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snp height

Suzanne C Dixon-Suen, Christina M Nagle, Aaron P Thrift, Paul D P Pharoah, Ailith Ewing, Celeste Leigh Pearce, Wei Zheng, Georgia Chenevix-Trench, Peter A Fasching, Matthias W Beckmann, Diether Lambrechts, Ignace Vergote, Sandrina Lambrechts, Els Van Nieuwenhuysen, Mary Anne Rossing, Jennifer A Doherty, Kristine G Wicklund, Jenny Chang-Claude, Audrey Y Jung, Kirsten B Moysich, Kunle Odunsi, Marc T Goodman, Lynne R Wilkens, Pamela J Thompson, Yurii B Shvetsov, Thilo Dörk, Tjoung-Won Park-Simon, Peter Hillemanns, Natalia Bogdanova, Ralf Butzow, Heli Nevanlinna, Liisa M Pelttari, Arto Leminen, Francesmary Modugno, Roberta B Ness, Robert P Edwards, Joseph L Kelley, Florian Heitz, Andreas du Bois, Philipp Harter, Ira Schwaab, Beth Y Karlan, Jenny Lester, Sandra Orsulic, Bobbie J Rimel, Susanne K Kjær, Estrid Høgdall, Allan Jensen, Ellen L Goode, Brooke L Fridley, Julie M Cunningham, Stacey J Winham, Graham G Giles, Fiona Bruinsma, Roger L Milne, Melissa C Southey, Michelle A T Hildebrandt, Xifeng Wu, Karen H Lu, Dong Liang, Douglas A Levine, Maria Bisogna, Joellen M Schildkraut, Andrew Berchuck, Daniel W Cramer, Kathryn L Terry, Elisa V Bandera, Sara H Olson, Helga B Salvesen, Liv Cecilie Vestrheim Thomsen, Reidun K Kopperud, Line Bjorge, Lambertus A Kiemeney, Leon F A G Massuger, Tanja Pejovic, Amanda Bruegl, Linda S Cook, Nhu D Le, Kenneth D Swenerton, Angela Brooks-Wilson, Linda E Kelemen, Jan Lubiński, Tomasz Huzarski, Jacek Gronwald, Janusz Menkiszak, Nicolas Wentzensen, Louise Brinton, Hannah Yang, Jolanta Lissowska, Claus K Høgdall, Lene Lundvall, Honglin Song, Jonathan P Tyrer, Ian Campbell, Diana Eccles, James Paul, Rosalind Glasspool, Nadeem Siddiqui, Alice S Whittemore, Weiva Sieh, Valerie McGuire, Joseph H Rothstein, Steven A Narod, Catherine Phelan, Harvey A Risch, John R McLaughlin, Hoda Anton-Culver, Argyrios Ziogas, Usha Menon, Simon A Gayther, Susan J Ramus, Aleksandra Gentry-Maharaj, Anna H Wu, Malcolm C Pike, Chiu-Chen Tseng, Jolanta Kupryjanczyk, Agnieszka Dansonka-Mieszkowska, Agnieszka Budzilowska, Iwona K Rzepecka, Penelope M Webb
BACKGROUND: Observational studies suggest greater height is associated with increased ovarian cancer risk, but cannot exclude bias and/or confounding as explanations for this. Mendelian randomisation (MR) can provide evidence which may be less prone to bias. METHODS: We pooled data from 39 Ovarian Cancer Association Consortium studies (16,395 cases; 23,003 controls). We applied two-stage predictor-substitution MR, using a weighted genetic risk score combining 609 single-nucleotide polymorphisms...
March 20, 2018: British Journal of Cancer
Alexandra Shadrina, Yakov Tsepilov, Ekaterina Sokolova, Mariya Smetanina, Elena Voronina, Eugene Pakhomov, Kseniya Sevost'ianova, Andrey Shevela, Evgeny Ilyukhin, Evgeny Seliverstov, Igor Zolotukhin, Maxim Filipenko
Heredity is a well-known risk factor for varicose veins, but genetic basis of this condition remains poorly studied. Our aim was to conduct a large-scale genetic association study for primary varicose veins (PVVs) in the population of ethnic Russians. An initial scan using Illumina HumanExome-12 v1.0 BeadChip was performed for 273 patients with PVVs and 250 controls without a history of chronic venous disease and other venous disorders. After quality control and removal of monomorphic markers, 25,424 common and 48,232 rare variants were included in the analysis...
March 15, 2018: Gene
Zhong-Feng Li, Yong Guo, Lin Ou, Huilong Hong, Jun Wang, Zhang-Xiong Liu, Bingfu Guo, Lijuan Zhang, Lijuan Qiu
GmDW1 encodes an ent-kaurene synthase (KS) acting at the early step of the biosynthesis pathway for gibberellins (GAs) and regulates the development of plant height in soybean. Plant height is an important component of plant architecture, and significantly affects crop breeding practices and yield. Here, we report the characterization of an EMS-induced dwarf mutant (dw) of the soybean cultivar Zhongpin 661 (ZDD23893). The dw mutant displayed reduced plant height and shortened internodes, both of which were mainly attributed to the longitudinally decreased cell length...
March 17, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Huihui Sun, Naijun Wan, Xinli Wang, Liang Chang, Dazhi Cheng
18p deletion syndrome is a rare chromosomal disease caused by deletion of the short arm of chromosome 18. By using cytogenetic and SNP array analysis, we identified a girl with 18p deletion syndrome exhibiting craniofacial anomalies, intellectual disability, and short stature. G-banding analysis of metaphase cells revealed an abnormal karyotype 46,XX,del(18)(p10). Further, SNP array detected a 15.3-Mb deletion at 18p11.21p11.32 (chr18:12842-15375878) including 61 OMIM genes. Genotype-phenotype correlation analysis showed that clinical manifestations of the patient were correlated with LAMA1, TWSG1, and GNAL deletions...
March 16, 2018: Cytogenetic and Genome Research
Roberta Pastorino, Anna Puggina, Robert Carreras-Torres, Pagona Lagiou, Ivana Holcátová, Lorenzo Richiardi, Kristina Kjaerheim, Antonio Agudo, Xavier Castellsagué, Tatiana V Macfarlane, Luigi Barzan, Cristina Canova, Nalin S Thakker, David I Conway, Ariana Znaor, Claire M Healy, Wolfgang Ahrens, David Zaridze, Neonilia Szeszenia-Dabrowska, Jolanta Lissowska, Eleonora Fabianova, Ioan Nicolae Mates, Vladimir Bencko, Lenka Foretova, Vladimir Janout, Paul Brennan, Valérie Gaborieau, James D McKay, Stefania Boccia
With the aim to dissect the effect of adult height on head and neck cancer (HNC), we use the Mendelian randomization (MR) approach to test the association between genetic instruments for height and the risk of HNC. 599 single nucleotide polymorphisms (SNPs) were identified as genetic instruments for height, accounting for 16% of the phenotypic variation. Genetic data concerning HNC cases and controls were obtained from a genome-wide association study. Summary statistics for genetic association were used in complementary MR approaches: the weighted genetic risk score (GRS) and the inverse-variance weighted (IVW)...
March 14, 2018: Scientific Reports
Li Zheng, Gui-Min Zhang, Yan-Peng Dong, Yi-Fan Wen, Dong Dong, Chu-Zhao Lei, Xing-Lei Qi, Hong Chen, Li-Jun Huo, Yong-Zhen Huang
As a member of MYLK family, MYLK4 gene may play a vital role in muscle development. In this study, one novel single-nucleotide polymorphism (SNP) was identified the bovine MYLK4 by sequencing pooled DNA samples (pool-Seq) and forced polymerase chain reaction-restriction fragment length polymorphism (forced PCR-RFLP) methods. Overall, we reported one mutation (SNP1) in the intron 10 region within the bovine MYLK4 gene in 559 individuals representing five main cattle breeds from China (Nanyang, NY; Qinchuan; Jiaxian, JX; Pinan cattle; and Caidamu cattle, CDM)...
March 14, 2018: Animal Biotechnology
Yong-Zhen Huang, Li-Na Qian, Jian Wang, Chun-Lei Zhang, Xing-Tang Fang, Chu-Zhao Lei, Xian-Yong Lan, Yun Ma, Yue-Yu Bai, Feng-Peng Lin, Hong Chen
The α-adducin (ADD1) is a subunit of adducin which is a cytoskeleton heterodimeric protein. Adducin participates in oocytes chromosome meiosis of mice, prompting adducin has an effect on embryonic development. Adducin gene mutation has significantly functional change. So the present study was to identify and characterize polymorphisms within the coding region of the bovine ADD1 gene among different cattle breeds. Here, 11 novel single nucleotide polymorphisms (SNPs 1-11) were identified by DNA sequencing and polymerase chain reaction-single stranded conformational polymorphism, there were one synonymous mutation in exon 1 (SNP1); four missense mutations in exons 4, 7, and 8 (SNPs 3-6); and six mutations in introns 4, 12, 13, and 14 (SNPs 2, 7-10)...
March 12, 2018: Animal Biotechnology
Juan E Rosas, Sebastián Martínez, Pedro Blanco, Fernando Pérez de Vida, Victoria Bonnecarrère, Gloria Mosquera, Maribel Cruz, Silvia Garaycochea, Eliana Monteverde, Susan McCouch, Silvia Germán, Jean-Luc Jannink, Lucía Gutiérrez
Stem rot and aggregated sheath spot are the two major stem and sheath diseases affecting rice (Oryza sativa L.) in temperate areas. A third fungal disease, sheath blight, is a major disease in tropical areas. Resistance to these diseases is a key objective in rice breeding programs but phenotyping is challenged by the confounding effects of phenological and morphological traits such as flowering time (FT) and plant height (PH). This study sought to identify quantitative trait loci (QTL) for resistance to these three diseases after removing the confounding effects of FT and PH...
March 2018: Plant Genome
Junji Su, Libei Li, Chi Zhang, Caixiang Wang, Lijiao Gu, Hantao Wang, Hengling Wei, Qibao Liu, Long Huang, Shuxun Yu
Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton. A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting...
March 1, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Dawei Wei, Sayed Haidar Abbas Raza, Jiupan Zhang, Linsheng Gui, Siddiq Ur Rahman, Rajwali Khan, Seyed Mahdi Hosseini, Hubdar Ali Kaleri, Linsen Zan
The sine oculis homeobox homolog 4 (SIX4) gene belongs to the SIX gene family, which plays a critical role in muscle regeneration and early stages of ontogeny. This study aimed to detect promoter variations of bovine SIX4 genes in Qinchuan cattle, and to evaluate the effect of transcription regulations and body measurement traits. Quantitative real-time PCR (qPCR) results showed that the mRNA expression levels of SIX4 gene were found significantly highest in longissimus thoracis tissue and individual before attaining the stage of physiological maturity...
February 26, 2018: Gene
Jie Guo, Weiping Shi, Zheng Zhang, Jingye Cheng, Daizhen Sun, Jin Yu, Xinlei Li, Pingyi Guo, Chenyang Hao
BACKGROUND: Yield improvement is an ever-important objective of wheat breeding. Studying and understanding the phenotypes and genotypes of yield-related traits has potential for genetic improvement of crops. RESULTS: The genotypes of 215 wheat cultivars including 11 founder parents and 106 derivatives were analyzed by the 9 K wheat SNP iSelect assay. A total of 4138 polymorphic single nucleotide polymorphism (SNP) loci were detected on 21 chromosomes, of which 3792 were mapped to single chromosome locations...
February 20, 2018: BMC Plant Biology
Marina B Pioltine, Maria Edna de Melo, Aritânia S Santos, Alisson D Machado, Ariana E Fernandes, Clarissa T Fujiwara, Cintia Cercato, Marcio C Mancini
Childhood obesity is a major public health problem. It has a direct impact on the quality of life of children and adolescents, as well as on their future risk of developing chronic diseases. Dietary patterns rich in fats and sugars and lacking dietary fibers, vitamins, and minerals, as well as lack of physical exercise have been associated with the rise of obesity prevalence. However, factors that contribute to the preference for foods rich in these nutrients are not well established. Taste is recognized as an important predictor of food choices, and polymorphisms in taste-related genes may explain the variability of taste preference and food intake...
January 29, 2018: Journal of Personalized Medicine
L W Gao, M X Zhang, L J Wu, L W Fu, X Y Zhao, J Mi
Objective: To examine the association between rs10938397 polymorphism in glucosamine-6-phosphate deaminase 2 (GNPDA2) and risk of obesity in children at different stages of development and analyze the differences in the association. Methods: A total of 3 503 school-aged children were selected from the Beijing Child and Adolescent Metabolic Syndrome (BCAMS) study in Beijing and their complete anthropometry weight, height, fat mass percentage (FMP), fat mass index (FMI) and free fat mass index (FFMI) and sexual maturation (SM) data were used...
January 10, 2018: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
Chonlaphat Sukasem, Natchaya Vanwong, Pornpen Srisawasdi, Nattawat Ngamsamut, Nopphadol Nuntamool, Yaowaluck Hongkaew, Apichaya Puangpetch, Bhunnada Chamkrachangpada, Penkhae Limsila
The purpose of this study was to explore the association of genetic polymorphism of genes related to pharmacokinetics or pharmacodynamics with insulin resistance in children and adolescents with autism spectrum disorder (ASD) and treated with risperidone. All 89 subjects underwent measurement of fasting blood glucose and insulin levels, body weight and height. Genotyping was performed by Taqman real-time polymerase chain reaction (PCR) (pharmacokinetics genes: cytochrome P450 2D6 (CYP2D6) *4 (rs3892097), *5 (gene deletion), *10 (rs1065852), and *41 (rs28371725), ATP-binding cassette transporter B1 (ABCB1) 2677 G>T/A (rs2032582) and 3435C>T (rs1045642), and pharmacodynamics genes: dopamine receptor D2 (DRD2) Tag-SNP (C>T) (rs4436578), DRD2 Tag1A (C>T) (rs1800497), leptin gene (LEP) -2548G>A (rs7799039), ghrelin gene (GHRL) -604G>A (rs27647), and brain-derived neurotrophic factor (BDNF) 196G>A (rs6265)...
January 25, 2018: Basic & Clinical Pharmacology & Toxicology
Biyue Tan, Dario Grattapaglia, Harry X Wu, Pär K Ingvarsson
Non-additive genetic effects can be effectively exploited in control-pollinated families with the availability of genome-wide markers. We used 41,304 SNP markers and compared pedigree vs. marker-based genetic models by analysing height, diameter, basic density and pulp yield for Eucalyptus urophylla × E.grandis control-pollinated families represented by 949 informative individuals. We evaluated models accounting for additive, dominance, and first-order epistatic interactions (additive by additive, dominance by dominance, and additive by dominance)...
February 2018: Plant Science: An International Journal of Experimental Plant Biology
Yi Xu, Yajun Wu, Jixiang Wu
Genetic association mapping has been widely applied to determine genetic markers favorably associated with a trait of interest and provide information for marker-assisted selection. Many association mapping studies commonly focus on main effects due to intolerable computing intensity. This study aims to select several sets of DNA markers with potential epistasis to maximize genetic variations of some key agronomic traits in barley. By doing so, we integrated a MDR (multifactor dimensionality reduction) method with a forward variable selection approach...
January 18, 2018: Genetica
Zhihong Zhu, Zhili Zheng, Futao Zhang, Yang Wu, Maciej Trzaskowski, Robert Maier, Matthew R Robinson, John J McGrath, Peter M Visscher, Naomi R Wray, Jian Yang
Health risk factors such as body mass index (BMI) and serum cholesterol are associated with many common diseases. It often remains unclear whether the risk factors are cause or consequence of disease, or whether the associations are the result of confounding. We develop and apply a method (called GSMR) that performs a multi-SNP Mendelian randomization analysis using summary-level data from genome-wide association studies to test the causal associations of BMI, waist-to-hip ratio, serum cholesterols, blood pressures, height, and years of schooling (EduYears) with common diseases (sample sizes of up to 405,072)...
January 15, 2018: Nature Communications
Anja Rudolph, Minsun Song, Mark N Brook, Roger L Milne, Nasim Mavaddat, Kyriaki Michailidou, Manjeet K Bolla, Qin Wang, Joe Dennis, Amber N Wilcox, John L Hopper, Melissa C Southey, Renske Keeman, Peter A Fasching, Matthias W Beckmann, Manuela Gago-Dominguez, Jose E Castelao, Pascal Guénel, Thérèse Truong, Stig E Bojesen, Henrik Flyger, Hermann Brenner, Volker Arndt, Hiltrud Brauch, Thomas Brüning, Arto Mannermaa, Veli-Matti Kosma, Diether Lambrechts, Machteld Keupers, Fergus J Couch, Celine Vachon, Graham G Giles, Robert J MacInnis, Jonine Figueroa, Louise Brinton, Kamila Czene, Judith S Brand, Marike Gabrielson, Keith Humphreys, Angela Cox, Simon S Cross, Alison M Dunning, Nick Orr, Anthony Swerdlow, Per Hall, Paul D P Pharoah, Marjanka K Schmidt, Douglas F Easton, Nilanjan Chatterjee, Jenny Chang-Claude, Montserrat García-Closas
Background: Polygenic risk scores (PRS) for breast cancer can be used to stratify the population into groups at substantially different levels of risk. Combining PRS and environmental risk factors will improve risk prediction; however, integrating PRS into risk prediction models requires evaluation of their joint association with known environmental risk factors. Methods: Analyses were based on data from 20 studies; datasets analysed ranged from 3453 to 23 104 invasive breast cancer cases and similar numbers of controls, depending on the analysed environmental risk factor...
January 5, 2018: International Journal of Epidemiology
Raman Dhariwal, George Fedak, Yves Dion, Curtis Pozniak, André Laroche, François Eudes, Harpinder Singh Randhawa
Triticale (xTriticosecale Wittmack) is an important feed crop which suffers severe yield, grade and end-use quality losses due to Fusarium head blight (FHB). Development of resistant triticale cultivars is hindered by lack of effective genetic resistance sources. To dissect FHB resistance, a doubled haploid spring triticale population produced from the cross TMP16315/AC Ultima using a microspore culture method, was phenotyped for FHB incidence, severity, visual rating index (VRI), deoxynivalenol (DON) and some associated traits (ergot, grain protein content, test weight, yield, plant height and lodging) followed by single nucleotide polymorphism (SNP) genotyping...
January 5, 2018: Genes
Ashley DuVal, Salvador A Gezan, Guiliana Mustiga, Conrad Stack, Jean-Philippe Marelli, José Chaparro, Donald Livingstone, Stefan Royaert, Juan C Motamayor
Breeding programs of cacao (Theobroma cacao L.) trees share the many challenges of breeding long-living perennial crops, and genetic progress is further constrained by both the limited understanding of the inheritance of complex traits and the prevalence of technical issues, such as mislabeled individuals (off-types). To better understand the genetic architecture of cacao, in this study, 13 years of phenotypic data collected from four progeny trials in Bahia, Brazil were analyzed jointly in a multisite analysis...
2017: Frontiers in Plant Science
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