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https://www.readbyqxmd.com/read/29890628/-prdm16-gene-polymorphism-is-associated-with-obesity-and-blood-lipids-profiles-in-saudi-population
#1
Aishah AlAmrani, Mouaadh AbdelKarim, Mohammed AlZoghaibi
AIMS: The PR domain containing 16 ( PRDM16 ) gene and the Phosphodiesterase 4D ( PDE4 ) gene are both an essential regulators in the thermogenesis process in the brown adipose tissues (BAT). The influence of polymorphisms in those genes on obesity and blood lipids profile is unknown particularly in the Saudi population, so the current study is aiming to explore that. METHODS: A case control format was used that involved 89 obese individual and 84 non-obese (control)...
June 8, 2018: Journal of Clinical Medicine
https://www.readbyqxmd.com/read/29860625/qtl-mapping-of-pre-harvest-sprouting-resistance-in-a-white-wheat-cultivar-danby
#2
Mingqin Shao, Guihua Bai, Trevor W Rife, Jesse Poland, Meng Lin, Shubing Liu, Hui Chen, Tadele Kumssa, Allan Fritz, Harold Trick, Yan Li, Guorong Zhang
One major and three minor QTLs for resistance to pre-harvest sprouting (PHS) were identified from a white wheat variety "Danby." The major QTL on chromosome 3A is TaPHS1, and the sequence variation in its promoter region was responsible for the PHS resistance. Additive × additive effects were detected between two minor QTLs on chromosomes 3B and 5A, which can greatly enhance the PHS resistance. Pre-harvest sprouting (PHS) causes significant losses in yield and quality in wheat. White wheat is usually more susceptible to PHS than red wheat...
June 2, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29803923/the-association-of-lncrna-hulc-polymorphisms-with-hepatocellular-cancer-risk-and-prognosis
#3
Ben-Gang Wang, Zhi Lv, Han-Xi Ding, Xin-Xin Fang, Jing Wen, Qian Xu, Yuan Yuan
BACKGROUND: Genetic polymorphisms in lncRNA HULC may affect the susceptibility and clinical outcome of cancer. We aimed to investigate the association of HULC tagSNPs with the risk and prognosis of hepatocellular cancer, as well as the influence of the SNPs on lncRNA expression level. METHODS: A total of 1338 samples were recruited in the risk study. Among them, 351 HCC patients were involved in the prognosis study. SNP genotyping was performed using KASP method and lncRNA expression was detected by Real-time PCR...
May 24, 2018: Gene
https://www.readbyqxmd.com/read/29791233/association-of-a-chromosome-locus-9p21-3-cdkn2b-as1-variant-rs4977574-with-hypertension-the-tamrisk-study
#4
Tarja Kunnas, Jaakko Piesanen, Seppo T Nikkari
AIMS: Chromosome locus 9p21.3 CDKN2B antisense RNA 1 (CDKN2B-AS1) has been found to contain multiple genetic markers for coronary artery disease (CAD) by genome-wide association studies (GWAS). Of these, the association of variants rs4977574, rs10757274, and rs2383206 with hypertension was studied in the Tampere adult population cardiovascular risk study (TAMRISK). MATERIALS AND METHODS: A Finnish cohort of 336 subjects diagnosed with hypertension and 444 controls was analyzed...
May 2018: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/29746580/characterization-and-mapping-of-leaf-rust-resistance-in-four-durum-wheat-cultivars
#5
Dhouha Kthiri, Alexander Loladze, P R MacLachlan, Amidou N'Diaye, Sean Walkowiak, Kirby Nilsen, Susanne Dreisigacker, Karim Ammar, Curtis J Pozniak
Widening the genetic basis of leaf rust resistance is a primary objective of the global durum wheat breeding effort at the International Wheat and Maize Improvement Center (CIMMYT). Breeding programs in North America are following suit, especially after the emergence of new races of Puccinia triticina such as BBG/BP and BBBQD in Mexico and the United States, respectively. This study was conducted to characterize and map previously undescribed genes for leaf rust resistance in durum wheat and to develop reliable molecular markers for marker-assisted breeding...
2018: PloS One
https://www.readbyqxmd.com/read/29742137/genetic-characterization-of-indigenous-goat-breeds-in-romania-and-hungary-with-a-special-focus-on-genetic-resistance-to-mastitis-and-gastrointestinal-parasitism-based-on-40-snps
#6
Daniela Elena Ilie, Szilvia Kusza, Maria Sauer, Dinu Gavojdian
Goat breeding has become an important sector in Eastern Europe, with Romania and Hungary being among the major producer countries. Given the limited number of research done up-to-date concerning genetic studies of indigenous goat breeds reared in Romania and Hungary, the current preliminary study aimed to analyze the variability of genes related to mastitis and gastrointestinal parasitism by using Kompetitive Allele Specific PCR (KASP™). We studied 52 single nucleotide polymorphisms (SNPs) belonging to 19 genes in indigenous breeds from both countries, namely Banat's White (n = 36), Carpatina (n = 35) from Romania and Hungarian Milking (n = 79) and identified 16 polymorphic SNPs among 10 genes (PTX3, IL6, CLEC4E, IL8, IL1RN, IL15RA, TNFSF13, SOCS3, TNF and TLR3) in 150 animals...
2018: PloS One
https://www.readbyqxmd.com/read/29704936/associations-between-single-nucleotide-polymorphisms-in-the-calcium-sensing-receptor-and-chronic-kidney-disease-mineral-and-bone-disorder-in-cats
#7
R F Geddes, R E Jepson, Y Forcada, J Elliott, H M Syme
Feline chronic kidney disease (CKD) is associated with high variability in severity of CKD-mineral and bone disorder (CKD-MBD). The calcium sensing receptor (CaSR) regulates circulating parathyroid hormone (PTH) and calcium concentrations. Single nucleotide polymorphisms (SNPs) in the CaSR are associated with severity of secondary renal hyperparathyroidism and total calcium concentrations in human patients receiving haemodialysis. The objective of this study was to explore associations between polymorphisms in the feline CaSR (fCaSR) and biochemical changes observed in CKD-MBD...
May 2018: Veterinary Journal
https://www.readbyqxmd.com/read/29683944/slco1b1-polymorphisms-are-associated-with-drug-intolerance-in-childhood-leukemia-maintenance-therapy
#8
İrem Eldem, Duygu Yavuz, Özge Cumaoğullari, Talia İleri, Elif Ünal İnce, Mehmet Ertem, Beyza Doğanay Erdoğan, Recep Bindak, Hilal Özdağ, N Lale Şatiroğlu-Tufan, L Zümrüt Uysal
BACKGROUND: Therapy discontinuations and toxicities occur because of significant interindividual variations in 6-mercaptopurine (6-MP) and methotrexate (MTX) response during maintenance therapy of childhood acute lymphoblastic leukemia (ALL). 6-MP/MTX intolerance in some of the patients cannot be explained by thiopurine S-methyl transferase (TPMT) gene variants. In this study, we aimed to investigate candidate pharmacogenetic determinants of 6-MP and MTX intolerance in Turkish ALL children...
April 20, 2018: Journal of Pediatric Hematology/oncology
https://www.readbyqxmd.com/read/29666883/snp-based-pool-genotyping-and-haplotype-analysis-accelerate-fine-mapping-of-the-wheat-genomic-region-containing-stripe-rust-resistance-gene-yr26
#9
Jianhui Wu, Qingdong Zeng, Qilin Wang, Shengjie Liu, Shizhou Yu, Jingmei Mu, Shuo Huang, Hanan Sela, Assaf Distelfeld, Lili Huang, Dejun Han, Zhensheng Kang
NGS-assisted super pooling emerging as powerful tool to accelerate gene mapping and haplotype association analysis within target region uncovering specific linkage SNPs or alleles for marker-assisted gene pyramiding. Conventional gene mapping methods to identify genes associated with important agronomic traits require significant amounts of financial support and time. Here, a single nucleotide polymorphism (SNP)-based mapping approach, RNA-Seq and SNP array assisted super pooling analysis, was used for rapid mining of a candidate genomic region for stripe rust resistance gene Yr26 that has been widely used in wheat breeding programs in China...
April 17, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29665794/mapping-a-male-fertility-restoration-locus-for-the-a-4-cytoplasmic-genic-male-sterility-system-in-pearl-millet-using-a-genotyping-by-sequencing-based-linkage-map
#10
Anna Pucher, C Tom Hash, Jason G Wallace, Sen Han, Willmar L Leiser, Bettina I G Haussmann
BACKGROUND: Pearl millet (Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) R. Br) is an important cereal and fodder crop in hot and arid environments. There is great potential to improve pearl millet production through hybrid breeding. Cytoplasmic male sterility (CMS) and the corresponding nuclear fertility restoration / sterility maintenance genes (Rfs) are essential tools for economic hybrid seed production in pearl millet. Mapping the Rf genes of the A4 CMS system in pearl millet would enable more efficient introgression of both dominant male-fertility restoration alleles (Rf) and their recessive male-sterility maintenance counterparts (rf)...
April 17, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29659569/targeted-next-generation-sequencing-identifies-functionally-deleterious-germline-mutations-in-novel-genes-in-early-onset-familial-prostate-cancer
#11
Paula Paulo, Sofia Maia, Carla Pinto, Pedro Pinto, Augusta Monteiro, Ana Peixoto, Manuel R Teixeira
Considering that mutations in known prostate cancer (PrCa) predisposition genes, including those responsible for hereditary breast/ovarian cancer and Lynch syndromes, explain less than 5% of early-onset/familial PrCa, we have sequenced 94 genes associated with cancer predisposition using next generation sequencing (NGS) in a series of 121 PrCa patients. We found monoallelic truncating/functionally deleterious mutations in seven genes, including ATM and CHEK2, which have previously been associated with PrCa predisposition, and five new candidate PrCa associated genes involved in cancer predisposing recessive disorders, namely RAD51C, FANCD2, FANCI, CEP57 and RECQL4...
April 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29610576/comparison-of-three-pcr-based-assays-for-snp-genotyping-in-plants
#12
Chiara Broccanello, Claudia Chiodi, Andrew Funk, J Mitchell McGrath, Lee Panella, Piergiorgio Stevanato
Background: PCR allelic discrimination technologies have broad applications in the detection of single nucleotide polymorphisms (SNPs) in genetics and genomics. The use of fluorescence-tagged probes is the leading method for targeted SNP detection, but assay costs and error rates could be improved to increase genotyping efficiency. A new assay, rhAmp, based on RNase H2-dependent PCR (rhPCR) combined with a universal reporter system attempts to reduce error rates from primer/primer and primer/probe dimers while lowering costs compared to existing technologies...
2018: Plant Methods
https://www.readbyqxmd.com/read/29593764/genetic-dissection-and-simultaneous-improvement-of-drought-and-low-nitrogen-tolerances-by-designed-qtl-pyramiding-in-rice
#13
Bo Feng, Kai Chen, Yanru Cui, Zhichao Wu, Tianqing Zheng, Yajun Zhu, Jauhar Ali, Bingbing Wang, Jianlong Xu, Wenzhong Zhang, Zhikang Li
Drought and low nitrogen are the most common abiotic stresses limiting rice productivity in the rainfed rice areas of Asia and Africa. Development and adoption of green super rice (GSR) varieties with greatly improved drought tolerance (DT) and low nitrogen tolerance (LNT) are the most efficient way to resolve this problem. In this study, using three sets of trait-specific introgression lines (ILs) in a Xian (indica) variety Huanghuazhan (HHZ) background, we identified nine DT-QTL and seven LNT-QTL by a segregation distortion approach and a genome-wide association study, respectively...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29584564/association-between-mica-gene-variants-and-the-risk-of-hepatitis-c-virus-induced-hepatocellular-cancer-in-a-sicilian-population-sample
#14
Giuseppa Augello, Daniele Balasus, Caterina Fusilli, Tommaso Mazza, Maria Rita Emma, Lydia Giannitrapani, Rosalia Agliastro, Melchiorre Cervello, Giuseppe Montalto
There are currently no biomarkers that predict hepatocellular carcinoma (HCC) risk in patients with hepatitis C virus (HCV)-related cirrhosis. We investigated the relationships among major histocompatibility complex (MHC) class I chain-related gene A (MICA) polymorphisms, plasma levels of soluble MICA (sMICA), and HCC risk in patients with HCV-related HCC. One hundred fifty-four HCV-related HCC patients, 93 HCV-related liver cirrhosis (LC) cases, and 244 healthy controls, all sampled from the native Sicilian population, were genotyped using the KASP™ single-nucleotide polymorphism genotyping method...
April 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29563850/accelerating-public-sector-rice-breeding-with-high-density-kasp-markers-derived-from-whole-genome-sequencing-of-indica-rice
#15
Katherine A Steele, Mark J Quinton-Tulloch, Resham B Amgai, Rajeev Dhakal, Shambhu P Khatiwada, Darshna Vyas, Martin Heine, John R Witcombe
Few public sector rice breeders have the capacity to use NGS-derived markers in their breeding programmes despite rapidly expanding repositories of rice genome sequence data. They rely on > 18,000 mapped microsatellites (SSRs) for marker-assisted selection (MAS) using gel analysis. Lack of knowledge about target SNP and InDel variant loci has hampered the uptake by many breeders of Kompetitive allele-specific PCR (KASP), a proprietary technology of LGC genomics that can distinguish alleles at variant loci...
2018: Molecular Breeding: New Strategies in Plant Improvement
https://www.readbyqxmd.com/read/29560515/characterisation-and-mapping-of-adult-plant-stripe-rust-resistance-in-wheat-accession-aus27284
#16
Vallence Nsabiyera, Harbans S Bariana, Naeela Qureshi, Debbie Wong, Matthew J Hayden, Urmil K Bansal
A new adult plant stripe rust resistance gene, Yr80, was identified in a common wheat landrace Aus27284. Linked markers were developed and validated for their utility in marker-assisted selection. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the most important constraints to global wheat production. The identification and characterisation of new sources of host plant resistance enrich the gene pool and underpin deployment of resistance gene pyramids in new cultivars. Aus27284 exhibited resistance at the adult plant stage against predominant Pst pathotypes and was crossed with a susceptible genotype Avocet S...
March 20, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29560514/identification-and-rapid-mapping-of-a-gene-conferring-broad-spectrum-late-blight-resistance-in-the-diploid-potato-species-solanum-verrucosum-through-dna-capture-technologies
#17
Xinwei Chen, Dominika Lewandowska, Miles R Armstrong, Katie Baker, Tze-Yin Lim, Micha Bayer, Brian Harrower, Karen McLean, Florian Jupe, Kamil Witek, Alison K Lees, Jonathan D Jones, Glenn J Bryan, Ingo Hein
A broad-spectrum late blight disease-resistance gene from Solanum verrucosum has been mapped to potato chromosome 9. The gene is distinct from previously identified-resistance genes. We have identified and characterised a broad-spectrum resistance to Phytophthora infestans from the wild Mexican species Solanum verrucosum. Diagnostic resistance gene enrichment (dRenSeq) revealed that the resistance is not conferred by previously identified nucleotide-binding, leucine-rich repeat genes. Utilising the sequenced potato genome as a reference, two complementary enrichment strategies that target resistance genes (RenSeq) and single/low-copy number genes (Generic-mapping enrichment Sequencing; GenSeq), respectively, were deployed for the rapid, SNP-based mapping of the resistance through bulked-segregant analysis...
June 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29511035/the-association-of-polymorphisms-in-lncrna-h19-with-hepatocellular-cancer-risk-and-prognosis
#18
Ming-Li Yang, Zhe Huang, Qian Wang, Huan-Huan Chen, Sai-Nan Ma, Rong Wu, Wei-Song Cai
Background: Hepatocellular cancer (HCC) is one of the major causes of cancer related mortality. Genetic polymorphisms may affect the susceptibility and clinical outcome of cancers. We aim to manifest the association of single nucleotide polymorphisms (SNPs) of lncRNA- H19 gene with the risk and prognosis of HCC. Methods: A total of 944 samples composed of 472 HCC patients and 472 matched controls were included in the risk analysis and among them 350 HCC samples were investigated in the prognosis analysis. KASP method was conducted for the SNP genotyping...
March 6, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29492347/kompetitive-allele-specific-pcr-kasp%C3%A2-genotyping-of-48-polymorphisms-at-different-caprine-loci-in-french-alpine-and-saanen-goat-breeds-and-their-association-with-milk-composition
#19
Szilvia Kusza, Ludovic Toma Cziszter, Daniela Elena Ilie, Maria Sauer, Ioan Padeanu, Dinu Gavojdian
Using a novel and fast genotyping method called Kompetitive Allele Specific PCR (KASP™), we carried out a pilot study on 48 single nucleotide polymorphisms (SNPs) belonging to 40 genes in French Alpine ( n  = 24) and Saanen ( n  = 25) goats reared in Romania. Furthermore, the associations of the 13 polymorphic genetic variants with milk production and composition were investigated. Thirty-five SNPs did not show polymorphism in the studied populations. Polymorphic SNPs were detected in the following genes: CAST, CLEC4E, DES, GHRHR, HSP90AA1, IL15RA, IL1RN, IL8, MITF, PPRC1, SOCS3, TNF and TNFSF13 ...
2018: PeerJ
https://www.readbyqxmd.com/read/29449853/targeted-haplotype-comparisons-between-south-african-wheat-cultivars-appear-predictive-of-pre-harvest-sprouting-tolerance
#20
Scott L Sydenham, Annelie Barnard
Pre-harvest sprouting (PHS) has been a serious production constraint for over two decades, especially in the summer rainfall wheat production regions of South Africa. It is a complex genetic trait controlled by multiple genes, which are significantly influenced by environmental conditions. This complicates the accurate prediction of a cultivar's stability in terms of PHS tolerance. A number of reports have documented the presence of major QTL on chromosomes 3A and 4A of modern bread wheat cultivars, which confer PHS tolerance...
2018: Frontiers in Plant Science
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