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Expression quantitative trait loci

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https://www.readbyqxmd.com/read/27915454/round-fruit-shape-in-wi7239-cucumber-is-controlled-by-two-interacting-quantitative-trait-loci-with-one-putatively-encoding-a-tomato-sun-homolog
#1
Yupeng Pan, Xinjing Liang, Meiling Gao, Hanqiang Liu, Huanwen Meng, Yiqun Weng, Zhihui Cheng
QTL analysis revealed two interacting loci, FS1.2 and FS2.1, underlying round fruit shape in WI7239 cucumber; CsSUN , a homolog of tomato fruit shape gene SUN , was a candidate for FS1.2. Fruit size is an important quality and yield trait in cucumber, but its genetic basis remains poorly understood. Here we reported QTL mapping results on fruit size with segregating populations derived from the cross between WI7238 (long fruit) and WI7239 (round fruit) inbred cucumber lines. Phenotypic data of fruit length and diameter were collected at anthesis, immature and mature fruit stages in four environments...
December 3, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27914629/cytoplasmic-fmr1-interacting-protein-2-is-a-major-genetic-factor-underlying-binge-eating
#2
Stacey L Kirkpatrick, Lisa R Goldberg, Neema Yazdani, R Keith Babbs, Jiayi Wu, Eric R Reed, David F Jenkins, Amanda F Bolgioni, Kelsey I Landaverde, Kimberly P Luttik, Karen S Mitchell, Vivek Kumar, W Evan Johnson, Megan K Mulligan, Pietro Cottone, Camron D Bryant
BACKGROUND: Eating disorders are lethal and heritable; however, the underlying genetic factors are unknown. Binge eating is a highly heritable trait associated with eating disorders that is comorbid with mood and substance use disorders. Therefore, understanding its genetic basis will inform therapeutic development that could improve several comorbid neuropsychiatric conditions. METHODS: We assessed binge eating in closely related C57BL/6 mouse substrains and in an F2 cross to identify quantitative trait loci associated with binge eating...
October 25, 2016: Biological Psychiatry
https://www.readbyqxmd.com/read/27906459/integrative-genomic-analysis-identifies-ancestry-related-expression-quantitative-trait-loci-on-dna-polymerase-%C3%AE-and-supports-the-association-of-genetic-ancestry-with-survival-disparities-in-head-and-neck-squamous-cell-carcinoma
#3
Meganathan P Ramakodi, Karthik Devarajan, Elizabeth Blackman, Denise Gibbs, Danièle Luce, Jacqueline Deloumeaux, Suzy Duflo, Jeffrey C Liu, Ranee Mehra, Rob J Kulathinal, Camille C Ragin
BACKGROUND: African Americans with head and neck squamous cell carcinoma (HNSCC) have a lower survival rate than whites. This study investigated the functional importance of ancestry-informative single-nucleotide polymorphisms (SNPs) in HNSCC and also examined the effect of functionally important genetic elements on racial disparities in HNSCC survival. METHODS: Ancestry-informative SNPs, RNA sequencing, methylation, and copy number variation data for 316 oral cavity and laryngeal cancer patients were analyzed across 178 DNA repair genes...
December 1, 2016: Cancer
https://www.readbyqxmd.com/read/27903236/erratum-to-adrenal-cortex-expression-quantitative-trait-loci-in-a-german-holstein%C3%A2-%C3%A3-%C3%A2-charolais-cross
#4
Bodo Brand, Markus O Scheinhardt, Juliane Friedrich, Daisy Zimmer, Norbert Reinsch, Siriluck Ponsuksili, Manfred Schwerin, Andreas Ziegler
No abstract text is available yet for this article.
November 30, 2016: BMC Genetics
https://www.readbyqxmd.com/read/27902802/identification-and-characterization-of-quantitative-trait-loci-for-shattering-in-rice-landrace-jiucaiqing-from-taihu-lake-valley-china
#5
Jinping Cheng, Yongqi He, Chengfang Zhan, Bin Yang, Enshun Xu, Hongsheng Zhang, Zhoufei Wang
Easy shattering reduces yield from grain loss during rice ( L.) harvest. We characterized a nonshattering rice landrace Jiucaiqing from Taihu Lake valley in China. The breaking tensile strength (BTS; grams force, gf) of the grain pedicel was measured using a digital force gauge to evaluate the degree of shattering at 0, 7, 14, 21, 28, and 35 d after heading (DAH). The BTS of Jiucaiqing did not significantly decrease with increasing DAH, maintaining a level of 152.2 to 195.9 gf, while that of IR26 decreased greatly during 0 to 14 DAH and finally stabilized at ∼100 gf...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27898833/a-cluster-of-nucleotide-binding-site-leucine-rich-repeat-genes-resides-in-a-barley-powdery-mildew-resistance-quantitative-trait-loci-on-7hl
#6
Carlos P Cantalapiedra, Bruno Contreras-Moreira, Cristina Silvar, Dragan Perovic, Frank Ordon, María Pilar Gracia, Ernesto Igartua, Ana M Casas
Powdery mildew causes severe yield losses in barley production worldwide. Although many resistance genes have been described, only a few have already been cloned. A strong QTL (quantitative trait locus) conferring resistance to a wide array of powdery mildew isolates was identified in a Spanish barley landrace on the long arm of chromosome 7H. Previous studies narrowed down the QTL position, but were unable to identify candidate genes or physically locate the resistance. In this study, the exome of three recombinant lines from a high-resolution mapping population was sequenced and analyzed, narrowing the position of the resistance down to a single physical contig...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898807/identification-and-validation-of-candidate-genes-associated-with-domesticated-and-improved-traits-in-soybean
#7
Ling Zhou, Longhai Luo, Jian-Fang Zuo, Linfeng Yang, Li Zhang, Xuanmin Guang, Yuan Niu, Jianbo Jian, Qing-Chun Geng, Liping Liang, Qijian Song, Jim M Dunwell, Zhenzhen Wu, Jia Wen, Yu-Qin Liu, Yuan-Ming Zhang
Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898766/genomic-regions-influencing-seminal-root-traits-in-barley
#8
Hannah Robinson, Lee Hickey, Cecile Richard, Emma Mace, Alison Kelly, Andrew Borrell, Jerome Franckowiak, Glen Fox
Water availability is a major limiting factor for crop production, making drought adaptation and its many component traits a desirable attribute of plant cultivars. Previous studies in cereal crops indicate that root traits expressed at early plant developmental stages, such as seminal root angle and root number, are associated with water extraction at different depths. Here, we conducted the first study to map seminal root traits in barley ( L.). Using a recently developed high-throughput phenotyping method, a panel of 30 barley genotypes and a doubled-haploid (DH) population (ND24260 × 'Flagship') comprising 330 lines genotyped with diversity array technology (DArT) markers were evaluated for seminal root angle (deviation from vertical) and root number under controlled environmental conditions...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27890468/genetic-overlap-between-attention-deficit-hyperactivity-disorder-and-bipolar-disorder-evidence-from-genome-wide-association-study-meta-analysis
#9
Kimm J E van Hulzen, Claus J Scholz, Barbara Franke, Stephan Ripke, Marieke Klein, Andrew McQuillin, Edmund J Sonuga-Barke, John R Kelsoe, Mikael Landén, Ole A Andreassen, Klaus-Peter Lesch, Heike Weber, Stephen V Faraone, Alejandro Arias-Vasquez, Andreas Reif
BACKGROUND: Attention-deficit/hyperactivity disorder (ADHD) and bipolar disorder (BPD) are frequently co-occurring and highly heritable mental health conditions. We hypothesized that BPD cases with an early age of onset (≤21 years old) would be particularly likely to show genetic covariation with ADHD. METHODS: Genome-wide association study data were available for 4609 individuals with ADHD, 9650 individuals with BPD (5167 thereof with early-onset BPD), and 21,363 typically developing controls...
October 18, 2016: Biological Psychiatry
https://www.readbyqxmd.com/read/27886173/integrative-epigenome-wide-analysis-demonstrates-that-dna-methylation-may-mediate-genetic-risk-in-inflammatory-bowel-disease
#10
N T Ventham, N A Kennedy, A T Adams, R Kalla, S Heath, K R O'Leary, H Drummond, D C Wilson, I G Gut, E R Nimmo, J Satsangi
Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. We replicate the top DMP (RPS6KA2) and DMRs (VMP1, ITGB2 and TXK) in an independent cohort. Using paired genetic and epigenetic data, we delineate methylation quantitative trait loci; VMP1/microRNA-21 methylation associates with two polymorphisms in linkage disequilibrium with a known IBD susceptibility variant...
November 25, 2016: Nature Communications
https://www.readbyqxmd.com/read/27881992/molecular-mapping-and-qtl-for-expression-profiles-of-flavonoid-genes-in-brassica-napus
#11
Cunmin Qu, Huiyan Zhao, Fuyou Fu, Kai Zhang, Jianglian Yuan, Liezhao Liu, Rui Wang, Xinfu Xu, Kun Lu, Jia-Na Li
Flavonoids are secondary metabolites that are extensively distributed in the plant kingdom and contribute to seed coat color formation in rapeseed. To decipher the genetic networks underlying flavonoid biosynthesis in rapeseed, we constructed a high-density genetic linkage map with 1089 polymorphic loci (including 464 SSR loci, 97 RAPD loci, 451 SRAP loci, and 75 IBP loci) using recombinant inbred lines (RILs). The map consists of 19 linkage groups and covers 2775 cM of the B. napus genome with an average distance of 2...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27881077/sex-difference-in-egfr-pathways-in-mouse-kidney-potential-impact-on-the-immune-system
#12
Fengxia Liu, Yan Jiao, Yun Jiao, Franklin Garcia-Godoy, Weikuan Gu, Qingyi Liu
BACKGROUND: Epidermal growth factor receptor (Egfr) has been the target of several drugs for cancers. The potential gender differences in genes in the Egfr axis have been suggested in humans and in animal models. Female and male mice from the same recombinant inbred (RI) strain have the same genomic components except the sex difference. A population of different RI mouse strains allows to conduct precise analysis of molecular pathways and regulation of Egfr between female and male mice...
November 24, 2016: BMC Genetics
https://www.readbyqxmd.com/read/27880018/drought-related-secondary-metabolites-of-barley-hordeum-vulgare-l-leaves-and-their-mqtls
#13
Anna Piasecka, Aneta Sawikowska, Anetta Kuczyńska, Piotr Ogrodowicz, Krzysztof Mikołajczak, Karolina Krystkowiak, Kornelia Gudyś, Justyna Guzy-Wróbelska, Paweł Krajewski, Piotr Kachlicki
Determination of the role of plant secondary metabolites in stress conditions is problematic due to diversity of their structures and complexity of interdependence with different biological pathways. Correlation of the metabolomic data with the genetic background provides essential information on the features of metabolites. LC-MS analysis of leaf metabolites from 100 barley recombinant inbred lines (RILs) revealed that 98 traits among 135 detected phenolic and terpenoid compounds significantly changed the level as a result of drought stress...
November 23, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27866706/colocalization-of-gwas-and-eqtl-signals-detects-target-genes
#14
Farhad Hormozdiari, Martijn van de Bunt, Ayellet V Segrè, Xiao Li, Jong Wha J Joo, Michael Bilow, Jae Hoon Sul, Sriram Sankararaman, Bogdan Pasaniuc, Eleazar Eskin
The vast majority of genome-wide association study (GWAS) risk loci fall in non-coding regions of the genome. One possible hypothesis is that these GWAS risk loci alter the individual's disease risk through their effect on gene expression in different tissues. In order to understand the mechanisms driving a GWAS risk locus, it is helpful to determine which gene is affected in specific tissue types. For example, the relevant gene and tissue could play a role in the disease mechanism if the same variant responsible for a GWAS locus also affects gene expression...
December 1, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27863251/genetic-drivers-of-epigenetic-and-transcriptional-variation-in-human-immune-cells
#15
Lu Chen, Bing Ge, Francesco Paolo Casale, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Ying Yan, Kousik Kundu, Simone Ecker, Avik Datta, David Richardson, Frances Burden, Daniel Mead, Alice L Mann, Jose Maria Fernandez, Sophia Rowlston, Steven P Wilder, Samantha Farrow, Xiaojian Shao, John J Lambourne, Adriana Redensek, Cornelis A Albers, Vyacheslav Amstislavskiy, Sofie Ashford, Kim Berentsen, Lorenzo Bomba, Guillaume Bourque, David Bujold, Stephan Busche, Maxime Caron, Shu-Huang Chen, Warren Cheung, Oliver Delaneau, Emmanouil T Dermitzakis, Heather Elding, Irina Colgiu, Frederik O Bagger, Paul Flicek, Ehsan Habibi, Valentina Iotchkova, Eva Janssen-Megens, Bowon Kim, Hans Lehrach, Ernesto Lowy, Amit Mandoli, Filomena Matarese, Matthew T Maurano, John A Morris, Vera Pancaldi, Farzin Pourfarzad, Karola Rehnstrom, Augusto Rendon, Thomas Risch, Nilofar Sharifi, Marie-Michelle Simon, Marc Sultan, Alfonso Valencia, Klaudia Walter, Shuang-Yin Wang, Mattia Frontini, Stylianos E Antonarakis, Laura Clarke, Marie-Laure Yaspo, Stephan Beck, Roderic Guigo, Daniel Rico, Joost H A Martens, Willem H Ouwehand, Taco W Kuijpers, Dirk S Paul, Hendrik G Stunnenberg, Oliver Stegle, Kate Downes, Tomi Pastinen, Nicole Soranzo
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14(+) monocytes, CD16(+) neutrophils, and naive CD4(+) T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies...
November 17, 2016: Cell
https://www.readbyqxmd.com/read/27858853/genome-wide-linkage-analysis-and-regional-fine-mapping-identified-variants-in-the-ryr3-gene-as-a-novel-quantitative-trait-locus-for-circulating-adiponectin-in-chinese-population
#16
Yi-Cheng Chang, Yen-Feng Chiu, Chih-Tsueng He, Wayne Huey-Herng Sheu, Ming-Wei Lin, Todd B Seto, Themistocles Assimes, Yuh-Shan Jou, Lynn Su, Wei-Jei Lee, Po-Chu Lee, Shu-Huei Tsai, Lee-Ming Chuang
Adiponectin is adipocyte-secreted cytokine with potent insulin-sensitizing action in peripheral tissues. The heritability of plasma adiponectin is high in Han Chinese population.To identify genetic loci influencing plasma adiponectin levels in Chinese population, we performed a genome-wide linkage scan in 1949 Chinese participants of the Stanford Asia-Pacific Program for Hypertension and Insulin Resistance family study and mapped a quantitative trail locus located on chromosome 15 at 31 cM (logarithm of odds = 3...
November 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27856709/association-mapping-reveals-the-genetic-architecture-of-tomato-response-to-water-deficit-focus-on-major-fruit-quality-traits
#17
Elise Albert, Vincent Segura, Justine Gricourt, Julien Bonnefoi, Laurent Derivot, Mathilde Causse
Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions...
December 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/27854153/genetic-factors-affecting-pork-quality-halothane-and-rendement-napole-genes
#18
Ramon Cesar D Salas, Claro N Mingala
The most common pork quality problems are pale, soft, and exudative (PSE) and acid pork (AP). PSE is associated with the expression of recessive halothane (Hal) allele Hal(n). Recessive Hal pigs (Hal(nn)) have defective Ca(2+) release channels (CRC) or Ryanodine Receptors (RYR1) within the sarcoplasmic reticulum that allow uncontrolled release of Ca(2+) in response to stress. Abnormal lactic acid metabolism caused by stress prior to slaughter leads to the sudden drop in postmortem muscle pH producing the PSE pork...
November 17, 2016: Animal Biotechnology
https://www.readbyqxmd.com/read/27853371/the-ncan-gene-schizophrenia-susceptibility-and-cognitive-dysfunction
#19
Peirong Wang, Jun Cai, Jianliang Ni, Jiangtao Zhang, Wei Tang, Chen Zhang
BACKGROUND: Cognitive dysfunction has been recognized as a cardinal feature of schizophrenia. Elucidating the neurobiological substrates of cognitive dysfunction in schizophrenia would help identify the underlying mechanism of this disorder. The rs1064395 single nucleotide polymorphism, within the gene encoding neurocan (NCAN), is reported to be associated with schizophrenia in European populations and may influence brain structure in patients with schizophrenia. METHODS: In this study, we aimed to explore whether NCAN rs1064395 confers some risk for schizophrenia and cognitive dysfunction in Han Chinese...
2016: Neuropsychiatric Disease and Treatment
https://www.readbyqxmd.com/read/27835950/targeted-high-throughput-sequencing-of-candidate-genes-for-chronic-obstructive-pulmonary-disease
#20
Hans Matsson, Cilla Söderhäll, Elisabet Einarsdottir, Maxime Lamontagne, Sanna Gudmundsson, Helena Backman, Anne Lindberg, Eva Rönmark, Juha Kere, Don Sin, Dirkje S Postma, Yohan Bossé, Bo Lundbäck, Joakim Klar
BACKGROUND: Reduced lung function in patients with chronic obstructive pulmonary disease (COPD) is likely due to both environmental and genetic factors. We report here a targeted high-throughput DNA sequencing approach to identify new and previously known genetic variants in a set of candidate genes for COPD. METHODS: Exons in 22 genes implicated in lung development as well as 61 genes and 10 genomic regions previously associated with COPD were sequenced using individual DNA samples from 68 cases with moderate or severe COPD and 66 controls matched for age, gender and smoking...
November 11, 2016: BMC Pulmonary Medicine
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