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Complex traits and quantitative genetics

Section edited by Jim Reecy

This section incorporates all aspects of complex trait and quantitative genetics including but not limited to: mapping and association studies, the genetic basis of disease, genetics aspects of breeding and linkage analysis.

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  1. Content type: Research article

    Among SNP markers that become increasingly valuable in molecular breeding of crop plants are the CAPS and dCAPS markers derived from the genes of interest. To date, the number of such gene-based markers is sma...

    Authors: Fakhriddin N. Kushanov, Alan E. Pepper, John Z. Yu, Zabardast T. Buriev, Shukhrat E. Shermatov, Sukumar Saha, Mauricio Ulloa, Johnie N. Jenkins, Abdusattor Abdukarimov and Ibrokhim Y. Abdurakhmonov

    Citation: BMC Genetics 2016 17:141

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  2. Content type: Research article

    The use of wood as an industrial raw material has led to development of plantation forestry, in which trees are planted, managed, and harvested as crops. The productivity of such plantations often exceeds that...

    Authors: Jin S. Xiong, Steven E. McKeand, Fikret Isik, Jill Wegrzyn, David B. Neale, Zhao-Bang Zeng, Luciano da Costa e Silva and Ross W. Whetten

    Citation: BMC Genetics 2016 17:138

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  3. Content type: Research article

    Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influ...

    Authors: Marinela Dukić, Daniel Berner, Marius Roesti, Christoph R. Haag and Dieter Ebert

    Citation: BMC Genetics 2016 17:137

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  4. Content type: Research article

    The importance of the adrenal gland in regard to lactation and reproduction in cattle has been recognized early. Caused by interest in animal welfare and the impact of stress on economically important traits i...

    Authors: Bodo Brand, Markus O. Scheinhardt, Juliane Friedrich, Daisy Zimmer, Norbert Reinsch, Siriluck Ponsuksili, Manfred Schwerin and Andreas Ziegler

    Citation: BMC Genetics 2016 17:135

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    The Erratum to this article has been published in BMC Genetics 2016 17:148

  5. Content type: Research article

    Nitrogen use efficiency is an important breeding trait that can be modified to improve the sustainability of many crop species used in agriculture. Rapeseed is a major oil crop with low nitrogen use efficiency...

    Authors: Anne-Sophie Bouchet, Anne Laperche, Christine Bissuel-Belaygue, Cécile Baron, Jérôme Morice, Mathieu Rousseau-Gueutin, Jean-Eric Dheu, Pierre George, Xavier Pinochet, Thomas Foubert, Olivier Maes, Damien Dugué, Florent Guinot and Nathalie Nesi

    Citation: BMC Genetics 2016 17:131

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  6. Content type: Research article

    Kernel length is an important target trait in barley (Hordeum vulgare L.) breeding programs. However, the number of known quantitative trait loci (QTLs) controlling kernel length is limited. In the present study,...

    Authors: Hong Zhou, Shihang Liu, Yujiao Liu, Yaxi Liu, Jing You, Mei Deng, Jian Ma, Guangdeng Chen, Yuming Wei, Chunji Liu and Youliang Zheng

    Citation: BMC Genetics 2016 17:130

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  7. Content type: Research article

    Spotted wilt caused by tomato spotted wilt virus (TSWV) is one of the major peanut (Arachis hypogaea L.) diseases in the southeastern United States. Occurrence, severity, and symptoms of spotted wilt disease are ...

    Authors: Yu-Chien Tseng, Barry L. Tillman, Ze Peng and Jianping Wang

    Citation: BMC Genetics 2016 17:128

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  8. Content type: Research article

    Preeclampsia is a common and heterogeneous vascular syndrome of pregnancy. Its genetic risk profile is yet unknown and may vary between individuals and populations. The rs4606 3′ UTR polymorphism of the Regula...

    Authors: Tiina Karppanen, Tea Kaartokallio, Miira M. Klemetti, Seppo Heinonen, Eero Kajantie, Juha Kere, Katja Kivinen, Anneli Pouta, Anne Cathrine Staff and Hannele Laivuori

    Citation: BMC Genetics 2016 17:121

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  9. Content type: Research article

    Results from genome-wide association studies (GWAS) identified many loci and biological pathways that influence adult body mass index (BMI). We aimed to identify if biological pathways related to adult BMI als...

    Authors: Claire Monnereau, Suzanne Vogelezang, Claudia J. Kruithof, Vincent W. V. Jaddoe and Janine F. Felix

    Citation: BMC Genetics 2016 17:120

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  10. Content type: Research article

    Genome-wide association studies of Single Nucleotide Polymorphisms (SNPs) have identified 55 SNPs associated with lung function. However, little is known about the effect of copy number variants (CNVs) on lung...

    Authors: Nick Shrine, Martin D. Tobin, Claudia Schurmann, María Soler Artigas, Jennie Hui, Terho Lehtimäki, Olli T. Raitakari, Craig E. Pennell, Qi Wei Ang, David P. Strachan, Georg Homuth, Sven Gläser, Stephan B. Felix, David M. Evans, John Henderson, Raquel Granell…

    Citation: BMC Genetics 2016 17:116

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  11. Content type: Research article

    Earlobe color is a naturally and artificially selected trait in chicken. As a head furnishing trait, it has been selected as a breed characteristic. Research has demonstrated that white/red earlobe color was r...

    Authors: Changsheng Nie, Zebin Zhang, Jiangxia Zheng, Hongyan Sun, Zhonghua Ning, Guiyun Xu, Ning Yang and Lujiang Qu

    Citation: BMC Genetics 2016 17:115

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  12. Content type: Research article

    In the Western world bovine milk products are an important protein source in human diet. The major proteins in bovine milk are the four caseins (CN), αS1-, αS2-, β-, and k-CN and the two whey proteins, β-LG and α...

    Authors: Bart Buitenhuis, Nina A. Poulsen, Grum Gebreyesus and Lotte B. Larsen

    Citation: BMC Genetics 2016 17:114

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  13. Content type: Research article

    Considerable natural variation for lifespan exists within human and animal populations. Genetically dissecting this variation can elucidate the pathways and genes involved in aging, and help uncover the geneti...

    Authors: Chad A. Highfill, G. Adam Reeves and Stuart J. Macdonald

    Citation: BMC Genetics 2016 17:113

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  14. Content type: Research article

    Down syndrome incidence in humans increases dramatically with maternal age. This is mainly the result of increased meiotic errors, but factors such as differences in abortion rate may play a role as well. Sinc...

    Authors: Shani Stern, David Biron and Elisha Moses

    Citation: BMC Genetics 2016 17:105

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  15. Content type: Research article

    Most agronomical traits of crop species are complex traits controlled by multiple genes and affected by environmental factors. While considerable efforts have been made to fine-map and clone major quantitative...

    Authors: Hong-Wei Zhang, Ye-Yang Fan, Yu-Jun Zhu, Jun-Yu Chen, Si-Bin Yu and Jie-Yun Zhuang

    Citation: BMC Genetics 2016 17:98

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  16. Content type: Methodology article

    Selecting chromosome substitution strains (CSSs, also called consomic strains/lines) used in the search for quantitative trait loci (QTLs) consistently requires the identification of the respective phenotypic ...

    Authors: M. Labots, M. C. Laarakker, F. Ohl and H. A. van Lith

    Citation: BMC Genetics 2016 17:95

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  17. Content type: Research article

    The genetic determinism of the calving and suckling performance of beef cows is little known whereas these maternal traits are of major economic importance in beef cattle production systems. This paper aims to...

    Authors: Alexis Michenet, Marine Barbat, Romain Saintilan, Eric Venot and Florence Phocas

    Citation: BMC Genetics 2016 17:88

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  18. Content type: Research article

    The identification of lines resistant to ear diseases is of great importance in maize breeding because such diseases directly interfere with kernel quality and yield. Among these diseases, ear rot disease is w...

    Authors: Jhonathan Pedroso Rigal dos Santos, Luiz Paulo Miranda Pires, Renato Coelho de Castro Vasconcellos, Gabriela Santos Pereira, Renzo Garcia Von Pinho and Marcio Balestre

    Citation: BMC Genetics 2016 17:86

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  19. Content type: Research article

    Genome-wide association studies (GWAS) are a powerful tool for detecting genomic regions explaining variation in phenotype. The objectives of the present study were to identify or refine the positions of genom...

    Authors: Shadi Nayeri, Mehdi Sargolzaei, Mohammed K. Abo-Ismail, Natalie May, Stephen P. Miller, Flavio Schenkel, Stephen S. Moore and Paul Stothard

    Citation: BMC Genetics 2016 17:75

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  20. Content type: Research article

    Fibrotic idiopathic interstitial pneumonias (fIIP) are a group of fatal lung diseases with largely unknown etiology and without definitive treatment other than lung transplant to prolong life. There is strong ...

    Authors: Tasha E. Fingerlin, Weiming Zhang, Ivana V. Yang, Hannah C. Ainsworth, Pamela H. Russell, Rachel Z. Blumhagen, Marvin I. Schwarz, Kevin K. Brown, Mark P. Steele, James E. Loyd, Gregory P. Cosgrove, David A. Lynch, Steve Groshong, Harold R. Collard, Paul J. Wolters, Williamson Z. Bradford…

    Citation: BMC Genetics 2016 17:74

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  21. Content type: Research article

    The SMXA-5 mouse is an animal model of high-fat diet-induced fatty liver. The major QTL for fatty liver, Fl1sa on chromosome 12, was identified in a SM/J × SMXA-5 intercross. The SMXA-5 genome consists of the SM/...

    Authors: Misato Kobayashi, Miyako Suzuki, Tamio Ohno, Kana Tsuzuki, Chie Taguchi, Soushi Tateishi, Teruo Kawada, Young-il Kim, Atsushi Murai and Fumihiko Horio

    Citation: BMC Genetics 2016 17:73

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  22. Content type: Research article

    Tensin2 deficiency results in alterations in podocytes and subsequent glomerular and tubulointerstitial injuries. However, this pathology is critically dependent on genetic background. While the Tensin2-defici...

    Authors: Hayato Sasaki, Junpei Kimura, Ken-Ichi Nagasaki, Kiyoma Marusugi, Takashi Agui and Nobuya Sasaki

    Citation: BMC Genetics 2016 17:69

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  23. Content type: Research article

    Comparing QTL analyses of multiple pair-mating families can provide a better understanding of important allelic variations and distributions. However, most QTL mapping studies in common carp have been based on...

    Authors: Weihua Lv, Xianhu Zheng, Youyi Kuang, Dingchen Cao, Yunqin Yan and Xiaowen Sun

    Citation: BMC Genetics 2016 17:65

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  24. Content type: Research article

    White striping (WS) is an emerging quality defect with adverse consequences for the sensorial, technological, and nutritional qualities of breast meat in broiler chickens. The genetic determinism of this defec...

    Authors: Nabeel Alnahhas, Cécile Berri, Marie Chabault, Pascal Chartrin, Maryse Boulay, Marie Christine Bourin and Elisabeth Le Bihan-Duval

    Citation: BMC Genetics 2016 17:61

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  25. Content type: Research article

    The aim of the present study was to compare the power of single nucleotide polymorphism (SNP)-based genome-wide association study (GWAS) and haplotype-based GWAS for quantitative trait loci (QTL) detection, an...

    Authors: Shuji Sato, Yoshinobu Uemoto, Takashi Kikuchi, Sachiko Egawa, Kimiko Kohira, Tomomi Saito, Hironori Sakuma, Satoshi Miyashita, Shinji Arata, Takatoshi Kojima and Keiichi Suzuki

    Citation: BMC Genetics 2016 17:60

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  26. Content type: Research article

    Hybrid breakdown has been well documented in various species. Relationships between genomic heterozygosity and traits-fitness have been extensively explored especially in the natural populations. But correlati...

    Authors: Baosheng Dai, Huanle Guo, Cong Huang, Xianlong Zhang and Zhongxu Lin

    Citation: BMC Genetics 2016 17:58

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  27. Content type: Research article

    Residual biomass production for fuel conversion represents a unique opportunity to avoid concerns about compromising food supply by using dedicated feedstock crops. Developing tomato varieties suitable for bot...

    Authors: G. Caruso, L. D. Gomez, F. Ferriello, A. Andolfi, C. Borgonuovo, A. Evidente, R. Simister, S. J. McQueen-Mason, D. Carputo, L. Frusciante and M. R. Ercolano

    Citation: BMC Genetics 2016 17:56

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  28. Content type: Research article

    The Nordic Red Cattle consisting of three different populations from Finland, Sweden and Denmark are under a joint breeding value estimation system. The long history of recording of production and health trait...

    Authors: T. Iso-Touru, G. Sahana, B. Guldbrandtsen, M. S. Lund and J. Vilkki

    Citation: BMC Genetics 2016 17:55

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  29. Content type: Research article

    Artificial insemination is widely used in many cattle breeding programs. Semen samples of breeding bulls are collected and closely examined immediately after collection at artificial insemination centers. Only...

    Authors: Hubert Pausch, Heli Venhoranta, Christine Wurmser, Kalle Hakala, Terhi Iso-Touru, Anu Sironen, Rikke K. Vingborg, Hannes Lohi, Lennart Söderquist, Ruedi Fries and Magnus Andersson

    Citation: BMC Genetics 2016 17:49

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  30. Content type: Research article

    Reproductive efficiency has a great impact on the economic success of pork production. Gilts comprise a significant portion of breeding females and gilts that reach puberty earlier tend to stay in the herd lon...

    Authors: Dan J. Nonneman, James F. Schneider, Clay A. Lents, Ralph T. Wiedmann, Jeffrey L. Vallet and Gary A. Rohrer

    Citation: BMC Genetics 2016 17:50

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  31. Content type: Research article

    Although the effect of the fat mass and obesity-associated (FTO) gene on adiposity is well established, there is a lack of evidence whether physical activity (PA) modifies the effect of FTO variants on obesity...

    Authors: Joon Young Kim, Jacob T. DeMenna, Sobha Puppala, Geetha Chittoor, Jennifer Schneider, Ravindranath Duggirala, Lawrence J. Mandarino, Gabriel Q. Shaibi and Dawn K. Coletta

    Citation: BMC Genetics 2016 17:47

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  32. Content type: Research article

    Colorectal cancer is an abnormal tissue development in the colon or rectum. Most of CRCs develop due to somatic mutations, while only a small proportion is caused by inherited mutations. Familial adenomatous p...

    Authors: Alexandra Dorman, Daria Baer, Ian Tomlinson, Richard Mott and Fuad A. Iraqi

    Citation: BMC Genetics 2016 17:46

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    The Erratum to this article has been published in BMC Genetics 2016 17:147

  33. Content type: Research article

    Genetic susceptibility plays an important role in the risk of developing pain in individuals with cancer. As a complex trait, multiple genes underlie this susceptibility. We used gene network analyses to ident...

    Authors: Cielito C. Reyes-Gibby, Jian Wang, Mary Rose T. Silvas, Robert Yu, Sai-Ching J. Yeung and Sanjay Shete

    Citation: BMC Genetics 2016 17:40

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  34. Content type: Research article

    Heritable factors are well known to increase the risk of cancer in families. Known susceptibility genes account for a small proportion of all colorectal cancer cases. The aim of this study was to identify the ...

    Authors: Jessada Thutkawkorapin, Simone Picelli, Vinaykumar Kontham, Tao Liu, Daniel Nilsson and Annika Lindblom

    Citation: BMC Genetics 2016 17:41

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  35. Content type: Research article

    The existence of moderate to high levels of linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) affecting traits of interest is fundamental for the success of genome-wide asso...

    Authors: Patrícia Biegelmeyer, Claudia C. Gulias-Gomes, Alexandre R. Caetano, Juan P. Steibel and Fernando F. Cardoso

    Citation: BMC Genetics 2016 17:32

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  36. Content type: Research article

    Genetic factors play an important role in hearing loss, contributing to approximately 60 % of cases of congenital hearing loss. Autosomal dominant deafness accounts for approximately 20 % of cases of hereditar...

    Authors: Yongyi Yuan, Xue Gao, Bangqing Huang, Jingqiao Lu, Guojian Wang, Xi Lin, Yan Qu and Pu Dai

    Citation: BMC Genetics 2016 17:33

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  37. Content type: Research article

    Seed dormancy is an adaptive trait employed by flowering plants to avoid harsh environmental conditions for the continuity of their next generations. In cereal crops, moderate seed dormancy could help prevent ...

    Authors: Risper Auma Magwa, Hu Zhao and Yongzhong Xing

    Citation: BMC Genetics 2016 17:28

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  38. Content type: Research article

    Groupers (Epinephelus spp.) have been widely cultivated in China and South-East Asian countries. As a novel hybrid offspring crossed between E. fuscogutatus♀ and E. lanceolatus♂, Hulong grouper exhibits significa...

    Authors: Ying Sun, Chuan-Yu Guo, Deng-Dong Wang, Xiao Feng Li, Ling Xiao, Xinhui Zhang, Xinxin You, Qiong Shi, Guo-Jun Hu, Chao Fang, Hao-Ran Lin and Yong Zhang

    Citation: BMC Genetics 2016 17:24

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  39. Content type: Research article

    The prevalence of Type 2 Diabetes (T2D) mellitus in the past decades, has reached epidemic proportions. Several lines of evidence support the role of genetic variation in the pathogenesis of T2D and insulin re...

    Authors: Hanifa J. Abu-Toamih Atamni, Richard Mott, Morris Soller and Fuad A. Iraqi

    Citation: BMC Genetics 2016 17:10

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  40. Content type: Research article

    In animal breeding, genetic variance for complex traits is often estimated using linear mixed models that incorporate information from single nucleotide polymorphism (SNP) markers using a realized genomic rela...

    Authors: Pernille Sarup, Just Jensen, Tage Ostersen, Mark Henryon and Peter Sørensen

    Citation: BMC Genetics 2016 17:11

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  41. Content type: Research article

    The use of information across populations is an attractive approach to increase the accuracy of genomic prediction for numerically small populations. However, accuracies of across population genomic prediction...

    Authors: S. van den Berg, M. P. L. Calus, T. H. E. Meuwissen and Y. C. J. Wientjes

    Citation: BMC Genetics 2015 16:146

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  42. Content type: Research article

    Premature flowering or bolting is an undesirable characteristic that causes severe sugar yield losses and interferes with harvesting. Vernalization is a prerequisite for the floral induction, achieved by expos...

    Authors: Chiara Broccanello, Piergiorgio Stevanato, Filippo Biscarini, Dario Cantu and Massimo Saccomani

    Citation: BMC Genetics 2015 16:142

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  43. Content type: Research article

    Pulmonary function decline is a major contributor to morbidity and mortality among smokers. Post bronchodilator FEV1 and FEV1/FVC ratio are considered the standard assessment of airflow obstruction. We performed ...

    Authors: Sharon M. Lutz, Michael H. Cho, Kendra Young, Craig P. Hersh, Peter J. Castaldi, Merry-Lynn McDonald, Elizabeth Regan, Manuel Mattheisen, Dawn L. DeMeo, Margaret Parker, Marilyn Foreman, Barry J. Make, Robert L. Jensen, Richard Casaburi, David A. Lomas, Surya P. Bhatt…

    Citation: BMC Genetics 2015 16:138

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  44. Content type: Research article

    Located in the Pacific Ocean between Australia and New Zealand, the unique population isolate of Norfolk Island has been shown to exhibit increased prevalence of metabolic disorders (type-2 diabetes, cardiovas...

    Authors: M. C. Benton, R. A. Lea, D. Macartney-Coxson, C. Bellis, M. A. Carless, J. E. Curran, M. Hanna, D. Eccles, G. K. Chambers, J. Blangero and L. R. Griffiths

    Citation: BMC Genetics 2015 16:136

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  45. Content type: Research article

    Identification of genetic variants that are associated with fatty acid composition in beef will enhance our understanding of host genetic influence on the trait and also allow for more effective improvement of...

    Authors: Liuhong Chen, Chinyere Ekine-Dzivenu, Michael Vinsky, John Basarab, Jennifer Aalhus, Mike E. R. Dugan, Carolyn Fitzsimmons, Paul Stothard and Changxi Li

    Citation: BMC Genetics 2015 16:135

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  46. Content type: Research article

    Genetic variance that is not captured by single nucleotide polymorphisms (SNPs) is due to imperfect linkage disequilibrium (LD) between SNPs and quantitative trait loci (QTLs), and the extent of LD between SNP...

    Authors: Yoshinobu Uemoto, Shinji Sasaki, Takatoshi Kojima, Yoshikazu Sugimoto and Toshio Watanabe

    Citation: BMC Genetics 2015 16:134

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  47. Content type: Research article

    Individuals with dyslipidemia often develop type 2 diabetes, and diabetic patients often have dyslipidemia. It remains to be determined whether there are genetic connections between the 2 disorders.

    Authors: Qian Wang, Andrew T. Grainger, Ani Manichaikul, Emily Farber, Suna Onengut-Gumuscu and Weibin Shi

    Citation: BMC Genetics 2015 16:133

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  48. Content type: Research article

    The genetic structure of human populations is the outcome of the combined action of different processes such as demographic dynamics and natural selection. Several efforts toward the characterization of popula...

    Authors: Silvia Parolo, Antonella Lisa, Davide Gentilini, Anna Maria Di Blasio, Simona Barlera, Enrico B. Nicolis, Giorgio B. Boncoraglio, Eugenio A. Parati and Silvia Bione

    Citation: BMC Genetics 2015 16:132

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