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Methylation QTL

Eilis Hannon, Mike Weedon, Nicholas Bray, Michael O'Donovan, Jonathan Mill
Most genetic variants identified in genome-wide association studies (GWASs) of complex traits are thought to act by affecting gene regulation rather than directly altering the protein product. As a consequence, the actual genes involved in disease are not necessarily the most proximal to the associated variants. By integrating data from GWAS analyses with those from genetic studies of regulatory variation, it is possible to identify variants pleiotropically associated with both a complex trait and measures of gene regulation...
June 1, 2017: American Journal of Human Genetics
Lin Zhang, Hong Yu, Bin Ma, Guifu Liu, Jianjun Wang, Junmin Wang, Rongcun Gao, Jinjun Li, Jiyun Liu, Jing Xu, Yingying Zhang, Qun Li, Xuehui Huang, Jianlong Xu, Jianming Li, Qian Qian, Bin Han, Zuhua He, Jiayang Li
Super hybrid rice varieties with ideal plant architecture (IPA) have been critical in enhancing food security worldwide. However, the molecular mechanisms underlying their improved yield remain unclear. Here, we report the identification of a QTL, qWS8/ipa1-2D, in the super rice Yongyou12 (YY12) and related varieties. In-depth genetic molecular characterization of qWS8/ipa1-2D reveals that this newly identified QTL results from three distal naturally occurring tandem repeats upstream of IPA1, a key gene/locus previously shown to shape rice ideal plant architecture and greatly enhance grain yield...
March 20, 2017: Nature Communications
Meiling Zou, Cheng Lu, Shengkui Zhang, Qing Chen, Xianglai Sun, Pingan Ma, Meizhen Hu, Ming Peng, Zilong Ma, Xin Chen, Xincheng Zhou, Haiyan Wang, Subin Feng, Kaixin Fang, Hairong Xie, Zaiyun Li, Kede Liu, Qiongyao Qin, Jinli Pei, Shujuan Wang, Kun Pan, Wenbin Hu, Binxiao Feng, Dayong Fan, Bin Zhou, Chunling Wu, Ming Su, Zhiqiang Xia, Kaimian Li, Wenquan Wang
Cassava (Manihot esculenta Crantz) is an important tropical starchy root crop that is adapted to drought but extremely cold sensitive. A cold-tolerant, high-quality, and robust supply of cassava is urgently needed. Here, we clarify genome-wide distribution and classification of CCGG hemi-methylation and full-methylation, and detected 77 much candidate QTLs(epi) for cold stress and 103 much candidate QTLs(epi) for storage root quality and yield in 186 cassava population, generated by crossing two non-inbred lines with female parent KU50 and male parent SC124 (KS population)...
January 25, 2017: Scientific Reports
Monica Sharma, Rajat Sandhir, Anuradha Singh, Pankaj Kumar, Ankita Mishra, Sanjay Jachak, Sukhvinder P Singh, Jagdeep Singh, Joy Roy
Phenolic compounds (PCs) affect the bread quality and can also affect the other types of end-use food products such as chapatti (unleavened flat bread), now globally recognized wheat-based food product. The detailed analysis of PCs and their biosynthesis genes in diverse bread wheat (Triticum aestivum) varieties differing for chapatti quality have not been studied. In this study, the identification and quantification of PCs using UPLC-QTOF-MS and/or MS/MS and functional genomics techniques such as microarrays and qRT-PCR of their biosynthesis genes have been studied in a good chapatti variety, "C 306" and a poor chapatti variety, "Sonalika...
2016: Frontiers in Plant Science
Xuewen Xu, Jing Ji, Qiang Xu, Xiaohua Qi, Xuehao Chen
The hypocotyl-derived adventitious root (AR) is an important morphological acclimation to waterlogging stress; however, its genetic basis has not been adequately understood. In the present study, a mixed major gene plus polygene inheritance model was used to analyze AR numbers (ARN) 7 days after waterlogging treatment in six generations (P1, P2, F1, B1, B2, and F2), using cucumber waterlogging tolerant line Zaoer-N and sensitive Pepino as parents. The results showed that the genetic model D-4, mixed one negative dominance major gene and additive-dominance polygenes, is the best-fitting genetic model for waterlogging-triggered ARN phenotype...
April 2017: Molecular Genetics and Genomics: MGG
Åsa K Hedman, Mihkel Zilmer, Johan Sundström, Lars Lind, Erik Ingelsson
BACKGROUND: Oxidative stress has been related to type 2 diabetes (T2D) and cardiovascular disease (CVD), the leading global cause of death. Contributions of environmental factors such as oxidative stress on complex traits and disease may be partly mediated through changes in epigenetic marks (e.g. DNA methylation). Studies relating differential methylation with intermediate phenotypes and disease endpoints may be useful in identifying additional candidate genes and mechanisms involved in disease...
November 25, 2016: BMC Medical Genomics
Lu Chen, Bing Ge, Francesco Paolo Casale, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Ying Yan, Kousik Kundu, Simone Ecker, Avik Datta, David Richardson, Frances Burden, Daniel Mead, Alice L Mann, Jose Maria Fernandez, Sophia Rowlston, Steven P Wilder, Samantha Farrow, Xiaojian Shao, John J Lambourne, Adriana Redensek, Cornelis A Albers, Vyacheslav Amstislavskiy, Sofie Ashford, Kim Berentsen, Lorenzo Bomba, Guillaume Bourque, David Bujold, Stephan Busche, Maxime Caron, Shu-Huang Chen, Warren Cheung, Oliver Delaneau, Emmanouil T Dermitzakis, Heather Elding, Irina Colgiu, Frederik O Bagger, Paul Flicek, Ehsan Habibi, Valentina Iotchkova, Eva Janssen-Megens, Bowon Kim, Hans Lehrach, Ernesto Lowy, Amit Mandoli, Filomena Matarese, Matthew T Maurano, John A Morris, Vera Pancaldi, Farzin Pourfarzad, Karola Rehnstrom, Augusto Rendon, Thomas Risch, Nilofar Sharifi, Marie-Michelle Simon, Marc Sultan, Alfonso Valencia, Klaudia Walter, Shuang-Yin Wang, Mattia Frontini, Stylianos E Antonarakis, Laura Clarke, Marie-Laure Yaspo, Stephan Beck, Roderic Guigo, Daniel Rico, Joost H A Martens, Willem H Ouwehand, Taco W Kuijpers, Dirk S Paul, Hendrik G Stunnenberg, Oliver Stegle, Kate Downes, Tomi Pastinen, Nicole Soranzo
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14(+) monocytes, CD16(+) neutrophils, and naive CD4(+) T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies...
November 17, 2016: Cell
Sandeep K Singh, Philip J Lupo, Michael E Scheurer, Anshul Saxena, Amy E Kennedy, Boubakari Ibrahimou, Manuel Alejandro Barbieri, Ken I Mills, Jacob L McCauley, Mehmet Fatih Okcu, Mehmet Tevfik Dorak
Childhood acute lymphoblastic leukemia (ALL) occurs more frequently in males. Reasons behind sex differences in childhood ALL risk are unknown. In the present genome-wide association study (GWAS), we explored the genetic basis of sex differences by comparing genotype frequencies between male and female cases in a case-only study to assess effect-modification by sex.The case-only design included 236 incident cases of childhood ALL consecutively recruited at the Texas Children's Cancer Center in Houston, Texas from 2007 to 2012...
November 2016: Medicine (Baltimore)
Yoo-Jeong Han, Jing Zhang, Yonglan Zheng, Dezheng Huo, Olufunmilayo I Olopade
Genome wide association studies (GWAS) have identified low penetrance and high frequency single nucleotide polymorphisms (SNPs) that contribute to genetic susceptibility of breast cancer. The SNPs at 16q12, close to the TOX3 and CASC16 genes, represent one of the susceptibility loci identified by GWAS, showing strong evidence for breast cancer association across various populations. To examine molecular mechanisms of TOX3 regulation in breast cancer, we investigated both genetic and epigenetic factors using cell lines and datasets derived from primary breast tumors available through The Cancer Genome Atlas (TCGA)...
2016: PloS One
Peilin Jia, Guangchun Han, Junfei Zhao, Pinyi Lu, Zhongming Zhao
SZGR 2.0 is a comprehensive resource of candidate variants and genes for schizophrenia, covering genetic, epigenetic, transcriptomic, translational and many other types of evidence. By systematic review and curation of multiple lines of evidence, we included almost all variants and genes that have ever been reported to be associated with schizophrenia. In particular, we collected ∼4200 common variants reported in genome-wide association studies, ∼1000 de novo mutations discovered by large-scale sequencing of family samples, 215 genes spanning rare and replication copy number variations, 99 genes overlapping with linkage regions, 240 differentially expressed genes, 4651 differentially methylated genes and 49 genes as antipsychotic drug targets...
January 4, 2017: Nucleic Acids Research
Jiaxue Cao, Caihong Wei, Shuzhen Zhang, Terence D Capellini, Li Zhang, Fuping Zhao, Li Li, Tao Zhong, Linjie Wang, Lixin Du, Hongping Zhang
Extensive variation in reproduction has arisen in Chinese Mongolian sheep during recent domestication. Hu and Small-tailed Han sheep, for example, have become non-seasonal breeders and exhibit higher fecundity than Tan and Ujumqin breeds. We therefore scanned reproduction-related single-nucleotide variations from methylated DNA-immunoprecipitation sequencing data generated from each of those four breeds to uncover potential mechanisms underlying this breed variation. We generated a high-quality map of single nucleotide variations (SNVs) in DNA methylation enriched regions, and found that the majority of variants are located within non-coding regions...
November 2016: Molecular Reproduction and Development
Animesh Acharjee, Bjorn Kloosterman, Richard G F Visser, Chris Maliepaard
BACKGROUND: In order to find genetic and metabolic pathways related to phenotypic traits of interest, we analyzed gene expression data, metabolite data obtained with GC-MS and LC-MS, proteomics data and a selected set of tuber quality phenotypic data from a diploid segregating mapping population of potato. In this study we present an approach to integrate these ~ omics data sets for the purpose of predicting phenotypic traits. This gives us networks of relatively small sets of interrelated ~ omics variables that can predict, with higher accuracy, a quality trait of interest...
2016: BMC Bioinformatics
Xi Cheng, Harshal Waghulde, Blair Mell, Kathryn Smedlund, Guillermo Vazquez, Bina Joe
This study is focused on a translationally significant, genome-wide-association-study (GWAS) locus for cardiovascular disease (QT-interval) on human chromosome 17. We have previously validated and high resolution mapped the homologous genomic segment of this human locus to <42.5 kb on rat chromosome 10. This <42.5 kb segment in rats regulates both QT-interval and blood pressure and contains a single protein-coding gene, rififylin (Rffl). The expression of Rffl in the hearts and kidneys is differential between Dahl S and S...
2016: PloS One
Konstantin Shakhbazov, Joseph E Powell, Gibran Hemani, Anjali K Henders, Nicholas G Martin, Peter M Visscher, Grant W Montgomery, Allan F McRae
BACKGROUND: Expression QTLs and epigenetic marks are often employed to provide an insight into the possible biological mechanisms behind GWAS hits. A substantial proportion of the variation in gene expression and DNA methylation is known to be under genetic control. We address the proportion of genetic control that is shared between these two genomic features. RESULTS: An exhaustive search for pairwise phenotypic correlations between gene expression and DNA methylation in samples from human blood (n = 610) was performed...
April 6, 2016: BMC Genomics
Ali Soltani, Ajay Kumar, Mohamed Mergoum, Seyed Mostafa Pirseyedi, Justin B Hegstad, Mona Mazaheri, Shahryar F Kianian
Interspecific hybridization can be considered an accelerator of evolution, otherwise a slow process, solely dependent on mutation and recombination. Upon interspecific hybridization, several novel interactions between nuclear and cytoplasmic genomes emerge which provide additional sources of diversity. The magnitude and essence of intergenomic interactions between nuclear and cytoplasmic genomes remain unknown due to the direction of many crosses. This study was conducted to address the role of nuclear-cytoplasmic interactions as a source of variation upon hybridization...
March 2016: Functional & Integrative Genomics
Yong Xu, Weihua Yue, Yin Yao Shugart, Jianmin Yuan, Guoqiang Wang, Harold Z Wang, Benjamin Lehrman, Fuquan Zhang, Dai Zhang
OBJECTIVE: Accumulating evidence implicates inflammatory cytokines in the development of psychiatric disorders, including schizophrenia (SZ). IL-18 is one of cytokines that plays a crucial role in immune response and neurodevelopment. We aimed to investigate potential genetic alterations of the cytokine system underpinning SZ. METHODS: We tested the association of genetic variants within the cytokine-cytokine receptor interaction (CCRI) pathway with SZ, using GWAS-derived data involving 768 adult SZ patients and 1348 controls, and replicated the association of IL18R1 rs1035130 with SZ in an independent sample of 1957 adult patients and 1509 controls...
March 2016: Journal of Psychiatric Research
Joseph L McClay, Andrey A Shabalin, Mikhail G Dozmorov, Daniel E Adkins, Gaurav Kumar, Srilaxmi Nerella, Shaunna L Clark, Sarah E Bergen, Christina M Hultman, Patrik K E Magnusson, Patrick F Sullivan, Karolina A Aberg, Edwin J C G van den Oord
BACKGROUND: Genetic influence on DNA methylation is potentially an important mechanism affecting individual differences in humans. We use next-generation sequencing to assay blood DNA methylation at approximately 4.5 million loci, each comprising 2.9 CpGs on average, in 697 normal subjects. Methylation measures at each locus are tested for association with approximately 4.5 million single nucleotide polymorphisms (SNPs) to exhaustively screen for methylation quantitative trait loci (meQTLs)...
December 23, 2015: Genome Biology
B S Coates, A P Alves, H Wang, X Zhou, T Nowatzki, H Chen, M Rangasamy, H M Robertson, C W Whitfield, K K Walden, S D Kachman, B W French, L J Meinke, D Hawthorne, C A Abel, T W Sappington, B D Siegfried, N J Miller
The western corn rootworm, Diabrotica virgifera virgifera, is an insect pest of corn and population suppression with chemical insecticides is an important management tool. Traits conferring organophosphate insecticide resistance have increased in frequency amongst D. v. virgifera populations, resulting in the reduced efficacy in many corn-growing regions of the USA. We used comparative functional genomic and quantitative trait locus (QTL) mapping approaches to investigate the genetic basis of D. v. virgifera resistance to the organophosphate methyl-parathion...
February 2016: Insect Molecular Biology
Marcela K Tello-Ruiz, Joshua Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani, Vindhya Amarasinghe, Palitha Dharmawardhana, Yinping Jiao, Joseph Mulvaney, Sunita Kumari, Kapeel Chougule, Justin Elser, Bo Wang, James Thomason, Daniel M Bolser, Arnaud Kerhornou, Brandon Walts, Nuno A Fonseca, Laura Huerta, Maria Keays, Y Amy Tang, Helen Parkinson, Antonio Fabregat, Sheldon McKay, Joel Weiser, Peter D'Eustachio, Lincoln Stein, Robert Petryszak, Paul J Kersey, Pankaj Jaiswal, Doreen Ware
Gramene ( is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces...
January 4, 2016: Nucleic Acids Research
Vered Tzin, Penelope L Lindsay, Shawn A Christensen, Lisa N Meihls, Levi B Blue, Georg Jander
Plants in nature have inducible defences that sometimes lead to targeted resistance against particular herbivores, but susceptibility to others. The metabolic diversity and genetic resources available for maize (Zea mays) make this a suitable system for a mechanistic study of within-species variation in such plant-mediated interactions between herbivores. Beet armyworms (Spodoptera exigua) and corn leaf aphids (Rhopalosiphum maidis) are two naturally occurring maize herbivores with different feeding habits...
November 2015: Molecular Ecology
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