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Functional genetics

Section edited by Federico Canzian

This section incorporates all aspects of the functional analysis of genes and genomes including but not limited to: sequence analysis and genotyping approaches to finding functional variation in genes and gene families, experimental studies of gene function, transcriptional regulation and gene expression.

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  1. Content type: Research article

    In humans, muscle-specific nicotinergic acetylcholine receptor (AChR) is a transmembrane protein with five different subunits, coded by CHRNA1, CHRNB, CHRND and CHRNG/CHRNE. The gamma subunit of AChR encoded by C...

    Authors: Ariana Kariminejad, Navid Almadani, Atefeh Khoshaeen, Bjorn Olsson, Ali-Reza Moslemi and Homa Tajsharghi

    Citation: BMC Genetics 2016 17:71

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  2. Content type: Research article

    Multiple sclerosis is a chronic inflammatory, demyelinating disease of the central nervous system. Recent genome-wide studies have revealed more than 110 single nucleotide polymorphisms as associated with susc...

    Authors: Pankaj K. Keshari, Hanne F. Harbo, Kjell-Morten Myhr, Jan H. Aarseth, Steffan D. Bos and Tone Berge

    Citation: BMC Genetics 2016 17:59

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  3. Content type: Research article

    Foxtail millet (Setaria italica) is a diploid C4 panicoid species. Because of its prominent drought resistance, small genome size, self-pollination, and short life cycle, foxtail millet has become an ideal model ...

    Authors: Yongqiang Wang, Lin Li, Sha Tang, Jianguang Liu, Hanshuang Zhang, Hui Zhi, Guanqing Jia and Xianmin Diao

    Citation: BMC Genetics 2016 17:57

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  4. Content type: Research article

    Trehalose (a-D-glucopyranosyl a-D-glucopyranoside) is a nonreducing disaccharide and is widely distributed in bacteria, fungi, algae, plants and invertebrates. In the study, the identification of trehalose-6-p...

    Authors: Min Mu, Xu-Ke Lu, Jun-Juan Wang, De-Long Wang, Zu-Jun Yin, Shuai Wang, Wei-Li Fan and Wu-Wei Ye

    Citation: BMC Genetics 2016 17:54

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    The Erratum to this article has been published in BMC Genetics 2016 17:101

  5. Content type: Research article

    Dopamine β-hydroxylase (DBH) is a critical enzyme in the biosynthesis of catecholamines. This enzyme’s role in neuroendocrine regulation is well known, but there are some indications that it may also modulate ...

    Authors: Qi Xu, Yadong Song, Ran Liu, Yang Chen, Yang Zhang, Yang Li, Wenming Zhao, Guobin Chang and Guohong Chen

    Citation: BMC Genetics 2016 17:48

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  6. Content type: Research article

    The beak deformity (crossed beaks) was found in some indigenous chickens of China, such as Beijing-You (BJY), Qingyuan Partridge, and Huxu Chickens. Birds with deformed beaks have reduced feed intake and drink...

    Authors: Hao Bai, Yanyan Sun, Jing Zhu, Nian Liu, Dongli Li, Fuguang Xue, Yunlei Li and Jilan Chen

    Citation: BMC Genetics 2016 17:44

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  7. Content type: Research article

    This study was performed to identify the non- synonymous polymorphisms in the myosin heavy chain 1 gene (MYH1) association with skeletal muscle development in economically important Jeju Native Pig (JNP) and Berk...

    Authors: Mrinmoy Ghosh, Simrinder Singh Sodhi, Neelesh Sharma, Raj Kumar Mongre, Nameun Kim, Amit Kumar Singh, Sung Jin Lee, Dae Cheol Kim, Sung Woo Kim, Hak Kyo Lee, Ki-Duk Song and Dong Kee Jeong

    Citation: BMC Genetics 2016 17:35

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  8. Content type: Research article

    The transformer (tra) is a sex determining switch in different orders of insects, including Diptera, as in the family Tephritidae. The lifelong autoregulatory loop of tra female-specific splicing can be reset by ...

    Authors: Kamoltip Laohakieat, Nidchaya Aketarawong, Siriwan Isasawin, Siripong Thitamadee and Sujinda Thanaphum

    Citation: BMC Genetics 2016 17:34

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  9. Content type: Research article

    Despite the emergence of stereotactic body radiotherapy (SBRT) for treatment of medically inoperable early-stage non-small-cell lung cancer patients, the molecular effects of focal exposure of limited lung vol...

    Authors: Bu-Yeo Kim, Hee Jin, Yoon-Jin Lee, Ga-Young Kang, Jaeho Cho and Yun-Sil Lee

    Citation: BMC Genetics 2016 17:29

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  10. Content type: Research article

    Copy number variation (CNV) is an important source of genetic variability associated with phenotypic variation and disease susceptibility. Comprehensive genome-wide CNV maps provide valuable information for ge...

    Authors: Shinji Sasaki, Toshio Watanabe, Shota Nishimura and Yoshikazu Sugimoto

    Citation: BMC Genetics 2016 17:26

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  11. Content type: Research article

    Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial commun...

    Authors: Xian Zhang, Jiaojiao Niu, Yili Liang, Xueduan Liu and Huaqun Yin

    Citation: BMC Genetics 2016 17:21

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  12. Content type: Research article

    Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1–6 bp tandem repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies....

    Authors: Sonali Sachin Ranade, Yao-Cheng Lin, Yves Van de Peer and María Rosario García-Gil

    Citation: BMC Genetics 2015 16:149

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  13. Content type: Research article

    Etl4lacZ (Enhancer trap locus 4) and SktGt (Sickle tail) are lacZ reporter gene integrations into the same locus on mouse chromosome 2 targeting a gene that is expressed in the notochord of early embryos and in m...

    Authors: Katrin Serth, Anja Beckers, Karin Schuster-Gossler, Maria N. Pavlova, Julia Müller, Mariel C. Paul, Richard Reinhardt and Achim Gossler

    Citation: BMC Genetics 2015 16:143

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  14. Content type: Research article

    Adaption to cold temperatures, especially those below freezing, is essential for animal survival in cold environments. Freezing is also used for many medical, scientific, and industrial purposes. Natural freez...

    Authors: Jian-Ping Hu, Xiao-Ying Xu, Li-Ying Huang, Li-shun Wang and Ning-Yuan Fang

    Citation: BMC Genetics 2015 16:139

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  15. Content type: Research article

    Fish are remarkably diverse in repertoires of visual opsins by gene duplications. Differentiation of their spatiotemporal expression patterns and absorption spectra enables fine-tuning of feature detection in ...

    Authors: Taro Tsujimura, Ryoko Masuda, Ryuichi Ashino and Shoji Kawamura

    Citation: BMC Genetics 2015 16:130

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  16. Content type: Research article

    Adipose tissue is recognized as a highly active metabolic and endocrine organ. The hormones secreted by this tissue play an important role in many biochemical processes. It is known that dysfunction of adipocy...

    Authors: Joanna Nowacka-Woszuk, Ewa Pruszynska-Oszmalek, Maciej Szydlowski, Slawomir Sadkowski and Izabela Szczerbal

    Citation: BMC Genetics 2015 16:113

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  17. Content type: Research article

    Sea level sojourners, on ascent to high altitude, undergo acclimatization through integrated physiological processes for defending the body against oxygen deprivation while the high altitude natives (resident ...

    Authors: Arvind Tomar, Seema Malhotra and Soma Sarkar

    Citation: BMC Genetics 2015 16:112

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  18. Content type: Research article

    Accumulation of galactosphingolipids is a general characteristic of Fabry disease, a lysosomal storage disorder caused by the deficient activity of α-galactosidase A encoded by the GLA gene. Although many polymor...

    Authors: Javier Gervas-Arruga, Jorge J. Cebolla, Pilar Irun, Javier Perez-Lopez, Luis Plaza, Jose C. Roche, Jose L. Capablo, Jose C. Rodriguez-Rey, Miguel Pocovi and Pilar Giraldo

    Citation: BMC Genetics 2015 16:109

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  19. Content type: Research article

    Acid soil is a serious limitation to crop production all over the world. Toxic aluminium (Al) cations in acid soil inhibit root growth and reduce yield. Although a gene tolerant to acid soil has been identifie...

    Authors: Miao Bian, Xiaoli Jin, Sue Broughton, Xiao-Qi Zhang, Gaofeng Zhou, Meixue Zhou, Guoping Zhang, Dongfa Sun and Chengdao Li

    Citation: BMC Genetics 2015 16:92

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  20. Content type: Research article

    In a deep sequencing analysis of small RNAs prepared from a living fossil, the tadpole shrimp Triops cancriformis, a 32-nt small RNA was specifically detected in the adult stage. A nucleotide sequence comparison ...

    Authors: Yuka Hirose, Kahori T. Ikeda, Emiko Noro, Kiriko Hiraoka, Masaru Tomita and Akio Kanai

    Citation: BMC Genetics 2015 16:83

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  21. Content type: Research article

    Low weight at birth is associated with obesity in later life. One hypothesis to explain such an association is that genetic variants that increase the risk of obesity also reduce fetal weight. Recently, obesit...

    Authors: Olivier S Descamps, Eric Tarantino and Pierre-Francois Guilmot

    Citation: BMC Genetics 2014 15:145

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  22. Content type: Research article

    Sheep are valuable resources for the animal fibre industry. Therefore, identifying genes which regulate wool growth would offer strategies for improving the quality of fine wool. In this study, we employed Agi...

    Authors: Nan Liu, Hegang Li, Kaidong Liu, Juanjuan Yu, Ran Bu, Ming Cheng, Wei De, Jifeng Liu, Guangling He and Jinshan Zhao

    Citation: BMC Genetics 2014 15:144

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  23. Content type: Research article

    The factors determining sex are diverse in vertebrates and especially so in teleost fishes. Only a handful of master sex-determining genes have been identified, however great efforts have been undertaken to ch...

    Authors: Corina Heule, Carolin Göppert, Walter Salzburger and Astrid Böhne

    Citation: BMC Genetics 2014 15:140

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  24. Content type: Research article

    In order to assess genetic diversity of a set of 41 Caricaceae accessions, this study used 34 primer pairs designed from the conserved domains of bacterial leaf blight resistance genes from rice, in a PCR base...

    Authors: Samik Sengupta, Basabdatta Das, Pinaki Acharyya, Manoj Prasad and Tapas Kumar Ghose

    Citation: BMC Genetics 2014 15:137

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  25. Content type: Research article

    Human xylosyltransferase-I (XT-I) catalyzes the rate-limiting step in proteoglycan glycosylation. An increase in XYLT1 mRNA expression and serum XT activity is associated with diseases characterized by abnormal e...

    Authors: Isabel Faust, Kai Oliver Böker, Christoph Lichtenberg, Joachim Kuhn, Cornelius Knabbe and Doris Hendig

    Citation: BMC Genetics 2014 15:129

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  26. Content type: Research article

    Loss-of-function mutations in TBC1D20 cause Warburg Micro syndrome 4 (WARBM4), which is an autosomal recessive syndromic disorder characterized by eye, brain, and genital abnormalities. Blind sterile (bs) mice ca...

    Authors: Anna Kyunglim Park, Ryan P Liegel, Adam Ronchetti, Allison D Ebert, Aron Geurts and Duska J Sidjanin

    Citation: BMC Genetics 2014 15:135

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  27. Content type: Research article

    Success of meat production and selection for improvement of meat quality is among the primary aims in animal production. Meat quality traits are economically important in swine; however, the underlying genetic...

    Authors: Silvia Bongiorni, Francesca Tilesi, Silvia Bicorgna, Francesca Iacoponi, Daniela Willems, Maria Gargani, MariaSilvia D’Andrea, Fabio Pilla and Alessio Valentini

    Citation: BMC Genetics 2014 15:119

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  28. Content type: Research article

    Glycosphingolipids (GSLs) are important membrane components composed of a carbohydrate structure attached to a hydrophobic ceramide. They can serve as specific membrane receptors for microbes and microbial pro...

    Authors: Tiphanie Goetstouwers, Mario Van Poucke, Annelies Coddens, Van Ut Nguyen, Vesna Melkebeek, Dieter Deforce, Eric Cox and Luc J Peelman

    Citation: BMC Genetics 2014 15:103

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  29. Content type: Research article

    The novel organic cation transporter 2 (OCTN2) is the physiologically most important carnitine transporter in tissues and is responsible for carnitine absorption in the intestine, carnitine reabsorption in the...

    Authors: Huidi Luo, Yuanqing Zhang, Huihui Guo, Li Zhang, Xi Li, Robert Ringseis, Gaiping Wen, Dequan Hui, Aihua Liang, Klaus Eder and Dongchang He

    Citation: BMC Genetics 2014 15:90

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  30. Content type: Research article

    Traditional canola (Brassica napus L.; AACC, 2n = 38) cultivars yield seed oil with a relatively high proportion of α-linolenic acid (ALA; C18:3cisΔ9,12,15), which is desirable from a health perspective. Unfortun...

    Authors: Stacy D Singer, Randall J Weselake and Habibur Rahman

    Citation: BMC Genetics 2014 15:94

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  31. Content type: Research article

    The SPE-8 group gene products transduce the signal for spermatid activation initiated by extracellular zinc in C. elegans. Mutations in the spe-8 group genes result in hermaphrodite-derived spermatids that cannot...

    Authors: Paul J Muhlrad, Jessica N Clark, Ubaydah Nasri, Nicholas G Sullivan and Craig W LaMunyon

    Citation: BMC Genetics 2014 15:83

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  32. Content type: Methodology article

    Single-strand conformational polymorphism (SSCP) is still a frequently used genotyping method across different fields for the detection of single nucleotide polymorphisms (SNPs) due to its simplicity, requirem...

    Authors: Shavanthi Rajatileka, Karen Luyt, Maggie Williams, David Harding, David Odd, Elek Molnár and Anikó Váradi

    Citation: BMC Genetics 2014 15:80

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  33. Content type: Research article

    The aim of this study was to determine if variable number of tandem repeats (VNTR) in the second intron (STin2) of the serotonin transporter (SLC6A4) gene was associated with tobacco use disorder, successful smok...

    Authors: Márcia Regina Pizzo de Castro, Michael Maes, Roberta Losi Guembarovski, Carolina Batista Ariza, Edna Maria Vissoci Reiche, Heber Odebrecht Vargas, Mateus Medonça Vargas, Luiz Gustavo Piccoli de Melo, Seetal Dodd, Michael Berk, Maria Angelica Ehara Watanabe and Sandra Odebrecht Vargas Nunes

    Citation: BMC Genetics 2014 15:78

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  34. Content type: Research article

    Several lines of evidence associate misregulated genetic expression with risk factors for diabetes, Alzheimer’s, and other diseases that sporadically develop in healthy adults with no background of hereditary ...

    Authors: Minoru Nakayama, Tomoki Ishibashi, Hiroyuki O Ishikawa, Hiroyasu Sato, Takao Usui, Takayuki Okuda, Hiroyuki Yashiro, Hironori Ishikawa, Yoshie Taikou, Asako Minami, Kengo Kato, Masataka Taki, Toshiro Aigaki, Wataru Gunji, Masaya Ohtsu, Yasufumi Murakami…

    Citation: BMC Genetics 2014 15:46

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  35. Content type: Research article

    The molecular mechanisms causing pigment dispersion syndrome (PDS) and the pathway(s) by which it progresses to pigmentary glaucoma are not known. Mutations in two melanosomal protein genes (Tyrp1 ...

    Authors: K Saidas Nair, Jessica Barbay, Richard S Smith, Sharmila Masli and Simon WM John

    Citation: BMC Genetics 2014 15:42

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  36. Content type: Research article

    Phophoserine phosphatase-like (PSPHL) is expressed at significantly higher levels in breast tumors from African American women (AAW) compared to Caucasian women (CW). How overexpression of PSPHL contributes to ou...

    Authors: Seth Rummel, Cayla E Penatzer, Craig D Shriver and Rachel E Ellsworth

    Citation: BMC Genetics 2014 15:38

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  37. Content type: Research article

    Lipoxygenases are a family of enzymes which catalyse the hydroperoxidation of polyunsaturated fatty acids with a cis, cis-1,4-pentadiene to form conjugated hydroperoxydienes. Lipoxygenase-1 (LOX-1) in barley w...

    Authors: Hongxia Ye, Stefan Harasymow, Xiao-Qi Zhang, Blakely Paynter, Dianxing Wu, Michael Jones, Xiaoli Shu and Chengdao Li

    Citation: BMC Genetics 2014 15:36

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  38. Content type: Research article

    Few exceptions have been described from strict maternal inheritance of mitochondrial DNA in animals, including sea mussels (Mytilidae), clams (Donacidae, Veneridae and Solenidae) and freshwater mussels (Uniono...

    Authors: Tomasz J Sańko and Artur Burzyński

    Citation: BMC Genetics 2014 15:28

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  39. Content type: Research article

    Fatty acid desaturase 1 (FADS1) and 2 (FADS2) genes code respectively for the enzymes delta-5 and delta-6 desaturases which are rate limiting enzymes in the synthesis of polyunsaturated omega-3 and omega-6 fat...

    Authors: Eveline M Ibeagha-Awemu, Kingsley A Akwanji, Frédéric Beaudoin and Xin Zhao

    Citation: BMC Genetics 2014 15:25

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  40. Content type: Research article

    Mitochondrial cytopathies are characterized by a large variability of clinical phenotypes and severity. The amount of mutant mitochondrial DNA (mtDNA) in a cell, called the heteroplasmy level, is an important ...

    Authors: Yuhua Zhu, Shasha Huang, Dongyang Kang, Mingyu Han, Guojian Wang, Yongyi Yuan, Yu Su, Huijun Yuan, Suoqiang Zhai and Pu Dai

    Citation: BMC Genetics 2014 15:26

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  41. Content type: Research article

    There was ancient human selection on the wild progenitor of modern maize, Balsas teosinte, for decreased shoot branching (tillering), in order to allow more nutrients to be diverted to grain. Mechanistically, ...

    Authors: Amelie CM Gaudin, Sarah A McClymont, Sameh SM Soliman and Manish N Raizada

    Citation: BMC Genetics 2014 15:23

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  42. Content type: Research article

    Monozygotic twins (MZT) are an important resource for genetical studies in the context of normal and diseased genomes. In the present study we used DYZ1, a satellite fraction present in the form of tandem arra...

    Authors: Sandeep Kumar Yadav, Anju Kumari, Saleem Javed and Sher Ali

    Citation: BMC Genetics 2014 15:19

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  43. Content type: Research article

    VKORC1 has been identified some years ago as the gene encoding vitamin K epoxide reductase (VKOR) – the target protein for coumarin derivates like warfarin or phenprocoumon. Resistance against warfarin and oth...

    Authors: Elisabeth Müller, Alexander Keller, Andreas Fregin, Clemens R Müller and Simone Rost

    Citation: BMC Genetics 2014 15:17

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  44. Content type: Research article

    The greater epithelial ridge (GER) is a developmental structure in the maturation of the organ of Corti. Situated near the inner hair cells of neonatal mice, the GER undergoes a wave of apoptosis after postnat...

    Authors: Ayako Inoshita, Keiko Karasawa, Megumi Funakubo, Asuka Miwa, Katsuhisa Ikeda and Kazusaku Kamiya

    Citation: BMC Genetics 2014 15:1

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  45. Content type: Methodology article

    Pathogenic mutations range from single nucleotide changes to deletions or duplications that encompass a single exon to several genes. The use of gene-centric high-density array comparative genomic hybridizatio...

    Authors: S Hussain Askree, Ephrem LH Chin, Lora H Bean, Bradford Coffee, Alice Tanner and Madhuri Hegde

    Citation: BMC Genetics 2013 14:116

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  46. Content type: Methodology article

    Genotyping requires biological sample collection that must be reliable, convenient and acceptable for patients and clinicians. Finding the most optimal procedure of sample collection for premature neonates who...

    Authors: Shavanthi Rajatileka, Karen Luyt, Manal El-Bokle, Maggie Williams, Helena Kemp, Elek Molnár and Anikó Váradi

    Citation: BMC Genetics 2013 14:105

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  47. Content type: Research article

    Klippel-Feil syndrome (KFS) is characterized by the developmental failure of the cervical spine and has two dominantly inherited subtypes. Affected individuals who are the children of a consanguineous marriage...

    Authors: Fatih Bayrakli, Bulent Guclu, Cengiz Yakicier, Hatice Balaban, Ugur Kartal, Bekir Erguner, Mahmut Samil Sagiroglu, Sirin Yuksel, Ahmet Rasit Ozturk, Burak Kazanci, Unal Ozum and Hamit Zafer Kars

    Citation: BMC Genetics 2013 14:95

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  48. Content type: Research article

    Eggshell quality is important for the poultry industry. During eggshell formation a mass of inorganic minerals is deposited. The Sodium Channel (SCNN1) gene family plays an essential role in cation transportat...

    Authors: Yan-Feng Fan, Zhuo-Cheng Hou, Guo-Qiang Yi, Gui-Yun Xu and Ning Yang

    Citation: BMC Genetics 2013 14:90

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  49. Content type: Research article

    Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most challenging areas of research in animal genetics, particularly in livestock where few annotated ge...

    Authors: Bianca Moioli, Maria Carmela Scatà, Roberto Steri, Francesco Napolitano and Gennaro Catillo

    Citation: BMC Genetics 2013 14:76

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