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Quantitative trait loci

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https://www.readbyqxmd.com/read/28213629/transcriptome-based-snp-discovery-by-gbs-and-the-construction-of-a-genetic-map-for-olive
#1
Ahmet İpek, Meryem İpek, Sezai Ercişli, Nesrin Aktepe Tangu
Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique...
February 18, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28213390/epigenetic-patterns-in-blood-associated-with-lipid-traits-predict-incident-coronary-heart-disease-events-and-are-enriched-for-results-from-genome-wide-association-studies
#2
Åsa K Hedman, Michael M Mendelson, Riccardo E Marioni, Stefan Gustafsson, Roby Joehanes, Marguerite R Irvin, Degui Zhi, Johanna K Sandling, Chen Yao, Chunyu Liu, Liming Liang, Tianxiao Huan, Allan F McRae, Serkalem Demissie, Sonia Shah, John M Starr, L Adrienne Cupples, Panos Deloukas, Timothy D Spector, Johan Sundström, Ronald M Krauss, Donna K Arnett, Ian J Deary, Lars Lind, Daniel Levy, Erik Ingelsson
BACKGROUND: Genome-wide association studies have identified loci influencing circulating lipid concentrations in humans; further information on novel contributing genes, pathways, and biology may be gained through studies of epigenetic modifications. METHODS AND RESULTS: To identify epigenetic changes associated with lipid concentrations, we assayed genome-wide DNA methylation at cytosine-guanine dinucleotides (CpGs) in whole blood from 2306 individuals from 2 population-based cohorts, with replication of findings in 2025 additional individuals...
January 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28211582/what-can-genome-wide-association-studies-tell-us-about-the-evolutionary-forces-maintaining-genetic-variation-for-quantitative-traits
#3
REVIEW
Emily B Josephs, John R Stinchcombe, Stephen I Wright
I. II. III. IV. V. References SUMMARY: Understanding the evolutionary forces that shape genetic variation within species has long been a goal of evolutionary biology. Integrating data for the genetic architecture of traits from genome-wide association mapping studies (GWAS) along with the development of new population genetic methods for identifying selection in sequence data may allow us to evaluate the roles of mutation-selection balance and balancing selection in shaping genetic variation at various scales...
February 17, 2017: New Phytologist
https://www.readbyqxmd.com/read/28202015/variant-discovery-in-the-sheep-milk-transcriptome-using-rna-sequencing
#4
Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser-Klopp, Juan José Arranz
BACKGROUND: The identification of genetic variation underlying desired phenotypes is one of the main challenges of current livestock genetic research. High-throughput transcriptome sequencing (RNA-Seq) offers new opportunities for the detection of transcriptome variants (SNPs and short indels) in different tissues and species. In this study, we used RNA-Seq on Milk Sheep Somatic Cells (MSCs) with the goal of characterizing the genetic variation within the coding regions of the milk transcriptome in Churra and Assaf sheep, two common dairy sheep breeds farmed in Spain...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28199342/meta-qtl-for-resistance-to-white-mold-in-common-bean
#5
Renato C C Vasconcellos, O Blessing Oraguzie, Alvaro Soler, Haidar Arkwazee, James R Myers, Juan J Ferreira, Qijian Song, Phil McClean, Phillip N Miklas
White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a major disease that limits common bean production and quality worldwide. The host-pathogen interaction is complex, with partial resistance in the host inherited as a quantitative trait with low to moderate heritability. Our objective was to identify meta-QTL conditioning partial resistance to white mold from individual QTL identified across multiple populations and environments. The physical positions for 37 individual QTL were identified across 14 recombinant inbred bi-parental populations (six new, three re-genotyped, and five from the literature)...
2017: PloS One
https://www.readbyqxmd.com/read/28198669/ulfasqtl-an-ultra-fast-method-of-composite-splicing-qtl-analysis
#6
Qian Yang, Yue Hu, Jun Li, Xuegong Zhang
BACKGROUND: Alternative splicing plays important roles in many regulatory processes and diseases in human. Many genetic variants contribute to phenotypic differences in gene expression and splicing that determine variations in human traits. Detecting genetic variants that affect splicing phenotypes is essential for understanding the functional impact of genetic variations on alternative splicing. For many situations, the key phenotype is the relative splicing ratios of alternative isoforms rather than the expression values of individual isoforms...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28197153/genetic-dissection-of-novel-qtls-for-resistance-to-leaf-spots-and-tomato-spotted-wilt-virus-in-peanut-arachis-hypogaea-l
#7
Manish K Pandey, Hui Wang, Pawan Khera, Manish K Vishwakarma, Sandip M Kale, Albert K Culbreath, C Corley Holbrook, Xingjun Wang, Rajeev K Varshney, Baozhu Guo
Peanut is an important crop, economically and nutritiously, but high production cost is a serious challenge to peanut farmers as exemplified by chemical spray to control foliar diseases such as leaf spots and thrips, the vectors of tomato spotted wilt virus (TSWV). The objective of this research was to map the quantitative trait loci (QTLs) for resistance to leaf spots and TSWV in one recombinant inbred line (RIL) mapping population of "Tifrunner × GT-C20" for identification of linked markers for marker-assisted breeding...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28196526/the-genetic-architecture-of-low-temperature-adaptation-in-the-wine-yeast-saccharomyces-cerevisiae
#8
Estéfani García-Ríos, Miguel Morard, Leopold Parts, Gianni Liti, José M Guillamón
BACKGROUND: Low-temperature growth and fermentation of wine yeast can enhance wine aroma and make them highly desirable traits for the industry. Elucidating response to cold in Saccharomyces cerevisiae is, therefore, of paramount importance to select or genetically improve new wine strains. As most enological traits of industrial importance in yeasts, adaptation to low temperature is a polygenic trait regulated by many interacting loci. RESULTS: In order to unravel the genetic determinants of low-temperature fermentation, we mapped quantitative trait loci (QTLs) by bulk segregant analyses in the F13 offspring of two Saccharomyces cerevisiae industrial strains with divergent performance at low temperature...
February 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28193859/genetic-regulatory-signatures-underlying-islet-gene-expression-and-type-2-diabetes
#9
Arushi Varshney, Laura J Scott, Ryan P Welch, Michael R Erdos, Peter S Chines, Narisu Narisu, Ricardo D'O Albanus, Peter Orchard, Brooke N Wolford, Romy Kursawe, Swarooparani Vadlamudi, Maren E Cannon, John P Didion, John Hensley, Anthony Kirilusha, Lori L Bonnycastle, D Leland Taylor, Richard Watanabe, Karen L Mohlke, Michael Boehnke, Francis S Collins, Stephen C J Parker, Michael L Stitzel
Genome-wide association studies (GWAS) have identified >100 independent SNPs that modulate the risk of type 2 diabetes (T2D) and related traits. However, the pathogenic mechanisms of most of these SNPs remain elusive. Here, we examined genomic, epigenomic, and transcriptomic profiles in human pancreatic islets to understand the links between genetic variation, chromatin landscape, and gene expression in the context of T2D. We first integrated genome and transcriptome variation across 112 islet samples to produce dense cis-expression quantitative trait loci (cis-eQTL) maps...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193307/heritability-and-gwas-studies-for-monocyte-lymphocyte-ratio
#10
Bochao D Lin, Gonneke Willemsen, Iryna O Fedko, Rick Jansen, Brenda Penninx, E de Geus, C Kluft, JoukeJan Hottenga, Dorret I Boomsma
The monocyte-lymphocyte ratio (MLR) is a useful biomarker for disease development, but little is known about the extent to which genetic and environmental factors influence MLR variation. Here, we study the genetic architecture of MLR and determine the influence of demographic and lifestyle factors on MLR in data from a Dutch non-patient twin-family population. Data were obtained in 9,501 individuals from the Netherlands Twin Register. We used regression analyses to determine the effects of age, sex, smoking, and body mass index (BMI) on MLR and its subcomponents...
February 14, 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28193175/genome-wide-association-mapping-for-milk-fat-composition-and-fine-mapping-of-a-qtl-for-de-novo-synthesis-of-milk-fatty-acids-on-bovine-chromosome-13
#11
Hanne Gro Olsen, Tim Martin Knutsen, Achim Kohler, Morten Svendsen, Lars Gidskehaug, Harald Grove, Torfinn Nome, Marte Sodeland, Kristil Kindem Sundsaasen, Matthew Peter Kent, Harald Martens, Sigbjørn Lien
BACKGROUND: Bovine milk is widely regarded as a nutritious food source for humans, although the effects of individual fatty acids on human health is a subject of debate. Based on the assumption that genomic selection offers potential to improve milk fat composition, there is strong interest to understand more about the genetic factors that influence the biosynthesis of bovine milk and the molecular mechanisms that regulate milk fat synthesis and secretion. For this reason, the work reported here aimed at identifying genetic variants that affect milk fatty acid composition in Norwegian Red cattle...
February 13, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28193168/genome-wide-snp-identification-linkage-map-construction-and-qtl-mapping-for-seed-mineral-concentrations-and-contents-in-pea-pisum-sativum-l
#12
Yu Ma, Clarice J Coyne, Michael A Grusak, Michael Mazourek, Peng Cheng, Dorrie Main, Rebecca J McGee
BACKGROUND: Marker-assisted breeding is now routinely used in major crops to facilitate more efficient cultivar improvement. This has been significantly enabled by the use of next-generation sequencing technology to identify loci and markers associated with traits of interest. While rich in a range of nutritional components, such as protein, mineral nutrients, carbohydrates and several vitamins, pea (Pisum sativum L.), one of the oldest domesticated crops in the world, remains behind many other crops in the availability of genomic and genetic resources...
February 13, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28188333/use-of-modern-tomato-breeding-germplasm-for-deciphering-the-genetic-control-of-agronomical-traits-by-genome-wide-association-study
#13
Guillaume Bauchet, Stéphane Grenier, Nicolas Samson, Julien Bonnet, Laurent Grivet, Mathilde Causse
A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato...
February 10, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28187132/gwas-for-serum-galactose-deficient-iga1-implicates-critical-genes-of-the-o-glycosylation-pathway
#14
Krzysztof Kiryluk, Yifu Li, Zina Moldoveanu, Hitoshi Suzuki, Colin Reily, Ping Hou, Jingyuan Xie, Nikol Mladkova, Sindhuri Prakash, Clara Fischman, Samantha Shapiro, Robert A LeDesma, Drew Bradbury, Iuliana Ionita-Laza, Frank Eitner, Thomas Rauen, Nicolas Maillard, Francois Berthoux, Jürgen Floege, Nan Chen, Hong Zhang, Francesco Scolari, Robert J Wyatt, Bruce A Julian, Ali G Gharavi, Jan Novak
Aberrant O-glycosylation of serum immunoglobulin A1 (IgA1) represents a heritable pathogenic defect in IgA nephropathy, the most common form of glomerulonephritis worldwide, but specific genetic factors involved in its determination are not known. We performed a quantitative GWAS for serum levels of galactose-deficient IgA1 (Gd-IgA1) in 2,633 subjects of European and East Asian ancestry and discovered two genome-wide significant loci, in C1GALT1 (rs13226913, P = 3.2 x 10-11) and C1GALT1C1 (rs5910940, P = 2...
February 10, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28184981/association-mapping-utilizing-diverse-barley-lines-reveals-net-form-net-blotch-seedling-resistance-susceptibility-loci
#15
Jonathan K Richards, Timothy L Friesen, Robert S Brueggeman
A diverse collection of barley lines was phenotyped with three North American Pyrenophora teres f. teres isolates and association analyses detected 78 significant marker-trait associations at 16 genomic loci. Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the causal agent of the economically important foliar disease net form net blotch (NFNB) of barley. The deployment of effective and durable resistance against P. teres f. teres has been hindered by the complexity of quantitative resistance and susceptibility...
February 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28182695/two-three-loci-control-scleral-ossicle-formation-via-epistasis-in-the-cavefish-astyanax-mexicanus
#16
Anastasia Lyon, Amanda K Powers, Joshua B Gross, Kelly E O'Quin
The sclera is the protective outer layer of the eye. In fishes, birds, and reptiles, the sclera may be reinforced with additional bony elements called scleral ossicles. Teleost fish vary in the number and size of scleral ossicles; however, the genetic mechanisms responsible for this variation remain poorly understood. In this study, we examine the inheritance of scleral ossicles in the Mexican tetra, Astyanax mexicanus, which exhibits both a cave morph and a surface fish morph. As these morphs and their hybrids collectively exhibit zero, one, and two scleral ossicles, they represent a microcosm of teleost scleral ossicle diversity...
2017: PloS One
https://www.readbyqxmd.com/read/28181565/genetic-susceptibility-variants-for-lung-cancer-replication-study-and-assessment-as-expression-quantitative-trait-loci
#17
Giulia Pintarelli, Chiara Elisabetta Cotroneo, Sara Noci, Matteo Dugo, Antonella Galvan, Simona Delli Carpini, Lorena Citterio, Paolo Manunta, Matteo Incarbone, Davide Tosi, Luigi Santambrogio, Tommaso A Dragani, Francesca Colombo
Many single nucleotide polymorphisms (SNPs) have been associated with lung cancer but lack confirmation and functional characterization. We retested the association of 56 candidate SNPs with lung adenocarcinoma risk and overall survival in a cohort of 823 Italian patients and 779 healthy controls, and assessed their function as expression quantitative trait loci (eQTLs). In the replication study, eight SNPs (rs401681, rs3019885, rs732765, rs2568494, rs16969968, rs6495309, rs11634351, and rs4105144) associated with lung adenocarcinoma risk and three (rs9557635, rs4105144, and rs735482) associated with survival...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28179981/deep-assessment-of-genomic-diversity-in-cassava-for-herbicide-tolerance-and-starch-biosynthesis
#18
Jorge Duitama, Lina Kafuri, Daniel Tello, Ana María Leiva, Bernhard Hofinger, Sneha Datta, Zaida Lentini, Ericson Aranzales, Bradley Till, Hernán Ceballos
Cassava is one of the most important food security crops in tropical countries, and a competitive resource for the starch, food, feed and ethanol industries. However, genomics research in this crop is much less developed compared to other economically important crops such as rice or maize. The International Center for Tropical Agriculture (CIAT) maintains the largest cassava germplasm collection in the world. Unfortunately, the genetic potential of this diversity for breeding programs remains underexploited due to the difficulties in phenotypic screening and lack of deep genomic information about the different accessions...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28179367/genomic-rearrangements-in-arabidopsis-considered-as-quantitative-traits
#19
Martha Imprialou, André Kahles, Joshua G Steffen, Edward J Osborne, Xiangchao Gan, Janne Lempe, Amarjit Bhomra, Eric Belfield, Anne Visscher, Robert Greenhalgh, Nicholas P Harberd, Richard Goram, Jotun Hein, Alexandre Robert-Seilaniantz, Jonathan Jones, Oliver Stegle, Paula Kover, Miltos Tsiantis, Magnus Nordborg, Gunnar Rätsch, Richard M Clark, Richard Mott
To understand the population genetics of structural variants and their effects on phenotypes, we developed an approach to mapping structural variants that segregate in a population sequenced at low coverage. We avoid calling structural variants directly. Instead, the evidence for a potential structural variant at a locus is indicated by variation in the counts of short-reads that map anomalously to that locus. These structural variant traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study...
February 7, 2017: Genetics
https://www.readbyqxmd.com/read/28176342/identification-of-the-crucial-genes-in-the-elimination-and-survival-process-of-salmonella-enterica-ser-pullorum-in-the-chicken-spleen
#20
T Ma, L Xu, H Wang, X Guo, Z Li, F Wan, J Chen, L Liu, X Liu, G Chang, G Chen
Salmonella enterica ser. Pullorum is one of the most easily re-infecting pathogens in poultry production because of its mechanism of escaping from immune elimination. We used the transcriptome method to investigate the variation in gene expression in chicken spleen resulting from the interaction between hosts and S. Pullorum in the survival process. The expression of various genes related to the maturation and activation of B cells was activated before S. Pullorum was eliminated, which might help S. Pullorum escape from the elimination process...
February 7, 2017: Animal Genetics
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