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BMC Genetics

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https://www.readbyqxmd.com/read/29221444/genome-wide-association-study-of-coronary-artery-calcified-atherosclerotic-plaque-in-african-americans-with-type-2-diabetes
#1
Jasmin Divers, Nicholette D Palmer, Carl D Langefeld, W Mark Brown, Lingyi Lu, Pamela J Hicks, S Carrie Smith, Jianzhao Xu, James G Terry, Thomas C Register, Lynne E Wagenknecht, John S Parks, Lijun Ma, Gary C Chan, Sarah G Buxbaum, Adolfo Correa, Solomon Musani, James G Wilson, Herman A Taylor, Donald W Bowden, John Jeffrey Carr, Barry I Freedman
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. To identify genes associated with CAC in AAs with type 2 diabetes (T2D), a genome-wide association study (GWAS) was performed using the Illumina 5 M chip in 691 African American-Diabetes Heart Study participants (AA-DHS), with replication in 205 Jackson Heart Study (JHS) participants with T2D...
December 8, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29212449/maternal-variant-in-the-upstream-of-foxp3-gene-on-the-x-chromosome-is-associated-with-recurrent-infertility-in-japanese-black-cattle
#2
Taichi Arishima, Shinji Sasaki, Tomohiro Isobe, Yoshihisa Ikebata, Shinichi Shimbara, Shogo Ikeda, Keisuke Kawashima, Yutaka Suzuki, Manabu Watanabe, Sumio Sugano, Kazunori Mizoshita, Yoshikazu Sugimoto
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...
December 6, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29212447/on-the-impact-of-relatedness-on-snp-association-analysis
#3
Arnd Gross, Anke Tönjes, Markus Scholz
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. However, this reduces the power of the test when relatedness is of concern. In the present paper, we derive explicit formulae to investigate how heritability and strength of relatedness contribute to variance inflation of the effect estimate of the linear model...
December 6, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29207956/a-microsatellite-diversity-analysis-and-the-development-of-core-set-germplasm-in-a-large-hulless-barley-hordeum-vulgare-l-collection
#4
Qijun Xu, Xingquan Zeng, Bin Lin, Zeqing Li, Hongjun Yuan, Yulin Wang, Zhasang, Nyima Tashi
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.) accessions with worldwide geographic origins and evaluated their genetic variability and relatedness based on 93 simple sequence repeat (SSR) markers...
December 6, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29202713/intromap-a-signal-analysis-based-method-for-the-detection-of-genomic-introgressions
#5
Daniel J Shea, Motoki Shimizu, Namiko Nishida, Eigo Fukai, Takashi Abe, Ryo Fujimoto, Keiichi Okazaki
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...
December 4, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29197342/identification-and-integrated-analysis-of-differentially-expressed-lncrnas-and-circrnas-reveal-the-potential-cerna-networks-during-pdlsc-osteogenic-differentiation
#6
Xiuge Gu, Mengying Li, Ye Jin, Dongxu Liu, Fulan Wei
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...
December 2, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29179688/evaluating-genetic-ancestry-and-self-reported-ethnicity-in-the-context-of-carrier-screening
#7
Roman Shraga, Sarah Yarnall, Sonya Elango, Arun Manoharan, Sally Ann Rodriguez, Sara L Bristow, Neha Kumar, Mohammad Niknazar, David Hoffman, Shahin Ghadir, Rita Vassena, Serena H Chen, Avner Hershlag, Jamie Grifo, Oscar Puig
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...
November 28, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29149838/genetic-variation-in-populations-of-the-earthworm-lumbricus-rubellus-across-contaminated-mine-sites
#8
Craig Anderson, Luis Cunha, Pierfrancesco Sechi, Peter Kille, David Spurgeon
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...
November 17, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29149837/assessment-of-genetic-diversity-in-vigna-unguiculata-l-walp-accessions-using-inter-simple-sequence-repeat-issr-and-start-codon-targeted-scot-polymorphic-markers
#9
David Okeh Igwe, Celestine Azubike Afiukwa, Benjamin Ewa Ubi, Kenneth Idika Ogbu, Omena Bernard Ojuederie, George Nkem Ude
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...
November 17, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29132297/association-between-%C3%A3-2-adrenergic-receptor-gene-polymorphisms-and-adverse-events-of-ritodrine-in-the-treatment-of-preterm-labor-a-prospective-observational-study
#10
Jee Eun Chung, Soo An Choi, Han Sung Hwang, Jin Young Park, Kyung Eun Lee, Jeong Yee, Young Ju Kim, Hye Sun Gwak
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. Five single nucleotide polymorphisms (SNPs) of the ADRB2 gene (rs1042713, rs1042714, rs1042717, rs1042718, and rs1042719) were analyzed in 186 pregnant women with preterm labor...
November 13, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29121864/comparative-transcriptome-and-dna-methylation-analyses-of-the-molecular-mechanisms-underlying-skin-color-variations-in-crucian-carp-carassius-carassius-l
#11
Yongqin Zhang, Jinhui Liu, Wen Fu, Wenting Xu, Huiqin Zhang, Shujuan Chen, Wenbin Liu, Liangyue Peng, Yamei Xiao
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. RESULTS: Totals of 3434 and 3683 unigenes had significantly lower and higher expression in WCC, respectively, compared with unigenes expressed in RCC...
November 9, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29115942/detection-of-qtls-for-seedling-characteristics-in-barley-hordeum-vulgare-l-grown-under-hydroponic-culture-condition
#12
Qifei Wang, Genlou Sun, Xifeng Ren, Jibin Wang, Binbin Du, Chengdao Li, Dongfa Sun
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. In the present work, 21 seedling-related characteristics are assessed in a barley double haploid (DH) population, grown under hydroponic conditions...
November 7, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29110633/network-analysis-for-count-data-with-excess-zeros
#13
Hosik Choi, Jungsoo Gim, Sungho Won, You Jin Kim, Sunghoon Kwon, Changyi Park
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. Furthermore, when zero counts are more frequent than are expected, excess zeros should be considered in the model...
November 6, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29096606/genetic-variability-in-italian-populations-of-drosophila-suzukii
#14
Gabriella Tait, Silvia Vezzulli, Fabiana Sassù, Gloria Antonini, Antonio Biondi, Nuray Baser, Giorgia Sollai, Alessandro Cini, Lorenzo Tonina, Lino Ometto, Gianfranco Anfora
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. In particular, we analysed 15 previously characterised Simple Sequence Repeat (SSR) markers to estimate genetic differentiation across the genome of 278 flies collected from nine populations...
November 3, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29058610/whole-genome-population-genetics-analysis-of-sudanese-goats-identifies-regions-harboring-genes-associated-with-major-traits
#15
Siham A Rahmatalla, Danny Arends, Monika Reissmann, Ammar Said Ahmed, Klaus Wimmers, Henry Reyer, Gudrun A Brockmann
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. RESULTS: More than 96% of high quality SNPs were polymorphic with an average minor allele frequency of 0...
October 23, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29058616/correction-to-novel-snp-markers-in-invge-and-sssi-genes-are-associated-with-natural-variation-of-sugar-contents-and-frying-color-in-solanum-tuberosum-group-phureja
#16
D Duarte-Delgado, D Juyó, C Gebhardt, F Sarmiento, T Mosquera-Vásquez
No abstract text is available yet for this article.
October 20, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29037145/generalized-disequilibrium-test-for-association-in-qualitative-traits-incorporating-imprinting-effects-based-on-extended-pedigrees
#17
Jian-Long Li, Peng Wang, Wing Kam Fung, Ji-Yuan Zhou
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...
October 16, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29025415/genetic-evidence-of-multiple-invasions-and-a-small-number-of-founders-of-asian-palmyra-palm-borassus-flabellifer-in-thailand
#18
Kwanjai Pipatchartlearnwong, Akarapong Swatdipong, Supachai Vuttipongchaikij, Somsak Apisitwanich
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. flabellifer is believed to be originated in Africa, spread to South Asia and introduced into Southeast Asia through commercial routes and dissemination of cultures, however, the nature of its invasion and settlement in Thailand is unclear...
October 12, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29025391/identification-of-putative-markers-linked-to-grain-plumpness-in-rice-oryza-sativa-l-via-association-mapping
#19
Erbao Liu, Siyuan Zeng, Xiangong Chen, Xiaojing Dang, Lijun Liang, Hui Wang, Zhiyao Dong, Yang Liu, Delin Hong
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. Among 31 marker-GP association loci detected in two or more environments and determined using general linear model (GLM) analyses, seven association loci were also detected using mixed linear model (MLM) analyses...
October 12, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29020941/fine-mapping-of-a-qtl-affecting-levels-of-skatole-on-pig-chromosome-7
#20
Maren van Son, Matthew P Kent, Harald Grove, Rahul Agarwal, Hanne Hamland, Sigbjørn Lien, Eli Grindflek
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. Skatole is one of the main components causing boar taint, which gives an undesirable smell and taste to the pig meat when heated. Surgical castration of boars is a common practice to reduce the risk of boar taint, however, a selection for boars genetically predisposed for low levels of taint would help eliminating the need for castration and be advantageous for both economic and welfare reasons...
October 11, 2017: BMC Genetics
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