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Genome wide selection

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https://www.readbyqxmd.com/read/29777112/micrornas-as-potential-therapeutics-to-enhance-chemosensitivity-in-advanced-prostate-cancer
#1
Hui-Ming Lin, Iva Nikolic, Jessica Yang, Lesley Castillo, Niantao Deng, Chia-Ling Chan, Nicole K Yeung, Eoin Dodson, Benjamin Elsworth, Calan Spielman, Brian Y Lee, Zoe Boyer, Kaylene J Simpson, Roger J Daly, Lisa G Horvath, Alexander Swarbrick
Docetaxel and cabazitaxel are taxane chemotherapy treatments for metastatic castration-resistant prostate cancer (CRPC). However, therapeutic resistance remains a major issue. MicroRNAs are short non-coding RNAs that can silence multiple genes, regulating several signalling pathways simultaneously. Therefore, synthetic microRNAs may have therapeutic potential in CRPC by regulating genes involved in taxane response and minimise compensatory mechanisms that cause taxane resistance. To identify microRNAs that can improve the efficacy of taxanes in CRPC, we performed a genome-wide screen of 1280 microRNAs in the CRPC cell lines PC3 and DU145 in combination with docetaxel or cabazitaxel treatment...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29776387/integrative-genomics-approaches-validate-ppyuc11-like-as-candidate-gene-for-the-stony-hard-trait-in-peach-p-persica-l-batsch
#2
Marco Cirilli, Daniela Giovannini, Angelo Ciacciulli, Remo Chiozzotto, Stefano Gattolin, Laura Rossini, Alessandro Liverani, Daniele Bassi
BACKGROUND: Texture is one of the most important fruit quality attributes. In peach, stony hard (SH) is a recessive monogenic trait (hd/hd) that confers exceptionally prolonged firm flesh to fully ripe fruit. Previous studies have shown that the SH mutation affects the fruit ability to synthesize appropriate amounts of indol-3-acetic acid (IAA), which orchestrates the ripening processes through the activation of system 2 ethylene pathway. Allelic variation in a TC microsatellite located within the first intron of PpYUC11-like (a YUCCA-like auxin-biosynthesis gene) has been recently proposed as the causal mutation of the SH phenotype...
May 18, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29776331/genome-wide-detection-of-selection-signatures-in-chinese-indigenous-laiwu-pigs-revealed-candidate-genes-regulating-fat-deposition-in-muscle
#3
Minhui Chen, Jiying Wang, Yanping Wang, Ying Wu, Jinluan Fu, Jian-Feng Liu
BACKGROUND: Currently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, few studies have focused on selection footprints of indigenous breeds. Laiwu pig is an invaluable Chinese indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent model to detect footprint as the result of natural and artificial selection for fat deposition in muscle. RESULT: In this study, based on GeneSeek Genomic profiler Porcine HD data, three complementary methods, FST , iHS (integrated haplotype homozygosity score) and CLR (composite likelihood ratio), were implemented to detect selection signatures in the whole genome of Laiwu pigs...
May 18, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29776327/utility-of-whole-genome-sequence-data-for-across-breed-genomic-prediction
#4
Biaty Raymond, Aniek C Bouwman, Chris Schrooten, Jeanine Houwing-Duistermaat, Roel F Veerkamp
BACKGROUND: Genomic prediction (GP) across breeds has so far resulted in low accuracies of the predicted genomic breeding values. Our objective was to evaluate whether using whole-genome sequence (WGS) instead of low-density markers can improve GP across breeds, especially when markers are pre-selected from a genome-wide association study (GWAS), and to test our hypothesis that many non-causal markers in WGS data have a diluting effect on accuracy of across-breed prediction. METHODS: Estimated breeding values for stature and bovine high-density (HD) genotypes were available for 595 Jersey bulls from New Zealand, 957 Holstein bulls from New Zealand and 5553 Holstein bulls from the Netherlands...
May 18, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29775784/genome-wide-association-mapping-of-virulence-gene-in-rice-blast-fungus-magnaporthe-oryzae-using-a-genotyping-by-sequencing-approach
#5
Siripar Korinsak, Sithichoke Tangphatsornruang, Wirulda Pootakham, Samart Wanchana, Anucha Plabpla, Chatchawan Jantasuriyarat, Sujin Patarapuwadol, Apichart Vanavichit, Theerayut Toojinda
Magnaporthe oryzae is a fungal pathogen causing blast disease in many plant species. In this study, Seventy three isolates of M. oryzae collected from rice (Oryza sativa) in 1996-2014 were genotyped using a genotyping-by-sequencing approach to detect genetic variation. Association study was performed to identify single nucleotide polymorphism (SNP) associated with virulence genes using 831 selected SNP and infection phenotypes on local and improved rice varieties. Population structure analysis revealed eight subpopulations...
May 15, 2018: Genomics
https://www.readbyqxmd.com/read/29775471/host-directed-combinatorial-rnai-improves-inhibition-of-diverse-strains-of-influenza-a-virus-in-human-respiratory-epithelial-cells
#6
Michael A Estrin, Islam T M Hussein, Wendy B Puryear, Anne C Kuan, Stephen C Artim, Jonathan A Runstadler
Influenza A virus infections are important causes of morbidity and mortality worldwide, and currently available prevention and treatment methods are suboptimal. In recent years, genome-wide investigations have revealed numerous host factors that are required for influenza to successfully complete its life cycle. However, only a select, small number of influenza strains were evaluated using this platform, and there was considerable variation in the genes identified across different investigations. In an effort to develop a universally efficacious therapeutic strategy with limited potential for the emergence of resistance, this study was performed to investigate the effect of combinatorial RNA interference (RNAi) on inhibiting the replication of diverse influenza A virus subtypes and strains...
2018: PloS One
https://www.readbyqxmd.com/read/29774533/analysis-of-type-2-diabetes-and-obesity-genetic-variants-in-mexican-pima-indians-marked-allelic-differentiation-among-amerindians-at-hla
#7
Wen-Chi Hsueh, Peter H Bennett, Julian Esparza-Romero, Rene Urquidez-Romero, Mauro E Valencia, Eric Ravussin, Robert C Williams, William C Knowler, Leslie J Baier, Leslie O Schulz, Robert L Hanson
Prevalence of diabetes and obesity in Mexican Pima Indians is low, while prevalence in US Pima Indians is high. Although lifestyle likely accounts for much of the difference, the role of genetic factors is not well explored. To examine this, we genotyped 359 single nucleotide polymorphisms, including established type 2 diabetes and obesity variants from genome-wide association studies (GWAS) and 96 random markers, in 342 Mexican Pimas. A multimarker risk score of obesity variants was associated with body mass index (BMI; β = 0...
May 17, 2018: Annals of Human Genetics
https://www.readbyqxmd.com/read/29772750/the-late-embryogenesis-abundant-protein-family-in-cassava-manihot-esculenta-crantz-genome-wide-characterization-and-expression-during-abiotic-stress
#8
Chunlai Wu, Wei Hu, Yan Yan, Weiwei Tie, Zehong Ding, Jianchun Guo, Guangyuan He
Late embryogenesis abundant (LEA) proteins, as a highly diverse group of polypeptides, play an important role in plant adaptation to abiotic stress; however, LEAs from cassava have not been studied in cassava. In this study, 26 LEA members were genome-wide identified from cassava, which were clustered into seven subfamily according to evolutionary relationship, protein motif, and gene structure analyses. Chromosomal location and duplication event analyses suggested that 26 MeLEAs distributed in 10 chromosomes and 11 MeLEA paralogues were subjected to purifying selection...
May 17, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29772717/a-rapid-screen-for-host-encoded-mirnas-with-inhibitory-effects-against-ebola-virus-using-a-transcription-and-replication-competent-virus-like-particle-system
#9
Zhongyi Wang, Jiaming Li, Yingying Fu, Zongzheng Zhao, Chunmao Zhang, Nan Li, Jingjing Li, Hongliang Cheng, Xiaojun Jin, Bing Lu, Zhendong Guo, Jun Qian, Linna Liu
MicroRNAs (miRNAs) may become efficient antiviral agents against the Ebola virus (EBOV) targeting viral genomic RNAs or transcripts. We previously conducted a genome-wide search for differentially expressed miRNAs during viral replication and transcription. In this study, we established a rapid screen for miRNAs with inhibitory effects against EBOV using a tetracistronic transcription- and replication-competent virus-like particle (trVLP) system. This system uses a minigenome comprising an EBOV leader region, luciferase reporter, VP40, GP, VP24, EBOV trailer region, and three noncoding regions from the EBOV genome and can be used to model the life cycle of EBOV under biosafety level (BSL) 2 conditions...
May 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29770990/pool-based-genome-wide-association-study-identified-novel-candidate-regions-on-bta9-and-14-for-oleic-acid-percentage-in-japanese-black-cattle
#10
Fuki Kawaguchi, Hiroto Kigoshi, Ayaka Nakajima, Yuta Matsumoto, Yoshinobu Uemoto, Moriyuki Fukushima, Emi Yoshida, Eiji Iwamoto, Takayuki Akiyama, Namiko Kohama, Eiji Kobayashi, Takeshi Honda, Kenji Oyama, Hideyuki Mannen, Shinji Sasazaki
Fatty acid composition is an important indicator of beef quality. The objective of this study was to search the potential candidate region for fatty acid composition. We performed pool-based genome-wide association studies (GWAS) for oleic acid percentage (C18:1) in a Japanese Black cattle population from the Hyogo prefecture. GWAS analysis revealed two novel candidate regions on BTA9 and BTA14. The most significant single nucleotide polymorphisms (SNPs) in each region were genotyped in a population (n = 899) to verify their effect on C18:1...
May 17, 2018: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/29770973/genome-wide-based-model-predicting-recovery-from-portosystemic-shunting-after-liver-shunt-attenuation-in-dogs
#11
Lindsay Van den Bossche, Frank G van Steenbeek, Maarten F Weber, Bart Spee, Louis C Penning, Freek J van Sluijs, Flin Zomerdijk, Marian J A Groot Koerkamp, Jan Rothuizen, Iwan A Burgener, Anne Kummeling
BACKGROUND: In dogs with congenital portosystemic shunt (CPSS), recovery after surgical CPSS attenuation is difficult to predict. OBJECTIVES: Our aim was to build a model with plasma albumin concentration and mRNA expression levels of hepatic gene products as predictors of recovery from portosystemic shunting after surgery. ANIMALS: Seventy-three client-owned dogs referred for surgical attenuation of CPSS. METHODS: A prediction model was constructed using 2 case-control studies of recovered and nonrecovered dogs after surgical CPSS attenuation...
May 17, 2018: Journal of Veterinary Internal Medicine
https://www.readbyqxmd.com/read/29768192/nuclear-export-inhibition-enhances-hlh-30-tfeb-activity-autophagy-and-lifespan
#12
Melissa J Silvestrini, Joseph R Johnson, Anita V Kumar, Tara G Thakurta, Karine Blais, Zachary A Neill, Sarah W Marion, Victoria St Amand, Robert A Reenan, Louis R Lapierre
Transcriptional modulation of the process of autophagy involves the transcription factor HLH-30/TFEB. In order to systematically determine the regulatory network of HLH-30/TFEB, we performed a genome-wide RNAi screen in C. elegans and found that silencing the nuclear export protein XPO-1/XPO1 enhances autophagy by significantly enriching HLH-30 in the nucleus, which is accompanied by proteostatic benefits and improved longevity. Lifespan extension via xpo-1 silencing requires HLH-30 and autophagy, overlapping mechanistically with several established longevity models...
May 15, 2018: Cell Reports
https://www.readbyqxmd.com/read/29767356/rna-seq-and-expression-arrays-selection-guidelines-for-genome-wide-expression-profiling
#13
Jessica Minnier, Nathan D Pennock, Quichen Guo, Pepper Schedin, Christina A Harrington
The development of genome-wide gene expression profiling technologies over the past two decades has produced great opportunity for researchers to explore the transcriptome and to better understand biological systems and their perturbation. In this chapter we provide an overview of microarray and massively parallel sequencing technologies and their application to gene expression analysis. We discuss factors that impact expression data generation and analysis that which should be considered in the application of these technology platforms...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29767279/identification-and-validation-of-qtl-for-grain-yield-and-plant-water-status-under-contrasting-water-treatments-in-fall-sown-spring-wheats
#14
Junli Zhang, Shiferaw Abate Gizaw, Eligio Bossolini, Joshua Hegarty, Tyson Howell, Arron H Carter, Eduard Akhunov, Jorge Dubcovsky
Chromosome regions affecting grain yield, grain yield components and plant water status were identified and validated in fall-sown spring wheats grown under full and limited irrigation. Increases in wheat production are required to feed a growing human population. To understand the genetic basis of grain yield in fall-sown spring wheats, we performed a genome-wide association study (GWAS) including 262 photoperiod-insensitive spring wheat accessions grown under full and limited irrigation treatments. Analysis of molecular variance showed that 4...
May 16, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29766673/genomic-characterization-of-individuals-presenting-extreme-phenotypes-of-high-and-low-risk-to-develop-tobacco-induced-lung-cancer
#15
Juan Pablo Fusco, Guillermo Pita, María José Pajares, Maria Pilar Andueza, Ana Patiño-García, Juan P de-Torres, Alfonso Gurpide, Javier Zulueta, Rosario Alonso, Nuria Alvarez, Ruben Pio, Ignacio Melero, Miguel F Sanmamed, Maria Rodriguez Ruiz, Ignacio Gil-Bazo, Jose María Lopez-Picazo, Ciro Casanova, Rebeca Baz Davila, Antonio Agudo, Maria Dolores Lozano, Alvaro Gonzalez, Nuria Sala, Eva Ardanaz, Javier Benitez, Luis Montuenga, Anna Gonzalez-Neira, Jose Luis Perez-Gracia
Single nucleotide polymorphisms (SNPs) may modulate individual susceptibility to carcinogens. We designed a genome-wide association study to characterize individuals presenting extreme phenotypes of high and low risk to develop tobacco-induced non-small cell lung cancer (NSCLC), and we validated our results. We hypothesized that this strategy would enrich the frequencies of the alleles that contribute to the observed traits. We genotyped 2.37 million SNPs in 95 extreme phenotype individuals, that is: heavy smokers that either developed NSCLC at an early age (extreme cases); or did not present NSCLC at an advanced age (extreme controls), selected from a discovery set (n = 3631)...
May 15, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29764960/a-genomic-region-containing-rec8-and-rnf212b-is-associated-with-individual-recombination-rate-variation-in-a-wild-population-of-red-deer-cervus-elaphus
#16
Susan E Johnston, Jisca Huisman, Josephine M Pemberton
Recombination is a fundamental feature of sexual reproduction, ensuring proper disjunction, preventing mutation accumulation and generating new allelic combinations upon which selection can act. However it is also mutagenic, and breaks up favourable allelic combinations previously built up by selection. Identifying the genetic drivers of recombination rate variation is a key step in understanding the causes and consequences of this variation, how loci associated with recombination are evolving and how they affect the potential of a population to respond to selection...
May 15, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29764927/identification-of-genes-related-to-cold-tolerance-and-a-functional-allele-that-confers-cold-tolerance
#17
Ning Xiao, Yong Gao, Huangjun Qian, Qiang Gao, Yunyu Wu, Dongping Zhang, Zhiping Wang, Xiaoxiang Zhang, Ling Yu, Yuhong Li, Cunhong Pan, Guangqing Liu, Changhai Zhou, Min Jiang, Niansheng Huang, Zhuo Chen, Chengzhi Liang, Zhengyuan Dai, Jianmin Chen, Aihong Li
Cold stress is a major factor limiting rice (Oryza sativa L.) production worldwide, especially at the seedling and booting stages. Identification of genes associated with cold tolerance (CT) in rice is important for sustainable food production. Here, we report the results of a genome-wide association study (GWAS) to identify the genetic loci associated with CT by using a 1,033-accession diversity panel. We identified five CT-related genetic loci at the booting stage. Accessions carrying multiple cold-tolerant alleles displayed a higher seed setting rate than did accessions that had no cold-tolerant alleles or carried a single allele...
May 15, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29763729/in-silico-identification-of-molecular-mimics-involved-in-the-pathogenesis-of-clostridium-botulinum-atcc-3502-strain
#18
Tulika Bhardwaj, Shafiul Haque, Pallavi Somvanshi
Bacterial pathogens invade and disrupt the host defense system by means of protein sequences structurally similar at global and local level both. The sharing of homologous sequences between the host and the pathogenic bacteria mediates the infection and defines the concept of molecular mimicry. In this study, various computational approaches were employed to elucidate the pathogenicity of Clostridium at genome-wide level. Genome-wide study revealed that the pathogen mimics the host (Homo sapiens) and unraveled the complex pathogenic pathway of causing infections...
May 12, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29762716/crispor-intuitive-guide-selection-for-crispr-cas9-genome-editing-experiments-and-screens
#19
Jean-Paul Concordet, Maximilian Haeussler
CRISPOR.org is a web tool for genome editing experiments with the CRISPR-Cas9 system. It finds guide RNAs in an input sequence and ranks them according to different scores that evaluate potential off-targets in the genome of interest and predict on-target activity. The list of genomes is continuously expanded, with more 150 genomes added in the last two years. CRISPOR tries to provide a comprehensive solution from selection, cloning and expression of guide RNA as well as providing primers needed for testing guide activity and potential off-targets...
May 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29762663/population-genomic-data-reveal-genes-related-to-important-traits-of-quail
#20
Yan Wu, Yaolei Zhang, Zhuocheng Hou, Guangyi Fan, Jinsong Pi, Shuai Sun, Jiang Chen, Huaqiao Liu, Xiao Du, Jie Shen, Gang Hu, Wenbin Chen, Ailuan Pan, Pingping Yin, Xiaoli Chen, Yuejin Pu, He Zhang, Zhenhua Liang, Jianbo Jian, Hao Zhang, Bin Wu, Jing Sun, Jianwei Chen, Hu Tao, Ting Yang, Hongwei Xiao, Huan Yang, Chuanwei Zheng, Mingzhou Bai, Xiaodong Fang, David W Burt, Wen Wang, Qingyi Li, Xun Xu, Chengfeng Li, Huanming Yang, Jian Wang, Ning Yang, Xin Liu, Jinping Du
Background: Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution and functional studies. Results: Here, we present a quail genome assembly spanning 1...
May 11, 2018: GigaScience
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