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JOURNAL ARTICLE
Sam Benkwitz-Bedford, Martin Palm, Talip Yasir Demirtas, Ville Mustonen, Anne Farewell, Jonas Warringer, Leopold Parts, Danesh Moradigaravand
Escherichia coli is an important cause of bacterial infections worldwide, with multidrug-resistant strains incurring substantial costs on human lives. Besides therapeutic concentrations of antimicrobials in health care settings, the presence of subinhibitory antimicrobial residues in the environment and in clinics selects for antimicrobial resistance (AMR), but the underlying genetic repertoire is less well understood. Here, we used machine learning to predict the population doubling time and cell growth yield of 1,407 genetically diverse E...
August 24, 2021: MSystems
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JOURNAL ARTICLE
Carmen M Ávila, María Dolores Requena-Ramírez, Cristina Rodríguez-Suárez, Fernando Flores, Josefina C Sillero, Sergio G Atienza
Durum wheat landraces have a high potential for breeding but they remain underexploited due to several factors, including the insufficient evaluation of these plant materials and the lack of efficient selection tools for transferring target traits into elite backgrounds. In this work, we characterized 150 accessions of the Spanish durum wheat collection for stem cross section, height and heading date. Continuous variation and high heritabilities were recorded for the stem area, pith area, pith diameter, culm wall thickness, height and heading date...
June 1, 2021: Plants (Basel, Switzerland)
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JOURNAL ARTICLE
Jack C M Dekkers, Hailin Su, Jian Cheng
BACKGROUND: Mathematical models are needed for the design of breeding programs using genomic prediction. While deterministic models for selection on pedigree-based estimates of breeding values (PEBV) are available, these have not been fully developed for genomic selection, with a key missing component being the accuracy of genomic EBV (GEBV) of selection candidates. Here, a deterministic method was developed to predict this accuracy within a closed breeding population based on the accuracy of GEBV and PEBV in the reference population and the distance of selection candidates from their closest ancestors in the reference population...
June 29, 2021: Genetics, Selection, Evolution: GSE
#24
REVIEW
Xiaowei Zhu, Weiyang Bai, Houfeng Zheng
Osteoporosis is a common skeletal disease, affecting ~200 million people around the world. As a complex disease, osteoporosis is influenced by many factors, including diet (e.g. calcium and protein intake), physical activity, endocrine status, coexisting diseases and genetic factors. In this review, we first summarize the discovery from genome-wide association studies (GWASs) in the bone field in the last 12 years. To date, GWASs and meta-analyses have discovered hundreds of loci that are associated with bone mineral density (BMD), osteoporosis, and osteoporotic fractures...
April 29, 2021: Bone Research
#25
JOURNAL ARTICLE
Jared Crain, Atena Haghighattalab, Lee DeHaan, Jesse Poland
The development of perennial grain crops is driven by the vision of simultaneous food production and enhanced ecosystem services. Typically, perennial crops like intermediate wheatgrass (IWG)[Thinopyrum intermedium (Host) Barkworth & D.R Dewey] have low seed yield and other detrimental traits. Next-generation sequencing has made genomic selection (GS) a tractable and viable breeding method. To investigate how an IWG breeding program may use GS, we evaluated 3,658 genets over 2 yr for 46 traits to build a training population...
April 26, 2021: Plant Genome
#26
REVIEW
Xiangbo Zhang, Yongwen Qi
Conventional genome-wide association studies (GWAS) focused on the phenotypic mean differences (mGWAS) but often ignored genetic variants influencing differences in the variance between genotypes. In this study, we performed variance heterogeneity GWAS (vGWAS) analysis for 13 previously measured agronomic traits in a maize population. We discovered a total of 129 significant SNPs. We demonstrated that the genetic loci influencing mean differences and variance heterogeneity formed distinct groups, suggesting that breeders were able to independently select for phenotype mean and variance values...
April 8, 2021: Genomics
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JOURNAL ARTICLE
Xi Long, Hong Xue
BACKGROUND: Genetic variants, underlining phenotypic diversity, are known to distribute unevenly in the human genome. A comprehensive understanding of the distributions of different genetic variants is important for insights into genetic functions and disorders. METHODS: Herein, a sliding-window scan of regional densities of eight kinds of germline genetic variants, including single-nucleotide-polymorphisms (SNPs) and four size-classes of copy-number-variations (CNVs) in the human genome has been performed...
March 19, 2021: Human Genomics
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JOURNAL ARTICLE
Laavanya Rayaprolu, Sivasubramani Selvanayagam, D Manohar Rao, Rajeev Gupta, Roma Rani Das, Abhishek Rathore, Prasad Gandham, K N S Usha Kiranmayee, Santosh P Deshpande, Ashok Kumar Are
BACKGROUND: Production of biofuels from lignocellulosic crop biomass is an alternative to reduce greenhouse gas emissions. The biofuel production involves collecting biomass, breaking down cell wall components followed by the conversion of sugars to ethanol. The lingo-cellulosic biomass comprises 40-50% cellulose, 20-30% hemicellulose, and 10-25% lignin. Sorghum is a widely adapted energy crop for biofuel production. Biomass with low lignin, high cellulose, and high hemicellulose contents are exploited to attain maximum biofuel production efficiency...
2021: Protein and Peptide Letters
#29
JOURNAL ARTICLE
Francesco Tiezzi, Justin Fix, Clint Schwab, Caleb Shull, Christian Maltecca
A large number of studies have highlighted the importance of gut microbiome composition in shaping fat deposition in mammals. Several studies have also highlighted how host genome controls the abundance of certain species that make up the gut microbiota. We propose a systematic approach to infer how the host genome can control the gut microbiome, which in turn contributes to the host phenotype determination. We implemented a mediation test that can be applied to measured and latent dependent variables to describe fat deposition in swine ( Sus scrofa )...
2021: Computational and Structural Biotechnology Journal
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JOURNAL ARTICLE
Chang Liu, Yuan Tu, Shiyu Liao, Xiangkui Fu, Xingming Lian, Yuqing He, Weibo Xie, Gongwei Wang
Since domestication, rice has cultivated in a wide range of latitudes with different day lengths. Selection of diverse natural variations in heading date and photoperiod sensitivity is critical for adaptation of rice to different geographical environments. To unravel the genetic architecture underlying natural variation of rice flowering time, we conducted a genome wide association study (GWAS) using several association analysis strategies with a diverse worldwide collection of 529 O. sativa accessions. Heading date was investigated in three environments under long-day or short-day conditions, and photosensitivity was evaluated...
December 14, 2020: Gene
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JOURNAL ARTICLE
Emilia M Swietlik, Daniel Greene, Na Zhu, Karyn Megy, Marcella Cogliano, Smitha Rajaram, Divya Pandya, Tobias Tilly, Katie A Lutz, Carrie C L Welch, Michael W Pauciulo, Laura Southgate, Jennifer M Martin, Carmen M Treacy, Christopher J Penkett, Jonathan C Stephens, Harm J Bogaard, Colin Church, Gerry Coghlan, Anna W Coleman, Robin Condliffe, Christina A Eichstaedt, Mélanie Eyries, Henning Gall, Stefano Ghio, Barbara Girerd, Ekkehard Grünig, Simon Holden, Luke Howard, Marc Humbert, David G Kiely, Gabor Kovacs, Jim Lordan, Rajiv D Machado, Robert V Mackenzie Ross, Colm McCabe, Shahin Moledina, David Montani, Horst Olschewski, Joanna Pepke-Zaba, Laura Price, Christopher J Rhodes, Werner Seeger, Florent Soubrier, Jay Suntharalingam, Mark R Toshner, Anton Vonk Noordegraaf, John Wharton, James M Wild, Stephen John Wort, Allan Lawrie, Martin R Wilkins, Richard C Trembath, Yufeng Shen, Wendy K Chung, Andrew J Swift, William C Nichols, Nicholas W Morrell, Stefan Gräf
Background - Approximately 25% of patients with pulmonary arterial hypertension (PAH) have been found to harbor rare mutations in disease-causing genes. To identify missing heritability in PAH we integrated deep phenotyping with whole-genome sequencing data using Bayesian statistics. Methods - We analyzed 13,037 participants enrolled in the NIHR BioResource - Rare Diseases (NBR) study, of which 1,148 were recruited to the PAH domain. To test for genetic associations between genes and selected phenotypes of pulmonary hypertension (PH), we used the Bayesian rare-variant association method BeviMed...
December 15, 2020: Circulation. Genomic and Precision Medicine
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JOURNAL ARTICLE
Somayeh Kafaie, Ling Xu, Ting Hu
Though additive forms of heritability are primarily studied in genetics, nonlinear, non-additive gene-gene interactions, that is, epistasis, could explain a portion of the missing heritability in complex human diseases including cancer. In recent years, powerful computational methods have been introduced to understand multivariable genetic factors of these complex human diseases in extremely high-dimensional genome-wide data. In this study, we investigated the performance of three powerful methods, BOolean Operation-based Screening and Testing (BOOST), FastEpistasis, and Tree-based Epistasis Association Mapping (TEAM) to identify interacting genetic risk factors of colorectal cancer (CRC) for genome-wide association studies (GWAS)...
November 24, 2020: Genetic Epidemiology
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JOURNAL ARTICLE
S Tsuruta, T J Lawlor, D A L Lourenco, I Misztal
The objective of this study was to clarify how bias in genomic predictions is created by investigating a relationship among selection intensity, a change in heritability (Δh2 ), and assortative mating (ASM). A change in heritability, resulting from selection, reflects the impact that the Bulmer effect has on the reduction in between-family variation, whereas assortative mating impacts the within-family variance or Mendelian sampling variation. A partial data set up to 2014, including 841K genotyped animals, was used to calculate genomic predictions with a single-step genomic model for 18 linear type traits in US Holsteins...
November 5, 2020: Journal of Dairy Science
#34
JOURNAL ARTICLE
Achille Nyouma, Joseph Martin Bell, Florence Jacob, Virginie Riou, Aurore Manez, Virginie Pomiès, Leifi Nodichao, Indra Syahputra, Dadang Affandi, Benoit Cochard, Tristan Durand-Gasselin, David Cros
The prediction of clonal genetic value for yield is challenging in oil palm (Elaeis guineensis Jacq.). Currently, clonal selection involves two stages of phenotypic selection (PS): ortet preselection on traits with sufficient heritability among a small number of individuals in the best crosses in progeny tests, and final selection on performance in clonal trials. The present study evaluated the efficiency of genomic selection (GS) for clonal selection. The training set comprised almost 300 Deli × La Mé crosses phenotyped for eight palm oil yield components and the validation set 42 Deli × La Mé ortets...
October 2020: Plant Science: An International Journal of Experimental Plant Biology
#35
JOURNAL ARTICLE
Qiuyue Chen, Luis Fernando Samayoa, Chin Jian Yang, Peter J Bradbury, Bode A Olukolu, Michael A Neumeyer, Maria Cinta Romay, Qi Sun, Anne Lorant, Edward S Buckler, Jeffrey Ross-Ibarra, James B Holland, John F Doebley
The genetics of domestication has been extensively studied ever since the rediscovery of Mendel's law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication...
May 14, 2020: PLoS Genetics
#36
JOURNAL ARTICLE
Qiwen Zheng, Yan Zhang, Jie Jiang, Jia Jia, Fangfang Fan, Yanjun Gong, Zhi Wang, Qiuping Shi, Dafang Chen, Yong Huo
Genome-wide association studies have identified more than 150 susceptibility loci for coronary artery disease (CAD); however, there is still a large proportion of missing heritability remaining to be investigated. This study sought to identify population-based genetic variation associated with acute coronary syndromes (ACS) in individuals of Chinese Han descent. We proposed a novel strategy integrating a well-developed risk prediction model into control selection in order to lower the potential misclassification bias and increase the statistical power...
2020: Frontiers in Genetics
#37
JOURNAL ARTICLE
Gilles Charmet, Louis-Gautier Tran, Jérôme Auzanneau, Renaud Rincent, Sophie Bouchet
We developed an integrated R library called BWGS to enable easy computation of Genomic Estimates of Breeding values (GEBV) for genomic selection. BWGS, for BreedWheat Genomic selection, was developed in the framework of a cooperative private-public partnership project called Breedwheat (https://breedwheat.fr) and relies on existing R-libraries, all freely available from CRAN servers. The two main functions enable to run 1) replicated random cross validations within a training set of genotyped and phenotyped lines and 2) GEBV prediction, for a set of genotyped-only lines...
2020: PloS One
#38
JOURNAL ARTICLE
Yiru Wang, Jiayu Shi, Qian Zheng, Bing Shi, Zhonglin Jia
BACKGROUND: Genome-wide association studies (GWAS) have found more than 20 genes associated with a risk of non-syndromic cleft lip with or without cleft palate (NSCL/P). However, the interactions between these risk genes have been rarely reported. METHODS: Here we selected 47 Single Nucleotide Polymorphisms (SNP) from previous GWASs and tested for possible interactions among 302 NSCL/P case-parent trios from a western Han Chinese population to further explore the genetic etiology of NSCL/P...
2020: International Journal of Clinical and Experimental Pathology
#39
JOURNAL ARTICLE
Mohsin Ali, Yong Zhang, Awais Rasheed, Jiankang Wang, Luyan Zhang
Genomic selection (GS) is a strategy to predict the genetic merits of individuals using genome-wide markers. However, GS prediction accuracy is affected by many factors, including missing rate and minor allele frequency (MAF) of genotypic data, GS models, trait features, etc. In this study, we used one wheat population to investigate prediction accuracies of various GS models on yield and yield-related traits from various quality control (QC) scenarios, missing genotype imputation, and genome-wide association studies (GWAS)-derived markers...
February 17, 2020: International Journal of Molecular Sciences
#40
REVIEW
Amrita Chattopadhyay, Tzu-Pin Lu
Identified genetic variants from genome wide association studies frequently show only modest effects on the disease risk, leading to the "missing heritability" problem. An avenue, to account for a part of this "missingness" is to evaluate gene-gene interactions (epistasis) thereby elucidating their effect on complex diseases. This can potentially help with identifying gene functions, pathways, and drug targets. However, the exhaustive evaluation of all possible genetic interactions among millions of single nucleotide polymorphisms (SNPs) raises several issues, otherwise known as the "curse of dimensionality"...
December 2019: Annals of Translational Medicine
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