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Genome wide selection

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https://www.readbyqxmd.com/read/28724084/comparison-of-models-and-whole-genome-profiling-approaches-for-genomic-enabled-prediction-of-septoria-tritici-blotch-stagonospora-nodorum-blotch-and-tan-spot-resistance-in-wheat
#1
Philomin Juliana, Ravi P Singh, Pawan K Singh, Jose Crossa, Jessica E Rutkoski, Jesse A Poland, Gary C Bergstrom, Mark E Sorrells
The leaf spotting diseases in wheat that include Septoria tritici blotch (STB) caused by , Stagonospora nodorum blotch (SNB) caused by , and tan spot (TS) caused by pose challenges to breeding programs in selecting for resistance. A promising approach that could enable selection prior to phenotyping is genomic selection that uses genome-wide markers to estimate breeding values (BVs) for quantitative traits. To evaluate this approach for seedling and/or adult plant resistance (APR) to STB, SNB, and TS, we compared the predictive ability of least-squares (LS) approach with genomic-enabled prediction models including genomic best linear unbiased predictor (GBLUP), Bayesian ridge regression (BRR), Bayes A (BA), Bayes B (BB), Bayes Cπ (BC), Bayesian least absolute shrinkage and selection operator (BL), and reproducing kernel Hilbert spaces markers (RKHS-M), a pedigree-based model (RKHS-P) and RKHS markers and pedigree (RKHS-MP)...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724076/gbs-based-genomic-selection-for-pea-grain-yield-under-severe-terminal-drought
#2
Paolo Annicchiarico, Nelson Nazzicari, Luciano Pecetti, Massimo Romani, Barbara Ferrari, Yanling Wei, E Charles Brummer
Terminal drought is the main stress that limits pea ( L.) grain yield in Mediterranean-climate regions. This study provides an unprecedented assessment of the predictive ability of genomic selection (GS) for grain yield under severe terminal drought using genotyping-by-sequencing (GBS) data. Additional aims were to assess the GS predictive ability for different GBS data quality filters and GS models, comparing intrapopulation with interpopulation GS predictive ability and to perform genome-wide association (GWAS) studies...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724072/genome-wide-analysis-of-tar-spot-complex-resistance-in-maize-using-genotyping-by-sequencing-snps-and-whole-genome-prediction
#3
Shiliang Cao, Alexander Loladze, Yibing Yuan, Yongsheng Wu, Ao Zhang, Jiafa Chen, Gordon Huestis, Jingsheng Cao, Vijay Chaikam, Michael Olsen, Boddupalli M Prasanna, Felix San Vicente, Xuecai Zhang
Tar spot complex (TSC) is one of the most destructive foliar diseases of maize ( L.) in tropical and subtropical areas of Central and South America, causing significant grain yield losses when weather conditions are conducive. To dissect the genetic architecture of TSC resistance in maize, association mapping, in conjunction with linkage mapping, was conducted on an association-mapping panel and three biparental doubled-haploid (DH) populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs)...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724070/marker-trait-association-analysis-of-iron-and-zinc-concentration-in-lentil-lens-culinaris-medik-seeds
#4
Hamid Khazaei, Rajib Podder, Carolyn T Caron, Shudhangshu S Kundu, Marwan Diapari, Albert Vandenberg, Kirstin E Bett
Lentil ( Medik.) seeds are relatively rich in iron (Fe) and zinc (Zn), making lentil a potential crop to aid in the global battle against human micronutrient deficiency. Understanding the genetic basis for uptake of seed Fe and Zn is required to increase sustainable concentrations of these minerals in seeds. The objectives of this study were to characterize genetic variation in seed Fe and Zn concentration and to identify molecular markers associated with these traits across diverse lentil accessions. A set of 138 cultivated lentil accessions from 34 countries were evaluated in four environments (2 sites × 2 yr) in Saskatchewan, Canada...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724060/genome-wide-association-mapping-of-crown-rust-resistance-in-oat-elite-germplasm
#5
Kathy Esvelt Klos, Belayneh A Yimer, Ebrahiem M Babiker, Aaron D Beattie, J Michael Bonman, Martin L Carson, James Chong, Stephen A Harrison, Amir M H Ibrahim, Frederic L Kolb, Curt A McCartney, Michael McMullen, Jennifer Mitchell Fetch, Mohsen Mohammadi, J Paul Murphy, Nicholas A Tinker
Oat crown rust, caused by f. sp. , is a major constraint to oat ( L.) production in many parts of the world. In this first comprehensive multienvironment genome-wide association map of oat crown rust, we used 2972 single-nucleotide polymorphisms (SNPs) genotyped on 631 oat lines for association mapping of quantitative trait loci (QTL). Seedling reaction to crown rust in these lines was assessed as infection type (IT) with each of 10 crown rust isolates. Adult plant reaction was assessed in the field in a total of 10 location-years as percentage severity (SV) and as infection reaction (IR) in a 0-to-1 scale...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723906/genomic-prediction-with-parallel-computing-for-slaughter-traits-in-chinese-simmental-beef-cattle-using-high-density-genotypes
#6
Peng Guo, Bo Zhu, Lingyang Xu, Hong Niu, Zezhao Wang, Long Guan, Yonghu Liang, Hemin Ni, Yong Guo, Yan Chen, Lupei Zhang, Xue Gao, Huijiang Gao, Junya Li
Genomic selection has been widely used for complex quantitative trait in farm animals. Estimations of breeding values for slaughter traits are most important to beef cattle industry, and it is worthwhile to investigate prediction accuracies of genomic selection for these traits. In this study, we assessed genomic predictive abilities for average daily gain weight (ADG), live weight (LW), carcass weight (CW), dressing percentage (DP), lean meat percentage (LMP) and retail meat weight (RMW) using Illumina Bovine 770K SNP Beadchip in Chinese Simmental cattle...
2017: PloS One
https://www.readbyqxmd.com/read/28721852/effective-identification-of-lactobacillus-casei-group-species-genome-based-selection-of-the-gene-mutl-as-the-target-of-a-novel-multiplex-pcr-assay
#7
Benedetta Bottari, Giovanna E Felis, Elisa Salvetti, Anna Castioni, Ilenia Campedelli, Sandra Torriani, Valentina Bernini, Monica Gatti
Lactobacillus casei,Lactobacillus paracasei and Lactobacillusrhamnosus form a closely related taxonomic group (the L. casei group) within the facultatively heterofermentative lactobacilli. Strains of these species have been used for a long time as probiotics in a wide range of products, and they represent the dominant species of nonstarter lactic acid bacteria in ripened cheeses, where they contribute to flavour development. The close genetic relationship among those species, as well as the similarity of biochemical properties of the strains, hinders the development of an adequate selective method to identify these bacteria...
July 18, 2017: Microbiology
https://www.readbyqxmd.com/read/28721485/non-additive-and-epistatic-effects-of-hla-polymorphisms-contributing-to-risk-of-adult-glioma
#8
Chenan Zhang, Adam J de Smith, Ivan V Smirnov, John K Wiencke, Joseph L Wiemels, John S Witte, Kyle M Walsh
Although genome-wide association studies have identified several susceptibility loci for adult glioma, little is known regarding the potential contribution of genetic variation in the human leukocyte antigen (HLA) region to glioma risk. HLA associations have been reported for various malignancies, with many studies investigating selected candidate HLA polymorphisms. However, no systematic analysis has been conducted in glioma patients, and no investigation into potential non-additive effects has been described...
July 18, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28720371/genetic-risk-factors-for-idiopathic-urolithiasis-a-systematic-review-of-the-literature-and-causal-network-analysis
#9
REVIEW
Kazumi Taguchi, Takahiro Yasui, Dawn Schmautz Milliner, Bernd Hoppe, Thomas Chi
CONTEXT: Urolithiasis has a high prevalence and recurrence rate. Prevention is key to patient management, but risk stratification is challenging. In particular, genetic predisposition for urinary stones is not fully understood. OBJECTIVE: To review current evidence of potential causative genes for idiopathic urolithiasis and map their relationships to one another. This evidence is essential for future establishment of molecular targeted therapy. EVIDENCE ACQUISITION: A systematic literature review from 2007 to 2017 was performed in accordance with the Preferred Reporting Items for Systematic Review and Meta-analyses guidelines...
February 2017: European Urology Focus
https://www.readbyqxmd.com/read/28720099/association-between-genome-wide-copy-number-variation-and-arsenic-induced-skin-lesions-a-prospective-study
#10
Muhammad G Kibriya, Farzana Jasmine, Faruque Parvez, Maria Argos, Shantanu Roy, Rachelle Paul-Brutus, Tariqul Islam, Alauddin Ahmed, Muhammad Rakibuz-Zaman, Justin Shinkle, Vesna Slavkovich, Joseph H Graziano, Habibul Ahsan
BACKGROUND: Exposure to arsenic in drinking water is a global health problem and arsenic-induced skin lesions are hallmark of chronic arsenic toxicity. We and others have reported germline genetic variations as risk factors for such skin lesions. The role of copy number variation (CNV) in the germline DNA in this regard is unknown. METHODS: From a large prospectively followed-up cohort, exposed to arsenic, we randomly selected 2171 subjects without arsenic-induced skin lesions at enrollment and genotyped their whole blood DNA samples on Illumina Cyto12v2...
July 18, 2017: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/28718511/genome-wide-identification-of-genes-involved-in-the-potato-response-to-drought-indicates-functional-evolutionary-conservation-with-arabidopsis-plants
#11
M Pieczynski, A Wyrzykowska, K Milanowska, D Boguszewska-Mankowska, B Zagdanska, W Karlowski, A Jarmolowski, Z Szweykowska-Kulinska
Potato is one of the four most important food crop plants worldwide and is strongly affected by drought. The following two pairs of potato cultivars, which are related in ancestry but show different drought tolerances, were chosen for comparative gene expression studies: Gwiazda/Oberon and Tajfun/Owacja. Comparative RNA-seq analyses of gene expression differences in the transcriptomes obtained from drought-tolerant versus drought-sensitive plants during water shortage conditions were performed. The twenty-three top-ranking genes were selected, 22 of which are described here as novel potato drought-responsive genes...
July 17, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28717940/alopecia-areata-a-comprehensive-review-of-pathogenesis-and-management
#12
REVIEW
Ralph M Trüeb, Maria Fernanda Reis Gavazzoni Dias
Alopecia areata is a common hair loss condition that is characterized by acute onset of non-scarring hair loss in usually sharply defined areas ranging from small patches to extensive or less frequently diffuse involvement. Depending on its acuity and extent, hair loss is an important cause of anxiety and disability. The current understanding is that the condition represents an organ-specific autoimmune disease of the hair follicle with a genetic background. Genome-wide association studies provide evidence for the involvement of both innate and acquired immunity in the pathogenesis, and mechanistic studies in mouse models of alopecia areata have specifically implicated an IFN-γ-driven immune response, including IFNγ, IFNγ-induced chemokines and cytotoxic CD8 T cells as the main drivers of disease pathogenesis...
July 17, 2017: Clinical Reviews in Allergy & Immunology
https://www.readbyqxmd.com/read/28717847/exploring-the-genomic-diversity-and-cariogenic-differences-of-streptococcus-mutans-strains-through-pan-genome-and-comparative-genome-analysis
#13
Peiqi Meng, Chang Lu, Qian Zhang, Jiuxiang Lin, Feng Chen
Pan-genome refers to the sum of genes that can be found in a given bacterial species, including the core-genome and the dispensable genome. In this study, the genomes from 183 Streptococcus mutans (S. mutans) isolates were analyzed from the pan-genome perspective. This analysis revealed that S. mutans has an "open" pan-genome, implying that there are plenty of new genes to be found as more genomes are sequenced. Additionally, S. mutans has a limited core-genome, which is composed of genes related to vital activities within the bacterium, such as metabolism and hereditary information storage or processing, occupying 35...
July 17, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28716048/transcriptome-analysis-uncovers-arabidopsis-f-box-stress-induced-1-as-a-regulator-of-jasmonic-acid-and-abscisic-acid-stress-gene-expression
#14
Lauren E Gonzalez, Kristen Keller, Karen X Chan, Megan M Gessel, Bryan C Thines
BACKGROUND: The ubiquitin 26S proteasome system (UPS) selectively degrades cellular proteins, which results in physiological changes to eukaryotic cells. F-box proteins are substrate adaptors within the UPS and are responsible for the diversity of potential protein targets. Plant genomes are enriched in F-box genes, but the vast majority of these have unknown roles. This work investigated the Arabidopsis F-box gene F-BOX STRESS INDUCED 1 (FBS1) for its effects on gene expression in order elucidate its previously unknown biological function...
July 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28714975/association-analyses-based-on-false-discovery-rate-implicate-new-loci-for-coronary-artery-disease
#15
Christopher P Nelson, Anuj Goel, Adam S Butterworth, Stavroula Kanoni, Tom R Webb, Eirini Marouli, Lingyao Zeng, Ioanna Ntalla, Florence Y Lai, Jemma C Hopewell, Olga Giannakopoulou, Tao Jiang, Stephen E Hamby, Emanuele Di Angelantonio, Themistocles L Assimes, Erwin P Bottinger, John C Chambers, Robert Clarke, Colin N A Palmer, Richard M Cubbon, Patrick Ellinor, Raili Ermel, Evangelos Evangelou, Paul W Franks, Christopher Grace, Dongfeng Gu, Aroon D Hingorani, Joanna M M Howson, Erik Ingelsson, Adnan Kastrati, Thorsten Kessler, Theodosios Kyriakou, Terho Lehtimäki, Xiangfeng Lu, Yingchang Lu, Winfried März, Ruth McPherson, Andres Metspalu, Mar Pujades-Rodriguez, Arno Ruusalepp, Eric E Schadt, Amand F Schmidt, Michael J Sweeting, Pierre A Zalloua, Kamal AlGhalayini, Bernard D Keavney, Jaspal S Kooner, Ruth J F Loos, Riyaz S Patel, Martin K Rutter, Maciej Tomaszewski, Ioanna Tzoulaki, Eleftheria Zeggini, Jeanette Erdmann, George Dedoussis, Johan L M Björkegren, Heribert Schunkert, Martin Farrall, John Danesh, Nilesh J Samani, Hugh Watkins, Panos Deloukas
Genome-wide association studies (GWAS) in coronary artery disease (CAD) had identified 66 loci at 'genome-wide significance' (P < 5 × 10(-8)) at the time of this analysis, but a much larger number of putative loci at a false discovery rate (FDR) of 5% (refs. 1,2,3,4). Here we leverage an interim release of UK Biobank (UKBB) data to evaluate the validity of the FDR approach. We tested a CAD phenotype inclusive of angina (SOFT; ncases = 10,801) as well as a stricter definition without angina (HARD; ncases = 6,482) and selected cases with the former phenotype to conduct a meta-analysis using the two most recent CAD GWAS...
July 17, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28713859/fungus-causing-white-nose-syndrome-in-bats-accumulates-genetic-variability-in-north-america-with-no-sign-of-recombination
#16
Jigar Trivedi, Josianne Lachapelle, Karen J Vanderwolf, Vikram Misra, Craig K R Willis, John M Ratcliffe, Rob W Ness, James B Anderson, Linda M Kohn
Emerging fungal diseases of wildlife are on the rise worldwide, and the white-nose syndrome (WNS) epidemic in North American bats is a catastrophic example. The causal agent of WNS is a single clone of the fungus Pseudogymnoascus destructans. Early evolutionary change in this clonal population has major implications for disease ecology and conservation. Accumulation of variation in the fungus through mutation, and shuffling of variation through recombination, could affect the virulence and transmissibility of the fungus and the durability of what appears to be resistance arising in some bat populations...
July 2017: MSphere
https://www.readbyqxmd.com/read/28713819/differential-analysis-of-genetic-epigenetic-and-cytogenetic-abnormalities-in-aml
#17
Mirazul Islam, Zahurin Mohamed, Yassen Assenov
Acute myeloid leukemia (AML) is a haematological malignancy characterized by the excessive proliferation of immature myeloid cells coupled with impaired differentiation. Many AML cases have been reported without any known cytogenetic abnormalities and carry no mutation in known AML-associated driver genes. In this study, 200 AML cases were selected from a publicly available cohort and differentially analyzed for genetic, epigenetic, and cytogenetic abnormalities. Three genes (FLT3, DNMT3A, and NPMc) are found to be predominantly mutated...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28713414/divergent-evolutionary-patterns-of-nac-transcription-factors-are-associated-with-diversification-and-gene-duplications-in-angiosperm
#18
Xiaoli Jin, Jing Ren, Eviatar Nevo, Xuegui Yin, Dongfa Sun, Junhua Peng
NAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28713404/genome-wide-identification-and-analysis-of-genes-conserved-between-japonica-and-indica-rice-cultivars-that-respond-to-low-temperature-stress-at-the-vegetative-growth-stage
#19
Manu Kumar, Yun-Shil Gho, Ki-Hong Jung, Seong-Ryong Kim
Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28713401/genome-wide-association-study-reveals-natural-variations-contributing-to-drought-resistance-in-crops
#20
REVIEW
Hongwei Wang, Feng Qin
Crops are often cultivated in regions where they will face environmental adversities; resulting in substantial yield loss which can ultimately lead to food and societal problems. Thus, significant efforts have been made to breed stress tolerant cultivars in an attempt to minimize these problems and to produce more stability with respect to crop yields across broad geographies. Since stress tolerance is a complex and multi-genic trait, advancements with classical breeding approaches have been challenging. On the other hand, molecular breeding, which is based on transgenics, marker-assisted selection and genome editing technologies; holds great promise to enable farmers to better cope with these challenges...
2017: Frontiers in Plant Science
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