliminary study.
    BMC Genet 2017 Jun 21;18(1):57. Epub 2017 Jun 21.
    Department of Pathology and Molecular Medicine, McMaster University, 1280 Main St. W, MIP309A, Hamilton, ON, Canada.
    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. Read More

    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.
    BMC Genet 2017 Jun 12;18(1):55. Epub 2017 Jun 12.
    IUF-Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany.
    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. Read More

    Genome-wide identification and characterization of SnRK2 gene family in cotton (Gossypium hirsutum L.).
    BMC Genet 2017 Jun 12;18(1):54. Epub 2017 Jun 12.
    State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
    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.). Read More

    In vivo screening reveals interactions between Drosophila Manf and genes involved in the mitochondria and the ubiquinone synthesis pathway.
    BMC Genet 2017 Jun 2;18(1):52. Epub 2017 Jun 2.
    Department of Biosciences, University of Helsinki, FI-00014, Helsinki, Finland.
    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. Read More

    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.
    BMC Genet 2017 Jun 2;18(1):53. Epub 2017 Jun 2.
    CIRAD, UMR PVBMT, 7 chemin de l'Irat, Ligne Paradis, 97410, Saint Pierre, La Réunion, France.
    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. Read More

    Genomic prediction in early selection stages using multi-year data in a hybrid rye breeding program.
    BMC Genet 2017 May 31;18(1):51. Epub 2017 May 31.
    Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Fruwirthstrasse 23, Stuttgart, 70599, Germany.
    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. Read More

    Development of a SNP panel dedicated to parentage assignment in French sheep populations.
    BMC Genet 2017 May 26;18(1):50. Epub 2017 May 26.
    Institut de l'Elevage, DGEP, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France.
    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. Read More

    Determination of genetic effects of ATF3 and CDKN1A genes on milk yield and compositions in Chinese Holstein population.
    BMC Genet 2017 May 19;18(1):47. Epub 2017 May 19.
    Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China.
    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. Read More

    Genetic correlation of the plasma lipidome with type 2 diabetes, prediabetes and insulin resistance in Mexican American families.
    BMC Genet 2017 May 19;18(1):48. Epub 2017 May 19.
    South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA.
    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. Read More

    The distribution of mitochondrial DNA haplogroup H in southern Iberia indicates ancient human genetic exchanges along the western edge of the Mediterranean.
    BMC Genet 2017 May 19;18(1):46. Epub 2017 May 19.
    Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain.
    Background: The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring. Read More

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