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Quantitative trait loci

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https://www.readbyqxmd.com/read/28913655/quantitative-trait-loci-for-resistance-to-stripe-rust-of-wheat-revealed-using-global-field-nurseries-and-opportunities-for-stacking-resistance-genes
#1
Firdissa E Bokore, Richard D Cuthbert, Ron E Knox, Harpinder S Randhawa, Colin W Hiebert, Ron M DePauw, Asheesh K Singh, Arti Singh, Andrew G Sharpe, Amidou N'Diaye, Curtis J Pozniak, Curt McCartney, Yuefeng Ruan, Samia Berraies, Brad Meyer, Catherine Munro, Andy Hay, Karim Ammar, Julio Huerta-Espino, Sridhar Bhavani
Quantitative trait loci controlling stripe rust resistance were identified in adapted Canadian spring wheat cultivars providing opportunity for breeders to stack loci using marker-assisted breeding. Stripe rust or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is a devastating disease of common wheat (Triticum aestivum L.) in many regions of the world. The objectives of this research were to identify and map quantitative trait loci (QTL) associated with stripe rust resistance in adapted Canadian spring wheat cultivars that are effective globally, and investigate opportunities for stacking resistance...
September 14, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28913578/loci-on-chromosomes-1a-and-2a-affect-resistance-to-tan-yellow-spot-in-wheat-populations-not-segregating-for-tsn1
#2
Manisha Shankar, Dorthe Jorgensen, Julian Taylor, Ken J Chalmers, Rebecca Fox, Grant J Hollaway, Stephen M Neate, Mark S McLean, Elysia Vassos, Hossein Golzar, Robert Loughman, Diane E Mather
QTL for tan spot resistance were mapped on wheat chromosomes 1A and 2A. Lines were developed with resistance alleles at these loci and at the tsn1 locus on chromosome 5B. These lines expressed significantly higher resistance than the parent with tsn1 only. Tan spot (syn. yellow spot and yellow leaf spot) caused by Pyrenophora tritici-repentis is an important foliar disease of wheat in Australia. Few resistance genes have been mapped in Australian germplasm and only one, known as tsn1 located on chromosome 5B, is known in Australian breeding programs...
September 14, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28912790/development-and-evaluation-of-glycine-max-germplasm-lines-with-quantitative-resistance-to-sclerotinia-sclerotiorum
#3
Megan McCaghey, Jaime Willbur, Ashish Ranjan, Craig R Grau, Scott Chapman, Brian Diers, Carol Groves, Mehdi Kabbage, Damon L Smith
Sclerotinia sclerotiorum, the causal agent of Sclerotinia stem rot, is a devastating fungal pathogen of soybean that can cause significant yield losses to growers when environmental conditions are favorable for the disease. The development of resistant varieties has proven difficult. However, poor resistance in commercial cultivars can be improved through additional breeding efforts and understanding the genetic basis of resistance. The objective of this project was to develop soybean germplasm lines that have a high level of Sclerotinia stem rot resistance to be used directly as cultivars or in breeding programs as a source of improved Sclerotinia stem rot resistance...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28911167/in-utero-exposure-to-a-high-fat-diet-programs-hepatic-hypermethylation-and-gene-dysregulation-and-development-of-metabolic-syndrome-in-male-mice
#4
Yoshinori Seki, Masako Suzuki, Xingyi Guo, Alan Scott Glenn, Patricia M Vuguin, Ariana Fiallo, Quan Du, Yi-An Ko, Yiting Yu, Katalin Susztak, Deyou Zheng, John M Greally, Ellen B Katz, Maureen J Charron
Exposure to a high-fat (HF) diet in utero is associated with increased incidence of cardiovascular disease, diabetes, and metabolic syndrome later in life. However, the molecular basis of this enhanced susceptibility for metabolic disease is poorly understood. Gene expression microarray and genome-wide DNA methylation analyses of mouse liver revealed that exposure to a maternal HF milieu activated genes of immune response, inflammation, and hepatic dysfunction. DNA methylation analysis revealed 3360 differentially methylated loci, most of which (76%) were hypermethylated and distributed preferentially to hotspots on chromosomes 4 [atherosclerosis susceptibility quantitative trait loci (QTLs) 1] and 18 (insulin-dependent susceptibility QTLs 21)...
September 1, 2017: Endocrinology
https://www.readbyqxmd.com/read/28911016/quantifying-rooting-at-depth-in-a-wheat-doubled-haploid-population-with-introgression-from-wild-emmer
#5
Christina K Clarke, Peter J Gregory, Martin Lukac, Amanda J Burridge, Alexandra M Allen, Keith J Edwards, Mike J Gooding
Background and Aims: The genetic basis of increased rooting below the plough layer, post-anthesis in the field, of an elite wheat line (Triticum aestivum 'Shamrock') with recent introgression from wild emmer (T. dicoccoides), is investigated. Shamrock has a non-glaucous canopy phenotype mapped to the short arm of chromosome 2B (2BS), derived from the wild emmer. A secondary aim was to determine whether genetic effects found in the field could have been predicted by other assessment methods...
September 1, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28900432/assessing-and-exploiting-functional-diversity-in-germplasm-pools-to-enhance-abiotic-stress-adaptation-and-yield-in-cereals-and-food-legumes
#6
REVIEW
Sangam L Dwivedi, Armin Scheben, David Edwards, Charles Spillane, Rodomiro Ortiz
There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28899996/prediction-and-subtyping-of-hypertension-from-pan-tissue-transcriptomic-and-genetic-analyses
#7
Mahashweta Basu, Mahfuza Sharmin, Avinash Das, Nishanth Ulhas Nair, Kun Wang, Joo Sang Lee, Yen-Pei Christy Chang, Eytan Ruppin, Sridhar Hannenhalli
Hypertension is a complex systemic disease involving transcriptional changes in multiple organs. Here we systematically investigate the pan-tissue transcriptional and genetic landscape of hypertension spanning dozens of tissues in hundreds of individuals. We find that in several tissues previously identified hypertension-linked genes are dysregulated and the gene expression profile is predictive of hypertension. Importantly, many expression quantitative trait loci (eQTL) SNPs associated with the population variance of the dysregulated genes are linked with blood pressure in an independent genome-wide association study, suggesting that the functional effect of hypertension-associated SNPs may be mediated through tissue-specific transcriptional dysregulation...
September 12, 2017: Genetics
https://www.readbyqxmd.com/read/28894906/whole-exome-sequencing-reveals-a-functional-mutation-in-the-gain-domain-of-the-bai2-receptor-underlying-a-forward-mutagenesis-hyperactivity-qtl
#8
David J Speca, James S Trimmer, Andrew S Peterson, Elva Díaz
The identification of novel genes underlying complex mouse behavioral traits remains an important step in understanding normal brain function and its dysfunction in mental health disorders. To identify dominant mutations that influence locomotor activity, we performed a mouse N-ethyl-N-nitrosourea (ENU) forward mutagenesis screen and mapped several loci as quantitative traits. Here we describe the fine-mapping and positional cloning of a hyperactivity locus mapped to the medial portion of mouse chromosome four...
September 12, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28892072/neuregulin-signaling-pathway-in-smoking-behavior
#9
R Gupta, B Qaiser, L He, T S Hiekkalinna, A B Zheutlin, S Therman, M Ollikainen, S Ripatti, M Perola, V Salomaa, L Milani, T D Cannon, P A F Madden, T Korhonen, J Kaprio, A Loukola
Understanding molecular processes that link comorbid traits such as addictions and mental disorders can provide novel therapeutic targets. Neuregulin signaling pathway (NSP) has previously been implicated in schizophrenia, a neurodevelopmental disorder with high comorbidity to smoking. Using a Finnish twin family sample, we have previously detected association between nicotine dependence and ERBB4 (a neuregulin receptor), and linkage for smoking initiation at the ERBB4 locus on 2q33. Further, Neuregulin3 has recently been shown to associate with nicotine withdrawal in a behavioral mouse model...
August 22, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28892059/a-meta-analysis-of-genome-wide-association-studies-identifies-17-new-parkinson-s-disease-risk-loci
#10
Diana Chang, Mike A Nalls, Ingileif B Hallgrímsdóttir, Julie Hunkapiller, Marcel van der Brug, Fang Cai, Geoffrey A Kerchner, Gai Ayalon, Baris Bingol, Morgan Sheng, David Hinds, Timothy W Behrens, Andrew B Singleton, Tushar R Bhangale, Robert R Graham
Common variant genome-wide association studies (GWASs) have, to date, identified >24 risk loci for Parkinson's disease (PD). To discover additional loci, we carried out a GWAS comparing 6,476 PD cases with 302,042 controls, followed by a meta-analysis with a recent study of over 13,000 PD cases and 95,000 controls at 9,830 overlapping variants. We then tested 35 loci (P < 1 × 10(-6)) in a replication cohort of 5,851 cases and 5,866 controls. We identified 17 novel risk loci (P < 5 × 10(-8)) in a joint analysis of 26,035 cases and 403,190 controls...
September 11, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28887804/identification-of-major-quantitative-trait-loci-for-root-diameter-in-synthetic-hexaploid-wheat-under-phosphorus-deficient-conditions
#11
Fangkun Wu, Xilan Yang, Zhiqiang Wang, Mei Deng, Jian Ma, Guoyue Chen, Yuming Wei, Yaxi Liu
Synthetic hexaploid wheat (SHW) possesses numerous genes for resistance to stress, including phosphorus (P) deficiency. Root diameter (RDM) plays an important role in P-deficiency tolerance, but information related to SHW is still limited. Thus, the objective of this study was to investigate the genetic architecture of RDM in SHW under P-deficient conditions. To this end, we measured the RDM of 138 F9 recombinant inbred lines derived from an F2 population of a synthetic hexaploid wheat line (SHW-L1) and a common wheat line (Chuanmai32) under two P conditions, P sufficiency (PS) and P deficiency (PD), and mapped quantitative trait loci (QTL) for RDM using an enriched high-density genetic map, containing 120,370 single nucleotide polymorphisms, 733 diversity arrays technology markers, and 119 simple sequence repeats...
September 8, 2017: Journal of Applied Genetics
https://www.readbyqxmd.com/read/28887586/increased-genomic-prediction-accuracy-in-wheat-breeding-using-a-large-australian-panel
#12
Adam Norman, Julian Taylor, Emi Tanaka, Paul Telfer, James Edwards, Jean-Pierre Martinant, Haydn Kuchel
Genomic prediction accuracy within a large panel was found to be substantially higher than that previously observed in smaller populations, and also higher than QTL-based prediction. In recent years, genomic selection for wheat breeding has been widely studied, but this has typically been restricted to population sizes under 1000 individuals. To assess its efficacy in germplasm representative of commercial breeding programmes, we used a panel of 10,375 Australian wheat breeding lines to investigate the accuracy of genomic prediction for grain yield, physical grain quality and other physiological traits...
September 8, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28886448/exploring-hepsin-functional-genetic-variation-association-with-disease-specific-protein-expression-in-bipolar-disorder-applications-of-a-proteomic-informed-genomic-approach
#13
Malik Nassan, Yun-Fang Jia, Greg Jenkins, Colin Colby, Scott Feeder, Doo-Sup Choi, Marin Veldic, Susan L McElroy, David J Bond, Richard Weinshilboum, Joanna M Biernacka, Mark A Frye
In a prior discovery study, increased levels of serum Growth Differentiation Factor 15 (GDF15), Hepsin (HPN), and Matrix Metalloproteinase-7 (MMP7) were observed in bipolar depressed patients vs controls. This exploratory post-hoc analysis applied a proteomic-informed genomic research strategy to study the potential functional role of these proteins in bipolar disorder (BP). Utilizing the Genotype-Tissue Expression (GTEx) database to identify cis-acting blood expression quantitative trait loci (cis-eQTLs), five eQTL variants from the HPN gene were analyzed for association with BP cases using genotype data of cases from the discovery study (n = 58) versus healthy controls (n = 777)...
July 4, 2017: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/28885228/genetic-and-transcriptomic-bases-of-intestinal-epithelial-barrier-dysfunction-in-inflammatory-bowel-disease
#14
Maaike Vancamelbeke, Tim Vanuytsel, Ricard Farré, Sare Verstockt, Marc Ferrante, Gert Van Assche, Paul Rutgeerts, Frans Schuit, Séverine Vermeire, Ingrid Arijs, Isabelle Cleynen
BACKGROUND: Intestinal barrier defects are common in patients with inflammatory bowel disease (IBD). To identify which components could underlie these changes, we performed an in-depth analysis of epithelial barrier genes in IBD. METHODS: A set of 128 intestinal barrier genes was selected. Polygenic risk scores were generated based on selected barrier gene variants that were associated with Crohn's disease (CD) or ulcerative colitis (UC) in our study. Gene expression was analyzed using microarray and quantitative reverse transcription polymerase chain reaction...
September 6, 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28883458/genetic-correlations-reveal-the-shared-genetic-architecture-of-transcription-in-human-peripheral-blood
#15
Samuel W Lukowski, Luke R Lloyd-Jones, Alexander Holloway, Holger Kirsten, Gibran Hemani, Jian Yang, Kerrin Small, Jing Zhao, Andres Metspalu, Emmanouil T Dermitzakis, Greg Gibson, Timothy D Spector, Joachim Thiery, Markus Scholz, Grant W Montgomery, Tonu Esko, Peter M Visscher, Joseph E Powell
Transcript co-expression is regulated by a combination of shared genetic and environmental factors. Here, we estimate the proportion of co-expression that is due to shared genetic variance. To do so, we estimated the genetic correlations between each pairwise combination of 2469 transcripts that are highly heritable and expressed in whole blood in 1748 unrelated individuals of European ancestry. We identify 556 pairs with a significant genetic correlation of which 77% are located on different chromosomes, and report 934 expression quantitative trait loci, identified in an independent cohort, with significant effects on both transcripts in a genetically correlated pair...
September 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/28882987/reply-to-hu-et-al-on-the-interpretation-of-gasdermin-b-expression-quantitative-trait-loci-data
#16
Lipika R Pal, Kinlin L Chao, John Moult, Osnat Herzberg
No abstract text is available yet for this article.
September 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28881962/applying-meta-analysis-to-genotype-tissue-expression-data-from-multiple-tissues-to-identify-eqtls-and-increase-the-number-of-egenes
#17
Dat Duong, Lisa Gai, Sagi Snir, Eun Yong Kang, Buhm Han, Jae Hoon Sul, Eleazar Eskin
Motivation: There is recent interest in using gene expression data to contextualize findings from traditional genome-wide association studies (GWAS). Conditioned on a tissue, expression quantitative trait loci (eQTLs) are genetic variants associated with gene expression, and eGenes are genes whose expression levels are associated with genetic variants. eQTLs and eGenes provide great supporting evidence for GWAS hits and important insights into the regulatory pathways involved in many diseases...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28880898/qtl-mapping-of-selenium-content-using-a-ril-population-in-wheat
#18
Pei Wang, Huinan Wang, Qing Liu, Xia Tian, Yanxi Shi, Xiaocun Zhang
Selenium (Se) is an essential trace element that plays various roles in human health. Understanding the genetic control of Se content and quantitative trait loci (QTL) mapping provide a basis for Se biofortification of wheat to enhance grain Se content. In the present study, a set of recombinant inbred lines (RILs) derived from two Chinese winter wheat varieties (Tainong18 and Linmai6) was used to detect QTLs for Se content in hydroponic and field trials. In total, 16 QTLs for six Se content-related traits were detected on eight chromosomes, 1B, 2B, 4B, 5A, 5B, 5D, 6A, and 7D...
2017: PloS One
https://www.readbyqxmd.com/read/28878784/quantitative-disease-resistance-under-elevated-temperature-genetic-basis-of-new-resistance-mechanisms-to-ralstonia-solanacearum
#19
Nathalie Aoun, Laetitia Tauleigne, Fabien Lonjon, Laurent Deslandes, Fabienne Vailleau, Fabrice Roux, Richard Berthomé
In the context of climate warming, plants will be facing an increased risk of epidemics as well as the emergence of new highly aggressive pathogen species. Although a permanent increase of temperature strongly affects plant immunity, the underlying molecular mechanisms involved are still poorly characterized. In this study, we aimed to uncover the genetic bases of resistance mechanisms that are efficient at elevated temperature to the Ralstonia solanacearum species complex (RSSC), one of the most harmful phytobacteria causing bacterial wilt...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28878296/genetic-variants-in-ercc1-and-xpc-predict-survival-outcome-of-non-small-cell-lung-cancer-patients-treated-with-platinum-based-therapy
#20
Ruoxin Zhang, Ming Jia, Huijing Xue, Yuan Xu, Mengyun Wang, Meiling Zhu, Menghong Sun, Jianhua Chang, Qingyi Wei
Nucleotide excision repair (NER) plays a vital role in platinum-induced DNA damage during chemotherapy. We hypothesize that regulatory single nucleotide polymorphisms (rSNPs) of the core NER genes modulate clinical outcome of patients with advanced non-small cell lung cancer (NSCLC) treated with platinum-based chemotherapy (PBS). We investigated associations of 25 rSNPs in eight NER genes with progression free survival (PFS) and overall survival (OS) in 710 NSCLC patients. We found that ERCC1 rs3212924 AG/GG and XPC rs2229090 GC/CC genotypes were associated with patients' PFS (HRadj = 1...
September 6, 2017: Scientific Reports
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