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Quantitative trait loci

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https://www.readbyqxmd.com/read/28449076/qtl-analysis-of-the-developmental-response-to-l-glutamate-in-arabidopsis-roots-and-its-genotype-by-environment-interactions
#1
Pia Walch-Liu, Rhonda C Meyer, Thomas Altmann, Brian G Forde
Primary root growth in Arabidopsis and a number of other species has previously been shown to be remarkably sensitive to the presence of external glutamate, with glutamate signalling eliciting major changes in root architecture. Using two recombinant inbred lines from reciprocal crosses between Arabidopsis accessions C24 and Col-0, we have identified one large-effect quantitative trait locus (QTL), GluS1, and two minor QTLs, GluS2 and GluS3, which together accounted for 41% of the phenotypic variance in glutamate sensitivity...
April 26, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28448537/mapping-of-quantitative-trait-loci-associated-with-resistance-to-net-form-net-blotch-pyrenophora-teres-f-teres-in-a-doubled-haploid-norwegian-barley-population
#2
Ronja Wonneberger, Andrea Ficke, Morten Lillemo
Barley net blotch caused by the necrotrophic fungus Pyrenophora teres is a major barley disease in Norway. It can cause grain shriveling and yield losses, and resistance in currently grown cultivars is insufficient. In this study, a set of 589 polymorphic SNP markers was used to map resistance loci in a population of 109 doubled haploid lines from a cross between the closely related Norwegian cultivars Arve (moderately susceptible) and Lavrans (moderately resistant). Resistance to three net form net blotch (P...
2017: PloS One
https://www.readbyqxmd.com/read/28445652/identification-of-quantitative-trait-loci-underlying-seed-protein-content-of-soybean-including-main-epistatic-and-qtl-%C3%A3-environment-effects-in-different-regions-of-northeast-china
#3
Weili Teng, Wen Li, Q I Zhang, Depeng Wu, Xue Zhao, Haiyan Li, Yingpeng Han, Wenbin Li
The objective here was to identify QTL, their epistatic effects and QTLs x environments interaction underlying soybean protein content (PC). The mapping population, consisted of 129 recombinant inbred lines (RILs), was created by crossing 'Dongnong46' and 'L-100'. Phenotypic data of the parents and RILs were collected for four years in three locations of Heilongjiang Province of China. A total of 213 simple sequence repeat markers were used to construct a genetic linkage map. Eight QTLs, located on seven chromosomes (Chr), were identified to be associated with PC among the ten tested environments...
April 26, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28444412/biochemical-and-genetic-analyses-of-n-metabolism-in-maize-testcross-seedlings-1-leaves
#4
Ignacio Trucillo Silva, Hari Kishan R Abbaraju, Lynne P Fallis, Hongjun Liu, Michael Lee, Kanwarpal S Dhugga
Aside from the identification of 32 QTL for N metabolism in the seedling leaves of a maize testcross population, alanine aminotransferase was found to be a central enzyme in N assimilation. Excessive application of nitrogen (N) fertilizer to grow commercial crops like maize is a cause of concern because of the runoff of excess N into streams and rivers. Breeding maize with improved N use efficiency (NUE) would reduce environmental pollution as well as input costs for the farmers. An understanding of the genetics underlying N metabolism is key to breeding for NUE...
April 25, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28442482/a-bag3-coding-variant-in-mice-determines-susceptibility-to-ischemic-limb-muscle-myopathy-by-directing-autophagy
#5
Joseph M McClung, Timothy J McCord, Terence E Ryan, Cameron A Schmidt, Thomas D Green, Kevin W Southerland, Jessica L Reinardy, Sarah B Mueller, Talaignair N Venkatraman, Christopher D Lascola, Sehoon Keum, Douglas A Marchuk, Espen E Spangenburg, Ayotunde O Dokun, Brian H Annex, Christopher D Kontos
Background -Critical limb ischemia (CLI) is a manifestation of peripheral artery disease (PAD) that carries significant mortality and morbidity risk in humans, although its genetic determinants remain largely unknown. We previously discovered two overlapping quantitative trait loci (QTL) in mice, Lsq-1 and Civq-1, that affected limb muscle survival and stroke volume following femoral artery or middle cerebral artery ligation, respectively. Here we report that a Bag3 variant (Ile81Met) segregates with tissue protection from hindlimb ischemia (HLI)...
April 25, 2017: Circulation
https://www.readbyqxmd.com/read/28442423/slc6a1-gene-involvement-in-susceptibility-to-attention-deficit-hyperactivity-disorder-a-case-control-study-and-gene-environment-interaction
#6
Fang-Fen Yuan, Xue Gu, Xin Huang, Yan Zhong, Jing Wu
Attention-deficit/hyperactivity disorder (ADHD) is an early onset childhood neurodevelopmental disorder with an estimated heritability of approximately 76%. We conducted a case-control study to explore the role of the SLC6A1 gene in ADHD. The genotypes of eight variants were determined using Sequenom MassARRAY technology. The participants in the study were 302 children with ADHD and 411 controls. ADHD symptoms were assessed using the Conners Parent Symptom Questionnaire. In our study, rs2944366 was consistently shown to be associated with the ADHD risk in the dominant model (odds ratio [OR]=0...
April 22, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28441456/genome-wide-association-study-of-facial-morphology-reveals-novel-associations-with-frem1-and-park2
#7
Myoung Keun Lee, John R Shaffer, Elizabeth J Leslie, Ekaterina Orlova, Jenna C Carlson, Eleanor Feingold, Mary L Marazita, Seth M Weinberg
Several studies have now shown evidence of association between common genetic variants and quantitative facial traits in humans. The reported associations generally involve simple univariate measures and likely represent only a small fraction of the genetic loci influencing facial morphology. In this study, we applied factor analysis to a set of 276 facial linear distances derived from 3D facial surface images of 2187 unrelated individuals of European ancestry. We retained 23 facial factors, which we then tested for genetic associations using a genome-wide panel of 10,677,593 single nucleotide polymorphisms (SNPs)...
2017: PloS One
https://www.readbyqxmd.com/read/28441029/variable-susceptibility-to-cigarette-smoke-induced-emphysema-in-34-inbred-strains-of-mice-implicates-abi3bp-in-emphysema-susceptibility
#8
Josiah E Radder, Alyssa D Gregory, Adriana S Leme, Michael H Cho, Yanxia Chu, Neil J Kelly, Per Bakke, Amund Gulsvik, Augusto A Litonjua, David Sparrow, Terri H Beaty, James D Crapo, Edwin K Silverman, Yingze Zhang, Annerose Berndt, Steven D Shapiro
RATIONALE: Chronic obstructive pulmonary disease (COPD) is caused by a complex interaction of environmental exposures, most commonly cigarette smoke, and genetic factors. Chronic cigarette smoke exposure in the mouse is a commonly used animal model of COPD. We aimed to expand our knowledge of the variable susceptibility of inbred strains to this model and test for genetic variants associated with this trait. OBJECTIVE: To measure differential susceptibility to cigarette smoke-induced emphysema in the mouse, identify genetic loci associated with this quantitative trait, and find homologous human genes associated with COPD...
April 25, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28437453/three-dominant-awnless-genes-in-common-wheat-fine-mapping-interaction-and-contribution-to-diversity-in-awn-shape-and-length
#9
Motohiro Yoshioka, Julio C M Iehisa, Ryoko Ohno, Tatsuro Kimura, Hiroyuki Enoki, Satoru Nishimura, Shuhei Nasuda, Shigeo Takumi
The awn is a long needle-like structure formed at the tip of the lemma in the florets of some grass species. It plays a role in seed dispersal and protection against animals, and can contribute to the photosynthetic activity of spikes. Three main dominant inhibitors of awn development (Hd, B1 and B2) are known in hexaploid wheat, but the causal genes have not been cloned yet and a genetic association with awn length diversity has been found only for the B1 allele. To analyze the prevalence of these three awning inhibitors, we attempted to predict the genotypes of 189 hexaploid wheat varieties collected worldwide using markers tightly linked to these loci...
2017: PloS One
https://www.readbyqxmd.com/read/28430897/genetic-variants-associated-with-the-root-system-architecture-of-oilseed-rape-brassica-napus-l-under-contrasting-phosphate-supply
#10
Xiaohua Wang, Yanling Chen, Catherine L Thomas, Guangda Ding, Ping Xu, Dexu Shi, Fabian Grandke, Kemo Jin, Hongmei Cai, Fangsen Xu, Bin Yi, Martin R Broadley, Lei Shi
Breeding crops with ideal root system architecture for efficient absorption of phosphorus is an important strategy to reduce the use of phosphate fertilizers. To investigate genetic variants leading to changes in root system architecture, 405 oilseed rape cultivars were genotyped with a 60K Brassica Infinium SNP array in low and high P environments. A total of 285 single-nucleotide polymorphisms were associated with root system architecture traits at varying phosphorus levels. Nine single-nucleotide polymorphisms corroborate a previous linkage analysis of root system architecture quantitative trait loci in the BnaTNDH population...
April 19, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28429576/suppression-of-osmads7-in-rice-endosperm-stabilizes-amylose-content-under-high-temperature-stress
#11
Hua Zhang, Heng Xu, Mengjie Feng, Ying Zhu
High temperature significantly alters the amylose content of rice, resulting in mature grains with poor eating quality. However, only few genes and/or quantitative trait loci (QTLs) involved in this process have been isolated and the molecular mechanisms of this effect remain unclear. Here, we describe a floral organ identity gene, OsMADS7, involved in stabilizing rice amylose content at high temperature. OsMADS7 is greatly induced by high temperature at the early filling stage. Constitutive suppression of OsMADS7 stabilizes amylose content under high temperature stress but results in low spikelet fertility...
April 20, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28429084/rs4878104-contributes-to-alzheimer-s-disease-risk-and-regulates-dapk1-gene-expression
#12
Yang Hu, Liang Cheng, Ying Zhang, Weiyang Bai, Wenyang Zhou, Tao Wang, Zhifa Han, Jian Zong, Shuilin Jin, Jun Zhang, Qinghua Jiang, Guiyou Liu
In 2006, a candidate gene study reported death-associated protein kinase 1 (DAPK1) rs4878104 variant to be significantly associated with Alzheimer's disease (AD) risk. However, the following studies showed inconsistent association results. Here, we conducted an updated analysis to investigate the potential association between rs4878104 and AD using a total of 60,751 samples (20,161 AD cases and 40,590 controls). In the pooled population, the results based on the allele and genotype genetic models show that rs4878104 variant is not significantly associated with AD risk...
April 20, 2017: Neurological Sciences
https://www.readbyqxmd.com/read/28428791/genome-wide-association-study-for-pre-harvest-sprouting-resistance-in-a-large-germplasm-collection-of-chinese-wheat-landraces
#13
Yong Zhou, Hao Tang, Meng-Ping Cheng, Kwame O Dankwa, Zhong-Xu Chen, Zhan-Yi Li, Shang Gao, Ya-Xi Liu, Qian-Tao Jiang, Xiu-Jin Lan, Zhi-En Pu, Yu-Ming Wei, You-Liang Zheng, Lee T Hickey, Ji-Rui Wang
Pre-harvest sprouting (PHS) is mainly caused by the breaking of seed dormancy in high rainfall regions, which leads to huge economic losses in wheat. In this study, we evaluated 717 Chinese wheat landraces for PHS resistance and carried out genome-wide association studies (GWAS) using to 9,740 DArT-seq and 178,803 SNP markers. Landraces were grown across six environments in China and germination testing of harvest-ripe grain was used to calculate the germination rate (GR) for each accession at each site. GR was highly correlated across all environments...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28427326/no-evidence-for-strong-cytonuclear-conflict-over-sex-allocation-in-a-simultaneously-hermaphroditic-flatworm
#14
Nikolas Vellnow, Dita B Vizoso, Gudrun Viktorin, Lukas Schärer
BACKGROUND: Cytoplasmic sex allocation distorters, which arise from cytonuclear conflict over the optimal investment into male versus female reproductive function, are some of the best-researched examples for genomic conflict. Among hermaphrodites, many such distorters have been found in plants, while, to our knowledge, none have been clearly documented in animals. METHODS: Here we provide a quantitative test for cytonuclear conflict over sex allocation in the simultaneously hermaphroditic flatworm Macrostomum lignano...
April 20, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28427324/genomic-prediction-from-observed-and-imputed-high-density-ovine-genotypes
#15
Nasir Moghaddar, Andrew A Swan, Julius H J van der Werf
BACKGROUND: Genomic prediction using high-density (HD) marker genotypes is expected to lead to higher prediction accuracy, particularly for more heterogeneous multi-breed and crossbred populations such as those in sheep and beef cattle, due to providing stronger linkage disequilibrium between single nucleotide polymorphisms and quantitative trait loci controlling a trait. The objective of this study was to evaluate a possible improvement in genomic prediction accuracy of production traits in Australian sheep breeds based on HD genotypes (600k, both observed and imputed) compared to prediction based on 50k marker genotypes...
April 20, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28427323/detection-of-qtl-for-traits-related-to-adaptation-to-sub-optimal-climatic-conditions-in-chickens
#16
Ching-Yi Lien, Michèle Tixier-Boichard, Shih-Wen Wu, Woei-Fuh Wang, Chen Siang Ng, Chih-Feng Chen
BACKGROUND: Growth traits can be used as indicators of adaptation to sub-optimal conditions. The current study aimed at identifying quantitative trait loci (QTL) that control performance under variable temperature conditions in chickens. METHODS: An F2 population was produced by crossing the Taiwan Country chicken L2 line (selected for body weight, comb area, and egg production) with an experimental line of Rhode Island Red layer R- (selected for low residual feed consumption)...
April 20, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28425976/prenatal-exposure-to-a-maternal-high-fat-diet-affects-histone-modification-of-cardiometabolic-genes-in-newborn-rats
#17
Bijaya Upadhyaya, Tricia Larsen, Shivon Barwari, Eli J Louwagie, Michelle L Baack, Moul Dey
Infants born to women with diabetes or obesity are exposed to excess circulating fuels during fetal heart development and are at higher risk of cardiac diseases. We have previously shown that late-gestation diabetes, especially in conjunction with a maternal high-fat (HF) diet, impairs cardiac functions in rat-offspring. This study investigated changes in genome-wide histone modifications in newborn hearts from rat-pups exposed to maternal diabetes and HF-diet. Chromatin-immunoprecipitation-sequencing revealed a differential peak distribution on gene promoters in exposed pups with respect to acetylation of lysines 9 and 14 and to trimethylation of lysines 4 and 27 in histone H3 (all, false discovery rate, FDR < 0...
April 20, 2017: Nutrients
https://www.readbyqxmd.com/read/28424719/comparative-analysis-of-root-traits-and-the-associated-qtls-for-maize-seedlings-grown-in-paper-roll-hydroponics-and-vermiculite-culture-system
#18
Zhigang Liu, Kun Gao, Shengchen Shan, Riling Gu, Zhangkui Wang, Eric J Craft, Guohua Mi, Lixing Yuan, Fanjun Chen
Root system architecture (RSA) plays an important role in the acquisition of both nitrogen (N) and phosphorus (P) from the environment. Currently RSA is rarely considered as criteria for selection to improve nutrient uptake efficiency in crop breeding. Under field conditions roots can be greatly influenced by uncontrolled environment factors. Therefore, it is necessary to develop fast selection methods for evaluating root traits of young seedlings in the lab which can then be related to high nutrient efficiency of adult plants in the field...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28424372/effects-of-drought-stress-on-global-gene-expression-profile-in-leaf-and-root-samples-of-dongxiang-wild-rice-oryza-rufipogon
#19
Fantao Zhang, Yi Zhou, Meng Zhang, Xiangdong Luo, Jiankun Xie
Drought is a serious constraint to rice production throughout the world, and although Dongxiang wild rice ( Oryza rufipogon , DXWR) possesses a high degree of drought resistance, the underlying mechanisms of this trait remains unclear. In the present study, cDNA libraries were constructed from the leaf and root tissues of drought-stressed and untreated DXWR seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in drought stress response. The results indicated that 11,231 transcripts were differentially expressed in the leaves (4,040 up-regulated and 7,191 down-regulated) and 7,025 transcripts were differentially expressed in the roots (3,097 up-regulated and 3,928 down-regulated)...
April 19, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28424047/deciphering-mechanisms-underlying-the-genetic-variation-of-general-production-and-liver-quality-traits-in-the-overfed-mule-duck-by-pqtl-analyses
#20
Yoannah François, Alain Vignal, Caroline Molette, Nathalie Marty-Gasset, Stéphane Davail, Laurence Liaubet, Christel Marie-Etancelin
BACKGROUND: The aim of this study was to analyse the mechanisms that underlie phenotypic quantitative trait loci (QTL) in overfed mule ducks by identifying co-localized proteomic QTL (pQTL). The QTL design consisted of three families of common ducks that were progeny-tested by using 294 male mule ducks. This population of common ducks was genotyped using a genetic map that included 334 genetic markers located across 28 APL chromosomes (APL for Anas platyrhynchos). Mule ducks were phenotyped for 49 traits related to growth, metabolism, overfeeding ability and meat and fatty liver quality, and 326 soluble fatty liver proteins were quantified...
April 19, 2017: Genetics, Selection, Evolution: GSE
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