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Research articles The B chromosomes of the African cichlid fish Haplochromis obliquidens harbour 18S rRNA gene copies Andréia B Poletto, Irani A Ferreira, and Cesar Martins PMCID: PMC2806386 A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment Kevin A Glover, Michael M Hansen, Sigbjørn Lien, Thomas D Als, Bjørn Høyheim, and Øystein Skaala PMCID: PMC2818610 Transcript profiling of candidate genes in testis of pigs exhibiting large differences in androstenone levels Eli Grindflek, Ingunn Berget, Maren Moe, Paul Oeth, and Sigbjørn Lien PMCID: PMC2823645 Compilation of a panel of informative single nucleotide polymorphisms for bovine identification in the Northern Irish cattle population Adrian R Allen, Malcolm Taylor, Brian McKeown, April I Curry, John F Lavery, Andy Mitchell, David Hartshorne, Rüdi Fries, and Robin A Skuce PMCID: PMC2826282 Calcineurin and Protein kinase G regulate C. elegans behavioral quiescence during locomotion in liquid Rajarshi Ghosh and Scott W Emmons PMCID: PMC2834598 Mitochondrial haplogroup U is associated with a reduced risk to develop exfoliation glaucoma in the German population Christiane Wolf, Eugen Gramer, Bertram Müller-Myhsok, Francesca Pasutto, Bernd Wissinger, and Nicole Weisschuh PMCID: PMC2834599 Dispersal and population structure at different spatial scales in the subterranean rodent Ctenomys australis Matías S Mora, Fernando J Mapelli, Oscar E Gaggiotti, Marcelo J Kittlein, and Enrique P Lessa PMCID: PMC2828403 A nonsense mutation in the beta-carotene oxygenase 2 (BCO2) gene is tightly associated with accumulation of carotenoids in adipose tissue in sheep (Ovis aries) Dag I Våge and Inger A Boman PMCID: PMC2828402 Regional differences in recombination hotspots between two chicken populations Martin G Elferink, Pieter van As, Tineke Veenendaal, Richard PMA Crooijmans, and Martien AM Groenen PMCID: PMC2834597 Sp1 and KLF15 regulate basal transcription of the human LRP5 gene Jiangxia Li, Yang Yang, Baichun Jiang, Xiyu Zhang, Yongxin Zou, and Yaoqin Gong PMCID: PMC2831824 A copy number variation in human NCF1 and its pseudogenes Tiffany Brunson, Qingwei Wang, Isfahan Chambers, and Qing Song PMCID: PMC2846862 Genome-wide linkage scan for factors of metabolic syndrome in a Chinese population Claudia HT Tam, Vincent KL Lam, Wing-Yee So, Ronald CW Ma, Juliana CN Chan, and Maggie CY Ng PMCID: PMC2838753 The "silver" Japanese quail and the MITF gene: causal mutation, associated traits and homology with the "blue" chicken plumage Francis Minvielle, Bertrand Bed'hom, Jean-Luc Coville, Shin'ichi Ito, Miho Inoue-Murayama, and David Gourichon PMCID: PMC2841575 Genetic dissection of rice grain shape using a recombinant inbred line population derived from two contrasting parents and fine mapping a pleiotropic quantitative trait locus qGL7 Xufeng Bai, Lijun Luo, Wenhao Yan, Mallikarjuna Rao Kovi, Wei Zhan, and Yongzhong Xing PMCID: PMC2846863 The genetic effects of the dopamine D1 receptor gene on chicken egg production and broodiness traits Haiping Xu, Xu Shen, Min Zhou, Meixia Fang, Hua Zeng, Qinghua Nie, and Xiquan Zhang PMCID: PMC2848132 Genetic evidence supports linguistic affinity of Mlabri - a hunter-gatherer group in Thailand Shuhua Xu, Daoroong Kangwanpong, Mark Seielstad, Metawee Srikummool, Jatupol Kampuansai, Li Jin, and The HUGO Pan-Asian SNP Consortium* PMCID: PMC2858090 A 2cM genome-wide scan of European Holstein cattle affected by classical BSE Brenda M Murdoch, Michael L Clawson, William W Laegreid, Paul Stothard, Matthew Settles, Stephanie McKay, Aparna Prasad, Zhiquan Wang, Stephen S Moore, and John L Williams PMCID: PMC2853485 Third chromosome candidate genes for conspecific sperm precedence between D. simulans and D. mauritiana Lisa Levesque, Barb Brouwers, Vignesh Sundararajan, and Alberto Civetta PMCID: PMC2864193 Little ROCK is a ROCK1 pseudogene expressed in human smooth muscle cells Maria Claudia Montefusco, Kristen Merlo, Crystal D Bryan, Howard K Surks, Steven E Reis, Michael E Mendelsohn, and Gordon S Huggins PMCID: PMC2867973 Polymorphisms in the gene encoding bovine interleukin-10 receptor alpha are associated with Mycobacterium avium ssp. paratuberculosis infection status Chris P Verschoor, Sameer D Pant, Qiumei You, Flavio S Schenkel, David F Kelton, and Niel A Karrow PMCID: PMC2873551 Impact of reduced marker set estimation of genomic relationship matrices on genomic selection for feed efficiency in Angus cattle Megan M Rolf, Jeremy F Taylor, Robert D Schnabel, Stephanie D McKay, Matthew C McClure, Sally L Northcutt, Monty S Kerley, and Robert L Weaber PMCID: PMC2868785 High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta Caroline Daelemans, Matthew E Ritchie, Guillaume Smits, Sayeda Abu-Amero, Ian M Sudbery, Matthew S Forrest, Susana Campino, Taane G Clark, Philip Stanier, Dominic Kwiatkowski, Panos Deloukas, Emmanouil T Dermitzakis, Simon Tavaré, Gudrun E Moore, and Ian Dunham PMCID: PMC2871261 Identification of Type 2 Diabetes-associated combination of SNPs using Support Vector Machine Hyo-Jeong Ban, Jee Yeon Heo, Kyung-Soo Oh, and Keun-Joon Park PMCID: PMC2875201 Multiple rearrangements in cryptic species of electric knifefish, Gymnotus carapo (Gymnotidae, Gymnotiformes) revealed by chromosome painting Cleusa Y Nagamachi, Julio C Pieczarka, Susana SR Milhomem, Patricia CM O'Brien, Augusto CP de Souza, and Malcolm A Ferguson-Smith PMCID: PMC2873553 Impacts of recent cultivation on genetic diversity pattern of a medicinal plant, Scutellaria baicalensis (Lamiaceae) Qing-Jun Yuan, Zhi-Yong Zhang, Juan Hu, Lan-Ping Guo, Ai-Juan Shao, and Lu-Qi Huang PMCID: PMC2877650 Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range Andrew M Griffiths, Gonzalo Machado-Schiaffino, Eileen Dillane, Jamie Coughlan, Jose L Horreo, Andrew E Bowkett, Peter Minting, Simon Toms, Willie Roche, Paddy Gargan, Philip McGinnity, Tom Cross, Dylan Bright, Eva Garcia-Vazquez, and Jamie R Stevens PMCID: PMC2882343 SNP identification, verification, and utility for population genetics in a non-model genus Larissa M Williams, Xin Ma, Adam R Boyko, Carlos D Bustamante, and Marjorie F Oleksiak PMCID: PMC2874759 Influence of mutation rate on estimators of genetic differentiation - lessons from Arabidopsis thaliana Ilkka Kronholm, Olivier Loudet, and Juliette de Meaux PMCID: PMC2888750 Phylogeography and historical demography of the Pacific Sierra mackerel (Scomberomorus sierra) in the Eastern Pacific Mónica Domínguez López, Manuel Uribe Alcocer, and Píndaro Díaz Jaimes PMCID: PMC2876057 Genome-wide linkage scan for loci associated with epilepsy in Belgian shepherd dogs Anita M Oberbauer, Janelle M Belanger, Deborah I Grossman, Kelly R Regan, and Thomas R Famula PMCID: PMC2877138 Evaluating the transferability of Hapmap SNPs to a Singapore Chinese population Anand Kumar Andiappan, Ramani Anantharaman, Pallavi Parate Nilkanth, De Yun Wang, and Fook Tim Chew PMCID: PMC2877651 Identification of genetic modifiers of behavioral phenotypes in serotonin transporter knockout rats Judith Homberg, Isaäc J Nijman, Sylvia Kuijpers, and Edwin Cuppen PMCID: PMC2874760 Phylogenetic nomenclature and evolution of mannose-binding lectin (MBL2) haplotypes Angelica BW Boldt, Iara J Messias-Reason, Diogo Meyer, Carlos G Schrago, Florian Lang, Bertrand Lell, Klaus Dietz, Peter G Kremsner, Maria Luiza Petzl-Erler, and Jürgen FJ Kun PMCID: PMC2885306 How old is this mutation? - a study of three Ashkenazi Jewish founder mutations Celia MT Greenwood, Shuying Sun, Justin Veenstra, Nancy Hamel, Bethany Niell, Stephen Gruber, and William D Foulkes PMCID: PMC2889843 A three-stage approach for genome-wide association studies with family data for quantitative traits Ming-Huei Chen, Martin G Larson, Yi-Hsiang Hsu, Gina M Peloso, Chao-Yu Guo, Caroline S Fox, Larry D Atwood, and Qiong Yang PMCID: PMC2892427 Characterisation of sugar beet (Beta vulgaris L. ssp. vulgaris) varieties using microsatellite markers Marinus JM Smulders, G Danny Esselink, Isabelle Everaert, Jan De Riek, and Ben Vosman PMCID: PMC2890681 A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6 Naomi Duijvesteijn, Egbert F Knol, Jan WM Merks, Richard PMA Crooijmans, Martien AM Groenen, Henk Bovenhuis, and Barbara Harlizius PMCID: PMC2889844 Analysis of vkorc1 polymorphisms in Norway rats using the roof rat as outgroup Juan C Díaz, Ying Song, Anthony Moore, Jeff N Borchert, and Michael H Kohn PMCID: PMC2896334 Revealing fine scale subpopulation structure in the Vietnamese H'mong cattle breed for conservation purposes C Berthouly, JC Maillard, L Pham Doan, T Nhu Van, B Bed'Hom, G Leroy, H Hoang Thanh, D Laloë, N Bruneau, C Vu Chi, V Nguyen Dang, E Verrier, and X Rognon PMCID: PMC2889845 The 341C/T polymorphism in the GSTP1 gene is associated with increased risk of oesophageal cancer Dongping Li, Collet Dandara, and M Iqbal Parker PMCID: PMC2891604 Identification of population substructure among Jews using STR markers and dependence on reference populations included Jennifer B Listman , Deborah Hasin, Henry R Kranzler, Robert T Malison, Apiwat Mutirangura, Atapol Sughondhabirom, Efrat Aharonovich, Baruch Spivak, and Joel Gelernter PMCID: PMC2896335 An application of Random Forests to a genome-wide association dataset: Methodological considerations & new findings Benjamin A Goldstein, Alan E Hubbard, Adele Cutler, and Lisa F Barcellos PMCID: PMC2896336 Chromosome differentiation patterns during cichlid fish evolution Andréia B Poletto, Irani A Ferreira, Diogo C Cabral-de-Mello, Rafael T Nakajima, Juliana Mazzuchelli, Heraldo B Ribeiro, Paulo C Venere, Mauro Nirchio, Thomas D Kocher, and Cesar Martins PMCID: PMC2896337 Genetic diversity in three invasive clonal aquatic species in New Zealand Carla Lambertini, Tenna Riis, Birgit Olesen, John S Clayton, Brian K Sorrell, and Hans Brix PMCID: PMC2902404 Vietnamese chickens: a gate towards Asian genetic diversity C Berthouly-Salazar, X Rognon, T Nhu Van, M Gély, C Vu Chi, M Tixier-Boichard, B Bed'Hom, N Bruneau, E Verrier, JC Maillard, and JR Michaux PMCID: PMC2897773 Review A symphony of inner ear developmental control genes Sumantra Chatterjee, Petra Kraus, and Thomas Lufkin PMCID: PMC2915946 Research Articles Recombination facilitates neofunctionalization of duplicate genes via originalization Cheng Xue, Ren Huang, Shu-Qun Liu, and Yun-Xin Fu PMCID: PMC2906408 Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project Deanna S Cross, Lynn C Ivacic, Elisha L Stefanski, and Catherine A McCarty PMCID: PMC2908055 Frequency of eNOS polymorphisms in the Colombian general population Norma C Serrano, Luis A Díaz, Juan P Casas, Aroon D Hingorani, Daniel Moreno de Lucca, and María C Páez PMCID: PMC2910657 Haplotypes that include the integrin alpha 11 gene are associated with tick burden in cattle Laercio R Porto Neto, Rowan J Bunch, Blair E Harrison, Kishore C Prayaga, and William Barendse PMCID: PMC2905322 Detection of quantitative trait loci affecting haematological traits in swine via genome scanning Yuan-Fang Gong, Xin Lu, Zhi-Peng Wang, Fang Hu, Yan-Ru Luo, Shao-Qian Cai, Chun-Mei Qi, Shan Li, Xiao-Yan Niu, Xiao-Tian Qiu, Jian Zeng, and Qin Zhang PMCID: PMC2906409 Differentiating Plasmodium falciparum alleles by transforming Cartesian X,Y data to polar coordinates Jeana T DaRe, Drew P Kouri, Peter A Zimmerman, and Peter J Thomas PMCID: PMC2912781 Generalist genes analysis of DNA markers associated with mathematical ability and disability reveals shared influence across ages and abilities Sophia J Docherty, Yulia Kovas, Stephen A Petrill, and Robert Plomin PMCID: PMC2909150 Male-like sexual behavior of female mouse lacking fucose mutarotase Dongkyu Park, Dongwook Choi, Junghoon Lee, Dae-sik Lim, and Chankyu Park PMCID: PMC2912782 Growth-related quantitative trait loci in domestic and wild rainbow trout (Oncorhynchus mykiss) Brendan F Wringe, Robert H Devlin, Moira M Ferguson, Hooman K Moghadam, Dionne Sakhrani, and Roy G Danzmann PMCID: PMC2914766 High variability in a mating type linked region in the dry rot fungus Serpula lacrymans caused by frequency-dependent selection? Ingeborg Bjorvand Engh, Inger Skrede, Glenn-Peter Sætre, and Håvard Kauserud PMCID: PMC2909151 Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies Pamela Orjuela-Sánchez, Nadira D Karunaweera, Mônica da Silva-Nunes, Natal S da Silva, Kézia KG Scopel, Raquel M Gonçalves, Chanaki Amaratunga, Juliana M Sá, Duong Socheat, Rick M Fairhust, Sharmini Gunawardena, Thuraisamy Thavakodirasah, Gawrie LN Galapaththy, Rabindra Abeysinghe, Fumihiko Kawamoto, Dyann F Wirth, and Marcelo U Ferreira PMCID: PMC2910014 Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers Xiaoying Li, Lingfei Shangguan, Changnian Song, Chen Wang, Zhihong Gao, Huaping Yu, and Jinggui Fang PMCID: PMC2920227 Genetic variation, population structure and linkage disequilibrium in peach commercial varieties Maria José Aranzana, El-Kadri Abbassi, Werner Howad, and Pere Arús PMCID: PMC2915947 Fleece variation in alpaca (Vicugna pacos): a two-locus model for the Suri/Huacaya phenotype Silvano Presciuttini, Alessandro Valbonesi, Nolberto Apaza, Marco Antonini, Teodosio Huanca, and Carlo Renieri PMCID: PMC2914767 A genetic dissection of breed composition and performance enhancement in the Alaskan sled dog Heather J Huson, Heidi G Parker, Jonathan Runstadler, and Elaine A Ostrander PMCID: PMC2920855 Landscape features influence gene flow as measured by cost-distance and genetic analyses: a case study for giant pandas in the Daxiangling and Xiaoxiangling Mountains Lifeng Zhu, Xiangjiang Zhan, Tao Meng, Shanning Zhang, and Fuwen Wei PMCID: PMC2918525 Association of bovine leptin polymorphisms with energy output and energy storage traits in progeny tested Holstein-Friesian dairy cattle sires Linda Giblin, Stephen T Butler, Breda M Kearney, Sinead M Waters, Michael J Callanan, and Donagh P Berry PMCID: PMC2920856 Association of HPA axis-related genetic variation with stress reactivity and aggressive behaviour in pigs Eduard Muráni, Siriluck Ponsuksili, Richard B D'Eath, Simon P Turner, Esra Kurt, Gary Evans, Ludger Thölking, Ronald Klont, Aline Foury, Pierre Mormède, and Klaus Wimmers PMCID: PMC2927472 Co-assortment in integron-associated gene cassette assemblages in environmental DNA samples Carolyn A Michael and Nigel R Andrew PMCID: PMC2927473 Methodology Articles EM algorithm for Bayesian estimation of genomic breeding values Takeshi Hayashi and Hiroyoshi Iwata PMCID: PMC2845064 PCA-based bootstrap confidence interval tests for gene-disease association involving multiple SNPs Qianqian Peng, Jinghua Zhao, and Fuzhong Xue PMCID: PMC2825231 An entropy test for single-locus genetic association analysis Manuel Ruiz-Marín, Mariano Matilla-García, José Antonio García Cordoba, Juan Luis Susillo-González, Alejandro Romo-Astorga, Antonio González-Pérez, Agustín Ruiz, and Javier Gayán PMCID: PMC2860340 Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome Hideaki Mizuno, Gurinder Atwal, Haijian Wang, Arnold J Levine, and Alexei Vazquez PMCID: PMC2873552 Bayesian shrinkage mapping of quantitative trait loci in variance component models Ming Fang PMCID: PMC2874758 Validation of dot blot hybridization and denaturing high performance liquid chromatography as reliable methods for TP53 codon 72 genotyping in molecular epidemiologic studies Tatiana Rabachini, Helen Trottier, Eduardo L Franco, and Luisa L Villa PMCID: PMC2891603 Improved IBD detection using incomplete haplotype information Giulio Genovese, Gregory Leibon, Martin R Pollak, and Daniel N Rockmore PMCID: PMC2914765 Other Issues: Journal List
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