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    1768 results match your criteria BMC Genetics [Journal]

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    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

    Candidate gene based association mapping in Fusarium culmorum for field quantitative pathogenicity and mycotoxin production in wheat.
    BMC Genet 2017 May 19;18(1):49. Epub 2017 May 19.
    State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany.
    Background: Quantitative traits are common in nature, but quantitative pathogenicity has received only little attention in phytopathology. In this study, we used 100 Fusarium culmorum isolates collected from natural field environments to assess their variation for two quantitative traits, aggressiveness and deoxynivalenol (DON) production on wheat plants grown in four different field environments (location-year combinations). Seventeen Fusarium graminearum pathogenicity candidate genes were assessed for their effect on the aggressiveness and DON production of F. Read More

    Effects of marker density and population structure on the genomic prediction accuracy for growth trait in Pacific white shrimp Litopenaeus vannamei.
    BMC Genet 2017 May 17;18(1):45. Epub 2017 May 17.
    Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
    Background: Due to the great advantages in selection accuracy and efficiency, genomic selection (GS) has been widely studied in livestock, crop and aquatic animals. Our previous study based on one full-sib family of Litopenaeus vannamei (L. vannamei) showed that GS was feasible in penaeid shrimp. Read More

    Network-based regularization for high dimensional SNP data in the case-control study of Type 2 diabetes.
    BMC Genet 2017 May 16;18(1):44. Epub 2017 May 16.
    Department of Statistics, Kansas State University, 1116 Mid-Campus Drive N., 66506, Manhattan, KS, USA.
    Background: Over the past decades, the prevalence of type 2 diabetes mellitus (T2D) has been steadily increasing around the world. Despite large efforts devoted to better understand the genetic basis of the disease, the identified susceptibility loci can only account for a small portion of the T2D heritability. Some of the existing approaches proposed for the high dimensional genetic data from the T2D case-control study are limited by analyzing a few number of SNPs at a time from a large pool of SNPs, by ignoring the correlations among SNPs and by adopting inefficient selection techniques. Read More

    FecX (Bar) a Novel BMP15 mutation responsible for prolificacy and female sterility in Tunisian Barbarine Sheep.
    BMC Genet 2017 May 15;18(1):43. Epub 2017 May 15.
    Laboratoire des Productions Animales et Fourragères, INRA-Tunisie, Université de Carthage, El Menzah, 1004, Tunis, Tunisia.
    Background: Naturally occurring mutations in growth and differentiation factor 9 (GDF9) or bone morphogenetic protein 15 (BMP15) genes are associated with increased ovulation rate (OR) and litter size (LS) but also sterility. Observing the Tunisian Barbarine ewes of the "W" flock selected for improved prolificacy, we found prolific and infertile ewes with streaky ovaries. Blood genomic DNA was extracted from a subset of low-ovulating, prolific and infertile ewes of the "W" flock, and the entire coding sequences of GDF9 and BMP15 were sequenced. Read More

    Sucrose non-ferment 1 related protein kinase 2 (SnRK2) genes could mediate the stress responses in potato (Solanum tuberosum L.).
    BMC Genet 2017 May 15;18(1):41. Epub 2017 May 15.
    Gansu Key Lab of Crop Improvement & Germplasm Enhancement, Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou, 730070, Gansu, People's Republic of China.
    Background: The SnRKs (sucrose non-fermenting 1 related protein kinase) are a gene family coding for Ser/Thr protein kinases and play important roles in linking the tolerance and metabolic responses of plants to abiotic stresses. To date, no genome-wide characterization of the sucrose non-ferment 1 related protein kinase 2 (SnRK2) subfamily has been conducted in potato (Solanum tuberosum L.). Read More

    A strategy to apply quantitative epistasis analysis on developmental traits.
    BMC Genet 2017 May 15;18(1):42. Epub 2017 May 15.
    Department of BioSciences, Rice University, Houston, TX, 77005, USA.
    Background: Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. Read More

    High-content behavioral profiling reveals neuronal genetic network modulating Drosophila larval locomotor program.
    BMC Genet 2017 May 12;18(1):40. Epub 2017 May 12.
    Department of BioSciences, Rice University, Houston, TX, 77005, USA.
    Background: Two key questions in understanding the genetic control of behaviors are: what genes are involved and how these genes interact. To answer these questions at a systems level, we conducted high-content profiling of Drosophila larval locomotor behaviors for over 100 genotypes.

    Results: We studied 69 genes whose C. Read More

    A novel nonsense mutation in the tyrosinase gene is related to the albinism in a capuchin monkey (Sapajus apella).
    BMC Genet 2017 May 5;18(1):39. Epub 2017 May 5.
    Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, Av. Professor Mello Moraes 1721 Bloco A Sala D9 - Butantã, São Paulo, SP, Brazil, 05508-030.
    Background: Oculocutaneous Albinism (OCA) is an autosomal recessive inherited condition that affects the pigmentation of eyes, hair and skin. The OCA phenotype may be caused by mutations in the tyrosinase gene (TYR), which expresses the tyrosinase enzyme and has an important role in the synthesis of melanin pigment. The aim of this study was to identify the genetic mutation responsible for the albinism in a captive capuchin monkey, and to describe the TYR gene of normal phenotype individuals. Read More

    Detection and comparison of microRNAs in the caprine mammary gland tissues of colostrum and common milk stages.
    BMC Genet 2017 May 2;18(1):38. Epub 2017 May 2.
    Animal Engineering Branch, Yangling Vocational & Technical College, No. 10 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China.
    Background: MicroRNAs (miRNAs) have a great influence on various physiological functions. A lot of high-throughput sequencing (HTS) research on miRNAs has been executed in the caprine mammary gland at different lactation periods (common milk lactation and dry period), but little is known about differentially expressed miRNAs in the caprine mammary gland of colostrum and peak lactation periods.

    Result: This study identified 131 differentially expressed miRNAs (P < 0. Read More

    Genetic diversity of Elaeis oleifera (HBK) Cortes populations using cross species SSRs: implication's for germplasm utilization and conservation.
    BMC Genet 2017 Apr 19;18(1):37. Epub 2017 Apr 19.
    School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
    Background: The Elaeis oleifera genetic materials were assembled from its center of diversity in South and Central America. These materials are currently being preserved in Malaysia as ex situ living collections. Maintaining such collections is expensive and requires sizable land. Read More

    Quantitative trait locus analysis of heterosis for plant height and ear height in an elite maize hybrid zhengdan 958 by design III.
    BMC Genet 2017 Apr 17;18(1):36. Epub 2017 Apr 17.
    State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China.
    Background: Plant height (PH) and ear height (EH) are two important agronomic traits in maize selection breeding. F1 hybrid exhibit significant heterosis for PH and EH as compared to their parental inbred lines. To understand the genetic basis of heterosis controlling PH and EH, we conducted quantitative trait locus (QTL) analysis using a recombinant inbreed line (RIL) based design III population derived from the elite maize hybrid Zhengdan 958 in five environments. Read More

    Karyotype diversity and chromosomal organization of repetitive DNA in Tityus obscurus (Scorpiones, Buthidae).
    BMC Genet 2017 Apr 17;18(1):35. Epub 2017 Apr 17.
    Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Avenida Augusto Corrêa, n°01, Av. Perimetral, s/n. Guamá, 66075-900, Belém, Pará, Brazil.
    Background: Holocentric chromosomes occur in approximately 750 species of eukaryotes. Among them, the genus Tityus (Scorpiones, Buthidae) has a labile karyotype that shows complex multivalent associations during male meiosis. Thus, taking advantage of the excellent model provided by the Buthidae scorpions, here we analyzed the chromosomal distribution of several repetitive DNA classes on the holocentric chromosomes of different populations of the species Tityus obscurus Gervais, 1843, highlighting their involvement in the karyotypic differences found among them. Read More

    Ploidy elicits a whole-genome dosage effect: growth of triploid Atlantic salmon is linked to the genetic origin of the second maternal chromosome set.
    BMC Genet 2017 Apr 11;18(1):34. Epub 2017 Apr 11.
    Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
    Background: The Atlantic salmon aquaculture industry is investigating the feasibility of using sterile triploids to mitigate genetic interactions with wild conspecifics, however, studies investigating diploid and triploid performance often show contrasting results. Studies have identified dosage and dosage-compensation effects for gene expression between triploid and diploid salmonids, but no study has investigated how ploidy and parent-origin effects interact on a polygenic trait in divergent lines of Atlantic salmon (i.e. Read More

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