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https://www.readbyqxmd.com/read/28527809/accuracy-of-genomic-predictions-in-gyr-bos-indicus-dairy-cattle
#1
S A Boison, A T H Utsunomiya, D J A Santos, H H R Neves, R Carvalheiro, G Mészáros, Y T Utsunomiya, A S do Carmo, R S Verneque, M A Machado, J C C Panetto, J F Garcia, J Sölkner, M V G B da Silva
Genomic selection may accelerate genetic progress in breeding programs of indicine breeds when compared with traditional selection methods. We present results of genomic predictions in Gyr (Bos indicus) dairy cattle of Brazil for milk yield (MY), fat yield (FY), protein yield (PY), and age at first calving using information from bulls and cows. Four different single nucleotide polymorphism (SNP) chips were studied. Additionally, the effect of the use of imputed data on genomic prediction accuracy was studied...
May 17, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28527390/on-filter-direct-amplification-of-legionella-pneumophila-for-rapid-assessment-of-its-abundance-and-viability
#2
Farag A Samhan, Tiffany M Stedtfeld, Hassan Waseem, Maggie R Williams, Robert D Stedtfeld, Syed A Hashsham
Guidelines and regulations to control Legionella pneumophila in cooling water systems of large buildings are evolving due to the increasing number of outbreaks. Rapid, on-site, simple, and sensitive quantification methods that are also able to assess viability may be extremely useful in monitoring and control. Culture-based methods for measuring L. pneumophila may take 4-10 days and qPCR-based methods are also slow, requiring at least a day from sample to result, albeit mainly due to the need for sample transport to a centralized laboratory...
May 13, 2017: Water Research
https://www.readbyqxmd.com/read/28527365/variation-in-the-ovine-myf5-gene-and-its-effect-on-carcass-lean-meat-yield-in-new-zealand-romney-sheep
#3
Jiqing Wang, Huitong Zhou, Rachel H J Forrest, Jiang Hu, Xiu Liu, Shaobin Li, Yuzhu Luo, Jon G H Hickford
Myogenic factor 5 (MYF5) plays an important role in regulating skeletal muscle, but to date there have been no reports on whether the gene is variable and whether this variation is associated with meat yield in sheep. In this study, four variants (A to D) of ovine MYF5 containing two Single Nucleotide Polymorphisms (SNPs) and one basepair (bp) insertion/deletion were detected by Polymerase Chain Reaction - Single Stranded Conformational Polymorphism (PCR-SSCP) analysis. Breed differences in variant frequencies were observed...
May 11, 2017: Meat Science
https://www.readbyqxmd.com/read/28527290/association-of-polymorphic-variants-of-ptpn22-tnf-and-vdr-genes-in-children-with-lupus-nephritis-a-study-in-colombian-family-triads
#4
Gloria Garavito, Eduardo Egea, Luis Fang, Clara Malagón, Carlos Olmos, Luz González, Pilar Guarnizo, Gustavo Aroca, Guillermo López, Antonio Iglesias
INTRODUCTION: Systemic lupus erythematosus is an autoimmune disease in which the severity varies according to race, sex and age of onset. This variation is also observed in the genetic markers associated with the disease, including PTPN22, VDR and TNF genes. The genetic stratification in different populations worldwide can influence the variability. OBJECTIVE: To analyze the heritability of PTPN22, VDR and TNF genetic variants and their association with pediatric lupus nephritis in Colombian families...
June 1, 2017: Biomédica: Revista del Instituto Nacional de Salud
https://www.readbyqxmd.com/read/28527015/a-genome-wide-association-study-identifies-the-genomic-region-associated-with-shell-color-in-yesso-scallop-patinopecten-yessoensis
#5
Liang Zhao, Yangping Li, Yajuan Li, Jiachen Yu, Huan Liao, Shuyue Wang, Jia Lv, Jun Liang, Xiaoting Huang, Zhenmin Bao
The shell color polymorphism widely exists in economic shellfish, which not only results in a better visual perception but also shows great value as an economic trait for breeding. Small numbers of reddish-orange shell Yesso scallops, Patinopecten yessoensis, were found in cultured populations compared to the brown majority. In this study, a genome-wide association study was conducted to understand the genetic basis of shell color. Sixty-six 2b-RAD libraries with equal numbers of reddish-orange and brown shell individuals were constructed and sequenced using the Illumina HiSeq 2000 platform...
May 19, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28527004/comparative-volumetric-analysis-of-the-extent-of-resection-of-molecularly-and-histologically-distinct-low-grade-gliomas-and-its-role-on-survival
#6
Chikezie I Eseonu, Francisco Eguia, Karim ReFaey, Oscar Garcia, Fausto J Rodriguez, Kaisorn Chaichana, Alfredo Quinones-Hinojosa
The authors investigate the role of extent of resection (EOR) and genetic markers on patient outcome and survival for LGGs. We conducted a retrospective cohort between 2005 and 2015, of 109 adult patients who underwent surgery for a LGG by a single surgeon. Volumetric computations of MRI studies were conducted to evaluate the EOR, and genetic markers (IDH1, 1p/19q co-deletion, and p53) were assessed and their effects on survival and neurological outcome were evaluated. The median EOR was 88.1%. Permanent postoperative neurological deficits were seen in 4...
May 19, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28526988/identification-of-candidate-genes-for-paratuberculosis-resistance-in-the-native-italian-garfagnina-goat-breed
#7
Francesca Cecchi, Claudia Russo, Daniela Iamartino, Alessia Galiero, Barbara Turchi, Filippo Fratini, Sara Degl'Innocenti, Raffaele Mazza, Stefano Biffani, Giovanna Preziuso, Carlo Cantile
Paratuberculosis disease is a chronic bacterial disease infection of ruminants of global relevance, caused by MAP (Mycobacterium avium subsp. paratuberculosis). The present study was conducted on the Garfagnina goat breed that is an Italian native goat population registered on the Tuscan regional repertory of genetic resources at risk of extinction. Forty-eight adult goats (27 serologically positive to MAP-positive and 21 serologically negative to MAP-negative) belonging to a single flock that had experienced annual mortalities due to MAP infection were identified and genotyped with the Illumina GoatSNP60 BeadChip...
May 19, 2017: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/28526937/molecular-confirmation-of-intraspecific-tomato-solanum-lycopersicum-hybrids-and-their-evaluation-against-late-blight-and-cucumber-mosaic-virus
#8
Amjad Hameed, Muhammad Yussouf Saleem, Khalid Pervaiz Akhtar, Muhammad Shoaib, Qumer Iqbal, Muhammad Asghar
Tomato is one of the most consumed vegetables in the world. Diseases are the number one concern in the development of high-yield and disease-resistant tomato hybrids which is the foremost priority of breeders. Present study was conducted (1) to develop DNA-based markers for genetic confirmation of tomato F1 hybrids, (2) to utilize sequenced characterized amplified region (SCAR) marker linked to the Ph-3 gene for Phytophthora infestans resistance in tomato and (3) to evaluate male and female parental genotypes and their F1 hybrids against late blight (LB) and cucumber mosaic virus (CMV)...
May 19, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/28526930/micrornas-in-parkinson-s-disease
#9
REVIEW
Abhishek Singh, Dwaipayan Sen
Parkinson's disease is the second most common neurodegenerative disease commonly affecting the older population. Loss of dopaminergic neurons in the substantia nigra of brain leads to impairment of motor activities as well as cognitive defects. There are many underlying causes to this disease, both genetic and epigenetic, which are yet to be fully explored. Non-coding RNAs are significant part of our genome and are involved in various cellular processes. MicroRNAs, which are small non-coding RNAs having 20-22 nucleotides, are involved in many underlying mechanisms of pathogenesis of several neurodegenerative diseases including Parkinson's...
May 19, 2017: Experimental Brain Research. Experimentelle Hirnforschung. Expérimentation Cérébrale
https://www.readbyqxmd.com/read/28526913/mapping-qtls-controlling-kernel-dimensions-in-a-wheat-inter-varietal-ril-mapping-population
#10
Ruiru Cheng, Zhongxin Kong, Liwei Zhang, Quan Xie, Haiyan Jia, Dong Yu, Yulong Huang, Zhengqiang Ma
Seven kernel dimension QTLs were identified in wheat, and kernel thickness was found to be the most important dimension for grain weight improvement. Kernel morphology and weight of wheat (Triticum aestivum L.) affect both yield and quality; however, the genetic basis of these traits and their interactions has not been fully understood. In this study, to investigate the genetic factors affecting kernel morphology and the association of kernel morphology traits with kernel weight, kernel length (KL), width (KW) and thickness (KT) were evaluated, together with hundred-grain weight (HGW), in a recombinant inbred line population derived from Nanda2419 × Wangshuibai, with data from five trials (two different locations over 3 years)...
May 19, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28526788/zinc-resistance-within-swine-associated-methicillin-resistant-staphylococcus-aureus-mrsa-isolates-in-the-usa-is-associated-with-mlst-lineage
#11
Samantha J Hau, Timothy Frana, Jisun Sun, Peter R Davies, Tracy L Nicholson
Zinc resistance in livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) sequence type (ST) 398 is primarily mediated by the czrC gene co-located with the mecA gene, encoding methicillin resistance, within the type V SCCmec element. Because czrC and mecA are located within the same mobile genetic element, it has been suggested that the use of in feed zinc as an antidiarrheal agent has the potential to contribute to the emergence and spread of MRSA in swine through increased selection pressure to maintain the SCCmec element in isolates obtained from pigs...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28526755/the-matrix-protein-tiggrin-regulates-plasmatocyte-maturation-in-drosophila-larva
#12
Chen U Zhang, Ken M Cadigan
The lymph gland (LG) is a major source of hematopoiesis during Drosophila development. In this tissue, prohemocytes differentiate into multiple lineages including macrophage-like plasmatocytes, which comprise the vast majority of mature hemocytes. Previous studies have uncovered genetic pathways that regulate prohemocyte maintenance and some cell fate choices between hemocyte lineages. However, less is known about how the plasmatocyte pool of the LG is established and matures. Here we report that Tiggrin, a matrix protein expressed in the LG, is a specific regulator of plasmatocyte maturation...
May 19, 2017: Development
https://www.readbyqxmd.com/read/28526731/validated-bayesian-differentiation-of-causative-and-passenger-mutations
#13
Frederick R Cross, Michal Breker, Kristi Lieberman
In many contexts, the problem arises of determining which of many candidate mutations is the most likely to be causative for some phenotype. It is desirable to have a way to evaluate this probability that relies as little as possible on previous knowledge, to avoid bias against discovering new genes or functions. We are isolating mutants with blocked cell cycle progression in Chlamydomonas, and determining mutant genome sequences. Due to the intensity of UV mutagenesis required for efficient mutant collection, the mutants contain multiple mutations altering coding sequence...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526729/phased-genotyping-by-sequencing-enhances-analysis-of-genetic-diversity-and-reveals-divergent-copy-number-variants-in-maize
#14
Heather Manching, Subhajit Sengupta, Keith R Hopper, Shawn W Polson, Yuan Ji, Randall J Wisser
High-throughput sequencing of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires a number of issues encountered with GBS be considered, including the sequencing of non-overlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526698/improving-response-in-genomic-selection-with-a-population-based-selection-strategy-optimal-population-value-selection
#15
Matthew Goiffon, Aaron Kusmec, Lizhi Wang, Guiping Hu, Patrick Schnable
Genomic selection (GS) identifies individuals for inclusion in breeding programs based on the sum of their estimated marker effects or genomic estimated breeding values (GEBVs). Due to significant correlation between GEBVs and true breeding values, this has resulted in enhanced rates of genetic gain as compared to traditional methods of selection. Three extensions to GS, weighted genomic selection (WGS), optimal haploid value (OHV) selection, and genotype building (GB) selection have been proposed to improve long-term response and to facilitate the efficient development of doubled haploids...
May 19, 2017: Genetics
https://www.readbyqxmd.com/read/28526288/the-association-between-mid-facial-morphology-and-climate-in-northeast-europe-differs-from-that-in-north-asia-implications-for-understanding-the-morphology-of-late-pleistocene-homo-sapiens
#16
Andrej A Evteev, Alla A Movsesian, Alexandra N Grosheva
The climate of northeastern Europe is likely to resemble in many ways Late Pleistocene periglacial conditions in Europe, but there have been relatively few studies exploring the association between climate and morphology in the mid-face of modern northeastern European populations. To fill this gap, we sampled 540 male skulls from 22 European and Near Eastern groups, including 314 skulls from 11 populations from northeastern Europe, to test for possible climate-morphology association at the continental scale...
June 2017: Journal of Human Evolution
https://www.readbyqxmd.com/read/28525989/determination-of-genetic-effects-of-atf3-and-cdkn1a-genes-on-milk-yield-and-compositions-in-chinese-holstein-population
#17
REVIEW
Bo Han, Weijun Liang, Lin Liu, Yanhua Li, Dongxiao Sun
BACKGROUND: Our previous RNA-sequencing study revealed that the ATF3 and CDKN1A genes were remarkably differentially expressed between the mammary glands of lactating Holstein cows with extremely high and low milk protein and fat percentage so that both of them were considered as candidates for milk composition. Herein, we further verified whether these genes have genetic effects on milk production traits in a Chinese Holstein cow population. RESULTS: By re-sequencing the entire coding and regulatory regions, we identified four SNPs in 5'promoter region, two in exons, seven in 3' un-translated region (UTR), and six in 3'flanking region of ATF3 gene, and one SNP in exon 5, two in 3'UTR, and two in 3'flanking region of CDKN1A gene...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525980/the-distribution-of-mitochondrial-dna-haplogroup-h-in-southern-iberia-indicates-ancient-human-genetic-exchanges-along-the-western-edge-of-the-mediterranean
#18
Candela L Hernández, Jean M Dugoujon, Andrea Novelletto, Juan N Rodríguez, Pedro Cuesta, Rosario Calderón
BACKGROUND: The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525661/comparison-between-mononucleotide-and-dinucleotide-marker-panels-in-gastric-cancer-with-loss-of-hmlh1-or-hmsh2-expression
#19
Jeong Goo Kim, Soyoung Shin, Joonhong Park
BACKGROUND: DNA mismatch repair deficiency is an important molecular mechanism of genetic instability in gastric cancer, and a high instability at microsatellites is associated with favorable prognosis. We compared mononucleotide and dinucleotide microsatellite instability (MSI) marker panels in 56 paired gastric tumor and normal samples. METHODS: The mononucleotide marker panel (mono panel) consisted of 8 markers: BAT25, BAT26, BAT40, BAT-RII, NR21, NR22, NR24 and NR27...
May 16, 2017: International Journal of Biological Markers
https://www.readbyqxmd.com/read/28525659/genetic-variability-in-jatropha-curcas-l-from-diallel-crossing
#20
D O Ribeiro, R Silva-Mann, S V Alvares-Carvalho, E M S Souza, M C Vasconcelos, A F Blank
Physic nut (Jatropha curcas L.) presents high oilseed yield and low production cost. However, technical-scientific knowledge on this crop is still limited. This study aimed to evaluate and estimate the genetic variability of hybrids obtained from dialell crossing. Genetic variability was carried out using ISSR molecular markers. For genetic variability, nine primers were used, and six were selected with 80.7% polymorphism. Genetic similarity was obtained using the NTSYS pc. 2.1 software, and cluster analysis was obtained by the UPGMA method...
May 18, 2017: Genetics and Molecular Research: GMR
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