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    Correction to: High density marker panels, SNPs prioritizing and accuracy of genomic selection.
    BMC Genet 2018 Feb 15;19(1):13. Epub 2018 Feb 15.
    Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA.
    Correction To: BMC GENETICS (2018) 19:4 DOI: 10.1186/S12863-017-0595-2: The original version of this article [1], published on 5 January 2018, contained 3 formatting errors. In this Correction the affected parts of the article are shown. Read More

    Genetic diversity and ex situ conservation of Loropetalum subcordatum, an endangered species endemic to China.
    BMC Genet 2018 Feb 13;19(1):12. Epub 2018 Feb 13.
    South China Limestone Plants Research Center, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
    Background: Loropetalum subcordatum is an endangered species endemic to China that is characterized by narrow distribution, small population size, and delayed fertilization. However, the genetic diversity of the entire extant natural and ex situ populations has not been assessed to date. In this study, we evaluated the genetic diversity and structure of six natural populations and a single ex situ population (the only known ex situ population of L. Read More

    Diversity of plant defense elicitor peptides within the Rosaceae.
    BMC Genet 2018 Jan 23;19(1):11. Epub 2018 Jan 23.
    Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain.
    Background: Plant elicitor peptides (Peps) are endogenous molecules that induce and amplify the first line of inducible plant defense, known as pattern-triggered immunity, contributing to protect plants against attack by bacteria, fungi and herbivores. Pep topic application and transgenic expression have been found to enhance disease resistance in a small number of model plant-pathogen systems. The action of Peps relies on perception by specific receptors, so displaying a family-specific activity. Read More

    Detecting TF-miRNA-gene network based modules for 5hmC and 5mC brain samples: a intra- and inter-species case-study between human and rhesus.
    BMC Genet 2018 Jan 22;19(1). Epub 2018 Jan 22.
    Machine Intelligence Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata, 700108, India.
    Background: Study of epigenetics is currently a high-impact research topic. Multi stage methylation is also an area of high-dimensional prospect. In this article, we provide a new study (intra and inter-species study) on brain tissue between human and rhesus on two methylation cytosine variants based data-profiles (viz. Read More

    DArT, SNP, and SSR analyses of genetic diversity in Lolium perenne L. using bulk sampling.
    BMC Genet 2018 Jan 22;19(1):10. Epub 2018 Jan 22.
    Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany.
    Background: Lolium perenne L. is the most important forage grass species in temperate regions. It is also considered as a sustainable source of biomass for energy production. Read More

    Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars.
    BMC Genet 2018 Jan 16;19(1). Epub 2018 Jan 16.
    Potato Research Group, Estación Experimental Agropecuaria Balcarce, Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta 226 km 73.5, Balcarce, Buenos Aires, Argentina.
    Background: Diversity in crops is fundamental for plant breeding efforts. An accurate assessment of genetic diversity, using molecular markers, such as single nucleotide polymorphism (SNP), must be able to reveal the structure of the population under study. A characterization of population structure using easy measurable phenotypic traits could be a preliminary and low-cost approach to elucidate the genetic structure of a population. Read More

    Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice.
    BMC Genet 2018 Jan 15;19(1). Epub 2018 Jan 15.
    Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
    Background: Balancing panicle-related traits such as panicle length and the numbers of primary and secondary branches per panicle, is key to improving the number of spikelets per panicle in rice. Identifying genetic information contributes to a broader understanding of the roles of gene and provides candidate alleles for use as DNA markers. Discovering relations between panicle-related traits and sequence variants allows opportunity for molecular application in rice breeding to improve the number of spikelets per panicle. Read More

    Rare variant association analysis in case-parents studies by allowing for missing parental genotypes.
    BMC Genet 2018 Jan 15;19(1). Epub 2018 Jan 15.
    Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, 70112, USA.
    Background: The development of next-generation sequencing technologies has facilitated the identification of rare variants. Family-based design is commonly used to effectively control for population admixture and substructure, which is more prominent for rare variants. Case-parents studies, as typical strategies in family-based design, are widely used in rare variant-disease association analysis. Read More

    Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton.
    BMC Genet 2018 Jan 15;19(1). Epub 2018 Jan 15.
    Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.
    Background: Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this research work was to characterize the late embryogenesis abundant (LEA) protein families and to carry out gene expression analysis to determine their potential role in drought stress tolerance in upland cotton. Read More

    High density marker panels, SNPs prioritizing and accuracy of genomic selection.
    BMC Genet 2018 Jan 5;19(1). Epub 2018 Jan 5.
    Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA.
    Background: The availability of high-density (HD) marker panels, genome wide variants and sequence data creates an unprecedented opportunity to dissect the genetic basis of complex traits, enhance genomic selection (GS) and identify causal variants of disease. The disproportional increase in the number of parameters in the genetic association model compared to the number of phenotypes has led to further deterioration in statistical power and an increase in co-linearity and false positive rates. At best, HD panels do not significantly improve GS accuracy and, at worst, reduce accuracy. Read More

    Genome-wide association study of seedling stage salinity tolerance in temperate japonica rice germplasm.
    BMC Genet 2018 Jan 3;19(1). Epub 2018 Jan 3.
    International Rice Research Institute, Laguna, 4031, Philippines.
    Background: Salinity has a significant impact on rice production in coastal, arid and semi-arid areas in many countries, including countries growing temperate rice, such as Kazakhstan. Recently, the complete genomes of 3000 rice accessions were sequenced through the 3 K rice genome project, and this set included 203 temperate japonica rice accessions. To identify salinity-tolerant germplasm and related genes for developing new salinity-tolerant breeding lines for the temperate japonica rice growing regions, we evaluated the seedling stage salinity tolerance of these sequenced temperate japonica rice accessions, and conducted genome-wide association studies (GWAS) for a series of salinity tolerance related traits. Read More

    De novo transcriptome sequencing and analysis of male and female swimming crab (Portunus trituberculatus) reproductive systems during mating embrace (stage II).
    BMC Genet 2018 Jan 3;19(1). Epub 2018 Jan 3.
    Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China.
    Background: The swimming crab Portunus trituberculatus is one of the most commonly farmed crustaceans in China. As one of the most widely known and high-value edible crabs, it crab supports large crab fishery and aquaculture in China. Only large and sexually mature crabs can provide the greatest economic benefits, suggesting the considerable effect of reproductive system development on fishery. Read More

    Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe.
    BMC Genet 2017 Dec 28;18(Suppl 1):110. Epub 2017 Dec 28.
    Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia.
    Background: The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia. Read More

    Upregulation of NETO2 gene in colorectal cancer.
    BMC Genet 2017 Dec 28;18(Suppl 1):117. Epub 2017 Dec 28.
    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
    Background: Neuropilin and tolloid-like 2 (NETO2) is a single-pass transmembrane protein that has been shown primarily implicated in neuron-specific processes. Upregulation of NETO2 gene was also detected in several cancer types. In colorectal cancer (CRC), it was associated with tumor progression, invasion, and metastasis, and seems to be involved in epithelial-mesenchymal transition (EMT). Read More

    A compendium and functional characterization of mammalian genes involved in adaptation to Arctic or Antarctic environments.
    BMC Genet 2017 Dec 28;18(Suppl 1):111. Epub 2017 Dec 28.
    The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia.
    Background: Many mammals are well adapted to surviving in extremely cold environments. These species have likely accumulated genetic changes that help them efficiently cope with low temperatures. It is not known whether the same genes related to cold adaptation in one species would be under selection in another species. Read More

    Generation of megabase-scale deletions, inversions and duplications involving the Contactin-6 gene in mice by CRISPR/Cas9 technology.
    BMC Genet 2017 Dec 28;18(Suppl 1):112. Epub 2017 Dec 28.
    Department of Molecular Mechanisms of Development, Institute of Cytology and Genetics, Russia Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia.
    Background: Copy Number Variation (CNV) of the human CNTN6 gene (encoding the contactin-6 protein), caused by deletions or duplications, is responsible for severe neurodevelopmental impairments, often in combination with facial dysmorphias. Conversely, deleterious point mutations of this gene do not show any clinical phenotypes. The aim of this study is to generate mice carrying large deletions, duplications and inversions involving the Cntn6 gene as a new experimental model to study CNV of the human CNTN6 locus. Read More

    Application of geographic population structure (GPS) algorithm for biogeographical analyses of populations with complex ancestries: a case study of South Asians from 1000 genomes project.
    BMC Genet 2017 Dec 28;18(Suppl 1):109. Epub 2017 Dec 28.
    Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India.
    Background: The utilization of biological data to infer the geographic origins of human populations has been a long standing quest for biologists and anthropologists. Several biogeographical analysis tools have been developed to infer the geographical origins of human populations utilizing genetic data. However due to the inherent complexity of genetic information these approaches are prone to misinterpretations. Read More

    DEP1 gene in wheat species with normal, compactoid and compact spikes.
    BMC Genet 2017 Dec 28;18(Suppl 1):106. Epub 2017 Dec 28.
    Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
    Background: In rice, a variant of DEP1 gene results in erect panicle architecture, well-developed vascular bundles, an increase in the number of grains per panicle and a consequent increase in the grain yield. Interestingly, DEP1 homologs are present in the other cereals including species of wheat and barley (Hordeum vulgare), even though they do not produce panicles but spikes. In barley, HvDEP1 alleles do not differ between strains of various ear types and geographic origins, while in at least three OsDEP1 variants have been described. Read More

    High resolution melting curve analysis targeting the HBB gene mutational hot-spot offers a reliable screening approach for all common as well as most of the rare beta-globin gene mutations in Bangladesh.
    BMC Genet 2018 Jan 2;19(1). Epub 2018 Jan 2.
    Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh.
    Background: Bangladesh lies in the global thalassemia belt, which has a defined mutational hot-spot in the beta-globin gene. The high carrier frequencies of beta-thalassemia trait and hemoglobin E-trait in Bangladesh necessitate a reliable DNA-based carrier screening approach that could supplement the use of hematological and electrophoretic indices to overcome the barriers of carrier screening. With this view in mind, the study aimed to establish a high resolution melting (HRM) curve-based rapid and reliable mutation screening method targeting the mutational hot-spot of South Asian and Southeast Asian countries that encompasses exon-1 (c. Read More

    Novel methods for genotype imputation to whole-genome sequence and a simple linear model to predict imputation accuracy.
    BMC Genet 2017 Dec 27;18(1):120. Epub 2017 Dec 27.
    Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
    Background: Accurate imputation plays a major role in genomic studies of livestock industries, where the number of genotyped or sequenced animals is limited by costs. This study explored methods to create an ideal reference population for imputation to Next Generation Sequencing data in cattle.

    Methods: Methods for clustering of animals for imputation were explored, using 1000 Bull Genomes Project sequence data on 1146 animals from a variety of beef and dairy breeds. Read More

    An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench).
    BMC Genet 2017 Dec 22;18(1):119. Epub 2017 Dec 22.
    South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Belleville, 7535, South Africa.
    Background: Drought is the most disastrous abiotic stress that severely affects agricultural productivity worldwide. Understanding the biological basis of drought-regulated traits, requires identification and an in-depth characterization of genetic determinants using model organisms and high-throughput technologies. However, studies on drought tolerance have generally been limited to traditional candidate gene approach that targets only a single gene in a pathway that is related to a trait. Read More

    Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat.
    BMC Genet 2017 Dec 20;18(1):118. Epub 2017 Dec 20.
    Linköping University, IFM Biology, SE-581 83, Linköping, Sweden.
    Background: The NAM-B1 gene in wheat has for almost three decades been extensively studied and utilized in breeding programs because of its significant impact on grain protein and mineral content and pleiotropic effects on senescence rate and grain size. First detected in wild emmer wheat, the wild-type allele of the gene has been introgressed into durum and bread wheat. Later studies have, however, also found the presence of the wild-type allele in some domesticated subspecies. Read More

    Comparison of weighting approaches for genetic risk scores in gene-environment interaction studies.
    BMC Genet 2017 Dec 16;18(1):115. Epub 2017 Dec 16.
    Mathematical Institute, Heinrich Heine University, Düsseldorf, Germany.
    Background: Weighted genetic risk scores (GRS), defined as weighted sums of risk alleles of single nucleotide polymorphisms (SNPs), are statistically powerful for detection gene-environment (GxE) interactions. To assign weights, the gold standard is to use external weights from an independent study. However, appropriate external weights are not always available. Read More

    Correction to: Mapping of leptin and its syntenic genes to chicken chromosome 1p.
    BMC Genet 2017 12 15;18(1):113. Epub 2017 Dec 15.
    Department of Animal Science, Agricultural Research Organization, Volcani Center, P.O. Box 15159, 7528809, Rishon LeTsiyon, Israel.
    Correction: After the publication of this work [1] an error was noticed in one of the author surnames. The author name Leif Anderson should be spelt as Leif Andersson. Read More

    Investigating population continuity with ancient DNA under a spatially explicit simulation framework.
    BMC Genet 2017 Dec 15;18(1):114. Epub 2017 Dec 15.
    AGP lab, Department of Genetics & Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.
    Background: Recent advances in sequencing technologies have allowed for the retrieval of ancient DNA data (aDNA) from skeletal remains, providing direct genetic snapshots from diverse periods of human prehistory. Comparing samples taken in the same region but at different times, hereafter called "serial samples", may indicate whether there is continuity in the peopling history of that area or whether an immigration of a genetically different population has occurred between the two sampling times. However, the exploration of genetic relationships between serial samples generally ignores their geographical locations and the spatiotemporal dynamics of populations. Read More

    Functional polymorphisms in asporin and CILP together with joint loading predispose to hand osteoarthritis.
    BMC Genet 2017 Dec 12;18(1):108. Epub 2017 Dec 12.
    Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Aapistie 5, 90220, Oulu, Finland.
    Background: Osteoarthritis (OA) is the most common degenerative joint disease afflicting people in the Western world and has a strong genetic influence. The aim of this study was to examine the association of two known functional polymorphisms in the TGF-β inhibiting genes, asporin (ASPN) and cartilage intermediate layer protein (CILP), with hand OA and potential gene-occupational hand loading interaction.

    Results: Statistically significant interaction of the CILP rs2073711 T and ASPN D15 alleles with hand OA was observed (OR = 2. Read More

    Evaluation of methods and marker Systems in Genomic Selection of oil palm (Elaeis guineensis Jacq.).
    BMC Genet 2017 Dec 11;18(1):107. Epub 2017 Dec 11.
    Institute of Biological Sciences, University Malaya, 50603, Kuala Lumpur, Malaysia.
    Background: Genomic selection (GS) uses genome-wide markers as an attempt to accelerate genetic gain in breeding programs of both animals and plants. This approach is particularly useful for perennial crops such as oil palm, which have long breeding cycles, and for which the optimal method for GS is still under debate. In this study, we evaluated the effect of different marker systems and modeling methods for implementing GS in an introgressed dura family derived from a Deli dura x Nigerian dura (Deli x Nigerian) with 112 individuals. Read More

    Genome-wide association study of coronary artery calcified atherosclerotic plaque in African Americans with type 2 diabetes.
    BMC Genet 2017 Dec 8;18(1):105. Epub 2017 Dec 8.
    Department of Internal Medicine-Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA.
    Background: Coronary artery calcified atherosclerotic plaque (CAC) predicts cardiovascular disease (CVD). Despite exposure to more severe conventional CVD risk factors, African Americans (AAs) are less likely to develop CAC, and when they do, have markedly lower levels than European Americans. Genetic factors likely contribute to the observed ethnic differences. Read More

    Maternal variant in the upstream of FOXP3 gene on the X chromosome is associated with recurrent infertility in Japanese Black cattle.
    BMC Genet 2017 Dec 6;18(1):103. Epub 2017 Dec 6.
    Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima, 961-8061, Japan.
    Background: Repeat breeding, which is defined as cattle failure to conceive after three or more inseminations in the absence of clinical abnormalities, is a substantial problem in cattle breeding. To identify maternal genetic variants of repeat breeding in Japanese Black cattle, we selected 29 repeat-breeding heifers that failed to conceive following embryo transfer (ET) and conducted a genome-wide association study (GWAS) using the traits.

    Results: We found that a single-nucleotide polymorphism (SNP; g. Read More

    On the impact of relatedness on SNP association analysis.
    BMC Genet 2017 Dec 6;18(1):104. Epub 2017 Dec 6.
    Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, Leipzig, 04107, Germany.
    Background: When testing for SNP (single nucleotide polymorphism) associations in related individuals, observations are not independent. Simple linear regression assuming independent normally distributed residuals results in an increased type I error and the power of the test is also affected in a more complicate manner. Inflation of type I error is often successfully corrected by genomic control. Read More

    A microsatellite diversity analysis and the development of core-set germplasm in a large hulless barley (Hordeum vulgare L.) collection.
    BMC Genet 2017 Dec 6;18(1):102. Epub 2017 Dec 6.
    Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China.
    Background: Clarifying genetic diversity in a large germplasm resource plays important roles in experimental designs that provides flexible utility in fundamental research and breeding in crops. However, the work is limited due to small collections of barley that are insufficient representatives.

    Results: In the present study, we collected 562 hulless barley (Hordeum vulgare L. Read More

    IntroMap: a signal analysis based method for the detection of genomic introgressions.
    BMC Genet 2017 Dec 4;18(1):101. Epub 2017 Dec 4.
    Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
    Background: Breeding programs often rely on marker-assisted tests or variant calling of next generation sequence (NGS) data to identify regions of genomic introgression arising from the hybridization of two plant species. In this paper we present IntroMap, a bioinformatics pipeline for the screening of candidate plants through the application of signal processing techniques to NGS data, using alignment to a reference genome sequence (annotation is not required) that shares homology with the recurrent parental cultivar, and without the need for de novo assembly of the read data or variant calling.

    Results: We show the accurate identification of introgressed genomic regions using both in silico simulated genomes, and a hybridized cultivar data set using our pipeline. Read More

    Identification and integrated analysis of differentially expressed lncRNAs and circRNAs reveal the potential ceRNA networks during PDLSC osteogenic differentiation.
    BMC Genet 2017 Dec 2;18(1):100. Epub 2017 Dec 2.
    Department of Orthodontics, Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Wenhua Xi Road No. 44-1, Jinan, Shandong, 250012, People's Republic of China.
    Background: Researchers have been exploring the molecular mechanisms underlying the control of periodontal ligament stem cell (PDLSC) osteogenic differentiation. Recently, long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) were shown to function as competitive endogenous RNAs (ceRNAs) to regulate the effect of microRNAs (miRNAs) on their target genes during cell differentiation. However, comprehensive identification and integrated analysis of lncRNAs and circRNAs acting as ceRNAs during PDLSC osteogenic differentiation have not been performed. Read More

    Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening.
    BMC Genet 2017 Nov 28;18(1):99. Epub 2017 Nov 28.
    Phosphorus, Inc, 25 West 26th St, New York, NY, 10010, USA.
    Background: Current professional society guidelines recommend genetic carrier screening be offered on the basis of ethnicity, or when using expanded carrier screening panels, they recommend to compute residual risk based on ethnicity. We investigated the reliability of self-reported ethnicity in 9138 subjects referred to carrier screening. Self-reported ethnicity gathered from test requisition forms and during post-test genetic counseling, and genetic ancestry predicted by a statistical model, were compared for concordance. Read More

    Genetic variation in populations of the earthworm, Lumbricus rubellus, across contaminated mine sites.
    BMC Genet 2017 Nov 17;18(1):97. Epub 2017 Nov 17.
    Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Wallingford, OX10 8BB, UK.
    Background: Populations of the earthworm, Lumbricus rubellus, are commonly found across highly contaminated former mine sites and are considered to have under-gone selection for mitigating metal toxicity. Comparison of adapted populations with those found on less contaminated soils can provide insights into ecological processes that demonstrate the long-term effects of soil contamination. Contemporary sequencing methods allow for portrayal of demographic inferences and highlight genetic variation indicative of selection at specific genes. Read More

    Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers.
    BMC Genet 2017 Nov 17;18(1):98. Epub 2017 Nov 17.
    Department of Natural Sciences, Bowie State University, 14000 Jericho Park Road, Bowie, USA.
    Background: Assessment of genetic diversity of Vigna unguiculata (L.) Walp (cowpea) accessions using informative molecular markers is imperative for their genetic improvement and conservation. Use of efficacious molecular markers to obtain the required knowledge of the genetic diversity within the local and regional germplasm collections can enhance the overall effectiveness of cowpea improvement programs, hence, the comparative assessment of Inter-simple sequence repeat (ISSR) and Start codon targeted (SCoT) markers in genetic diversity of V. Read More

    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 11 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 11 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 10 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 10 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 10 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 10 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 10 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 10 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 Fhybrids (4nF) (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 10 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

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