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Genome wide selection

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https://www.readbyqxmd.com/read/27920798/evolutionary-and-functional-features-of-copy-number-variation-in-the-cattle-genome
#1
Brittney N Keel, Amanda K Lindholm-Perry, Warren M Snelling
Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27920797/genome-wide-association-study-for-identifying-loci-that-affect-fillet-yield-carcass-and-body-weight-traits-in-rainbow-trout-oncorhynchus-mykiss
#2
Dianelys Gonzalez-Pena, Guangtu Gao, Matthew Baranski, Thomas Moen, Beth M Cleveland, P Brett Kenney, Roger L Vallejo, Yniv Palti, Timothy D Leeds
Fillet yield (FY, %) is an economically-important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has received little attention in breeding programs because it is difficult to measure on a large number of fish and cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the needed tool for studying the underlying genetic architecture of this trait. A genome-wide association study (GWAS) was conducted for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a pedigreed rainbow trout population selectively bred for improved growth performance...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27920788/vegetative-and-adaptive-traits-predict-different-outcomes-for-restoration-using-hybrids
#3
Philip A Crystal, Nathanael I Lichti, Keith E Woeste, Douglass F Jacobs
Hybridization has been implicated as a driver of speciation, extinction, and invasiveness, but can also provide resistant breeding stock following epidemics. However, evaluating the appropriateness of hybrids for use in restoration programs is difficult. Past the F1 generation, the proportion of a progenitor's genome can vary widely, as can the combinations of parental genomes. Detailed genetic analysis can reveal this information, but cannot expose phenotypic alterations due to heterosis, transgressive traits, or changes in metabolism or development...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27920780/genome-enabled-prediction-models-for-yield-related-traits-in-chickpea
#4
Manish Roorkiwal, Abhishek Rathore, Roma R Das, Muneendra K Singh, Ankit Jain, Samineni Srinivasan, Pooran M Gaur, Bharadwaj Chellapilla, Shailesh Tripathi, Yongle Li, John M Hickey, Aaron Lorenz, Tim Sutton, Jose Crossa, Jean-Luc Jannink, Rajeev K Varshney
Genomic selection (GS) unlike marker-assisted backcrossing (MABC) predicts breeding values of lines using genome-wide marker profiling and allows selection of lines prior to field-phenotyping, thereby shortening the breeding cycle. A collection of 320 elite breeding lines was selected and phenotyped extensively for yield and yield related traits at two different locations (Delhi and Patancheru, India) during the crop seasons 2011-12 and 2012-13 under rainfed and irrigated conditions. In parallel, these lines were also genotyped using DArTseq platform to generate genotyping data for 3000 polymorphic markers...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27919778/a-mutation-in-the-psst-homologue-of-complex-i-nadh-ubiquinone-oxidoreductase-from-tetranychus-urticae-is-associated-with-resistance-to-meti-acaricides
#5
Sabina Bajda, Wannes Dermauw, Rafaela Panteleri, Naoya Sugimoto, Vassilis Douris, Luc Tirry, Masahiro Osakabe, John Vontas, Thomas Van Leeuwen
The acaricidal compounds pyridaben, tebufenpyrad and fenpyroximate are frequently used in the control of phytophagous mites such as Tetranychus urticae, and are referred to as Mitochondrial Electron Transport Inhibitors, acting at the quinone binding pocket of complex I (METI-I acaricides). Because of their very frequent use, resistance evolved fast more than 20 years ago, and is currently wide-spread. Increased activity of P450 monooxygenases has been often associated with resistance, but target-site based resistance mechanisms were never reported...
December 2, 2016: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/27919371/a-machine-learning-based-framework-to-identify-type-2-diabetes-through-electronic-health-records
#6
Tao Zheng, Wei Xie, Liling Xu, Xiaoying He, Ya Zhang, Mingrong You, Gong Yang, You Chen
OBJECTIVE: To discover diverse genotype-phenotype associations affiliated with Type 2 Diabetes Mellitus (T2DM) via genome-wide association study (GWAS) and phenome-wide association study (PheWAS), more cases (T2DM subjects) and controls (subjects without T2DM) are required to be identified (e.g., via Electronic Health Records (EHR)). However, existing expert based identification algorithms often suffer in a low recall rate and could miss a large number of valuable samples under conservative filtering standards...
January 2017: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/27918076/genome-wide-association-analyses-of-54-traits-identified-multiple-loci-for-the-determination-of-floret-fertility-in-wheat
#7
Zifeng Guo, Dijun Chen, Ahmad M Alqudah, Marion S Röder, Martin W Ganal, Thorsten Schnurbusch
Increasing grain yield is still the main target of wheat breeding; yet today's wheat plants utilize less than half of their yield potential. Owing to the difficulty of determining grain yield potential in a large population, few genetic factors regulating floret fertility (i.e. the difference between grain yield potential and grain number) have been reported to date. In this study, we conducted a genome-wide association study (GWAS) by quantifying 54 traits (16 floret fertility traits and 38 traits for assimilate partitioning and spike morphology) in 210 European winter wheat accessions...
December 5, 2016: New Phytologist
https://www.readbyqxmd.com/read/27913567/drug-repositioning-screens-identify-triamterene-as-a-selective-drug-for-the-treatment-of-dna-mismatch-repair-deficient-cells
#8
Delphine Guillotin, Philip Austin, Rumena Begum, Marta O Freitas, Ashirwad Merve, Tim Brend, Susan C Short, Silvia Marino, Sarah A Martin
PURPOSE: The DNA Mismatch repair (MMR) pathway is required for the maintenance of genome stability. Unsurprisingly, mutations in MMR genes occur in a wide range of different cancers. Studies thus far have largely focused on specific tumor types or MMR mutations, however it is becoming increasingly clear that a therapy targeting MMR-deficiency in general would be clinically very beneficial. EXPERIMENTAL DESIGN: Based on a drug-repositioning approach, we screened a large panel of cell lines with various MMR deficiencies from a range of different tumor types with a compound drug library of previously approved drugs...
December 2, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27911958/advantages-of-an-improved-rhesus-macaque-genome-for-evolutionary-analyses
#9
Julien S Gradnigo, Abhishek Majumdar, Robert B Norgren, Etsuko N Moriyama
The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particularly to identify genes under adaptive or unique evolution in the human lineage. For such studies, it is necessary to align nucleotide sequences of homologous protein-coding genes among multiple species. The validity of these analyses is dependent on high quality genomic data. However, for most mammalian species (other than humans and mice), only draft genomes are available. There has been concern that some results obtained from evolutionary analyses using draft genomes may not be correct...
2016: PloS One
https://www.readbyqxmd.com/read/27910927/novel-chemoimmunotherapeutic-strategy-for-hepatocellular-carcinoma-based-on-a-genome-wide-association-study
#10
Kaku Goto, Dorcas A Annan, Tomoko Morita, Wenwen Li, Ryosuke Muroyama, Yasuo Matsubara, Sayaka Ito, Ryo Nakagawa, Yasushi Tanoue, Masahisa Jinushi, Naoya Kato
Pharmacotherapeutic options are limited for hepatocellular carcinoma (HCC). Recently, we identified the anti-tumor ligand MHC class I polypeptide-related sequence A (MICA) gene as a susceptibility gene for hepatitis C virus-induced HCC in a genome-wide association study (GWAS). To prove the concept of HCC immunotherapy based on the results of a GWAS, in the present study, we searched for drugs that could restore MICA expression. A screen of the FDA-approved drug library identified the anti-cancer agent vorinostat as the strongest hit, suggesting histone deacetylase inhibitors (HDACis) as potent candidates...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910110/runs-of-homozygosity-current-knowledge-and-applications-in-livestock
#11
REVIEW
E Peripolli, D P Munari, M V G B Silva, A L F Lima, R Irgang, F Baldi
This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome...
December 1, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27907911/genetic-variants-in-the-znf208-gene-are-associated-with-esophageal-cancer-in-a-chinese-han-population
#12
Huijie Wang, Jianzhong Yu, Yanling Guo, Zhengxing Zhang, Guoqi Liu, Jingjie Li, Xiyang Zhang, Tianbo Jin, Zhaoxia Wang
Previous studies showed an association between the ZNF208 gene and gastric cancer. In this study, we investigated the association between single nucleotide polymorphisms (SNPs) in ZNF208 and the risk of esophageal cancer in a Chinese Han population. We conducted a case-control study that included 386 cases and 495 controls. Five SNPs were selected from previous genome-wide association studies and genotyped using the Sequenom MassARRAY platform. Unconditional logistic regression was used to calculate odds ratios and 95% confidence intervals after adjustment for age and gender...
November 19, 2016: Oncotarget
https://www.readbyqxmd.com/read/27905878/genomic-prediction-using-preselected-dna-variants-from-a-gwas-with-whole-genome-sequence-data-in-holstein-friesian-cattle
#13
Roel F Veerkamp, Aniek C Bouwman, Chris Schrooten, Mario P L Calus
BACKGROUND: Whole-genome sequence data is expected to capture genetic variation more completely than common genotyping panels. Our objective was to compare the proportion of variance explained and the accuracy of genomic prediction by using imputed sequence data or preselected SNPs from a genome-wide association study (GWAS) with imputed whole-genome sequence data. METHODS: Phenotypes were available for 5503 Holstein-Friesian bulls. Genotypes were imputed up to whole-genome sequence (13,789,029 segregating DNA variants) by using run 4 of the 1000 bull genomes project...
December 1, 2016: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/27904879/the-establishment-and-diversification-of-epidemic-associated-serogroup-w-meningococcus-in-the-african-meningitis-belt-1994-to-2012
#14
Adam C Retchless, Fang Hu, Abdoul-Salam Ouédraogo, Seydou Diarra, Kristen Knipe, Mili Sheth, Lori A Rowe, Lassana Sangaré, Absetou Ky Ba, Soumeya Ouangraoua, Dhwani Batra, Ryan T Novak, Rasmata Ouédraogo Traoré, Xin Wang
Epidemics of invasive meningococcal disease (IMD) caused by meningococcal serogroup A have been eliminated from the sub-Saharan African so-called "meningitis belt" by the meningococcal A conjugate vaccine (MACV), and yet, other serogroups continue to cause epidemics. Neisseria meningitidis serogroup W remains a major cause of disease in the region, with most isolates belonging to clonal complex 11 (CC11). Here, the genetic variation within and between epidemic-associated strains was assessed by sequencing the genomes of 92 N...
November 2016: MSphere
https://www.readbyqxmd.com/read/27902807/improving-genetic-gain-with-genomic-selection-in-autotetraploid-potato
#15
Anthony T Slater, Noel O I Cogan, John W Forster, Benjamin J Hayes, Hans D Daetwyler
Potato ( L.) breeders consider a large number of traits during cultivar development and progress in conventional breeding can be slow. There is accumulating evidence that some of these traits, such as yield, are affected by a large number of genes with small individual effects. Recently, significant efforts have been applied to the development of genomic resources to improve potato breeding, culminating in a draft genome sequence and the identification of a large number of single nucleotide polymorphisms (SNPs)...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902805/genome-wide-association-mapping-reveals-novel-qtl-for-seedling-leaf-rust-resistance-in-a-worldwide-collection-of-winter-wheat
#16
Genqiao Li, Xiangyang Xu, Guihua Bai, Brett F Carver, Robert Hunger, J Michael Bonman, James Kolmer, Hongxu Dong
Leaf rust of wheat ( L.) is a major disease that causes significant yield losses worldwide. The short-lived nature of leaf rust resistance () genes necessitates a continuous search for novel sources of resistance. We performed a genome-wide association study (GWAS) on a panel of 1596 wheat accessions. The panel was evaluated for leaf rust reaction by testing with a bulk of Eriks. () isolates collected from multiple fields of Oklahoma in 2013 and two predominant races in the fields of Oklahoma in 2015. The panel was genotyped with a set of 5011 single-nucleotide polymorphism (SNP) markers...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902796/target-amplicon-sequencing-for-genotyping-genome-wide-single-nucleotide-polymorphisms-identified-by-whole-genome-resequencing-in-peanut
#17
Kenta Shirasawa, Chikara Kuwata, Manabu Watanabe, Masanobu Fukami, Hideki Hirakawa, Sachiko Isobe
Genome-wide genotyping data regarding breeding materials are essential resources for improving breeding efficiency, especially in plants with complex genomes with a high degree of polyploidy. Several current breeding efforts in cultivated peanut ( L.), which has a tetraploid genome, are devoted to developing high oleic acid cultivars. Genetic maps for such breeding programs have been developed using simple-sequence repeat (SSR) markers, the use of which requires time-consuming electrophoretic analyses. Next-generation sequencing (NGS) technology can overcome this technical hurdle...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902727/hybrid-origins-of-citrus-varieties-inferred-from-dna-marker-analysis-of-nuclear-and-organelle-genomes
#18
Tokurou Shimizu, Akira Kitajima, Keisuke Nonaka, Terutaka Yoshioka, Satoshi Ohta, Shingo Goto, Atsushi Toyoda, Asao Fujiyama, Takako Mochizuki, Hideki Nagasaki, Eli Kaminuma, Yasukazu Nakamura
Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins...
2016: PloS One
https://www.readbyqxmd.com/read/27900493/mining-the-cicer-arietinum-genome-for-the-mildew-locus-o-mlo-gene-family-and-comparative-evolutionary-analysis-of-the-mlo-genes-from-medicago-truncatula-and-some-other-plant-species
#19
Reena Deshmukh, V K Singh, Brahma Deo Singh
The mildew locus O (Mlo) gene family is ubiquitous in land plants. Some members of this gene family are involved in negative regulation of powdery mildew resistance, while others are involved in several other biological functions. Mlo proteins have characteristic seven transmembrane domains and a calmodulin-binding domain at their C-termini, and are associated with plasma membrane. The Mlo gene family has been studied in several economically important cereals, but little information is available on this gene family in the important legumes, Medicago truncatula Gaertn...
November 30, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27899914/how-useful-are-monogenic-rodent-models-for-the-study-of-human-non-alcoholic-fatty-liver-disease
#20
REVIEW
Jake P Mann, Robert K Semple, Matthew J Armstrong
Improving understanding of the genetic basis of human non-alcoholic fatty liver disease (NAFLD) has the potential to facilitate risk stratification of affected patients, permit personalized treatment, and inform development of new therapeutic strategies. Animal models have been widely used to interrogate the pathophysiology of, and genetic predisposition to, NAFLD. Nevertheless, considerable interspecies differences in intermediary metabolism potentially limit the extent to which results can be extrapolated to humans...
2016: Frontiers in Endocrinology
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