1,940 results match your criteria BMC Genetics [Journal]


No genetic erosion after five generations for Impatiens glandulifera populations across the invaded range in Europe.

BMC Genet 2019 Feb 19;20(1):20. Epub 2019 Feb 19.

Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, NO-7034, Trondheim, Norway.

Background: The observation that many alien species become invasive despite low genetic diversity has long been considered the 'genetic paradox' in invasion biology. This paradox is often resolved through the temporal buildup genetic diversity through multiple introduction events. These temporal dynamics in genetic diversity are especially important for annual invasive plants that lack a persistent seed bank, for which population persistence is strongly dependent on consecutive seed 're-establishment' in each growing season. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-019-0721-4DOI Listing
February 2019

Subcongenic analysis of a quantitative trait locus affecting body weight and glucose metabolism in zinc transporter 7 (znt7)-knockout mice.

BMC Genet 2019 Feb 18;20(1):19. Epub 2019 Feb 18.

Department of Nutrition, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.

Background: A genome-wide mapping study using male F zinc transporter 7-knockout mice (znt7-KO) and their wild type littermates in a mixed 129P1/ReJ (129P1) and C57BL/6J (B6) background identified a quantitative trait locus (QTL) on chromosome 7, which had a synergistic effect on body weight gain and fat deposit with the znt7-null mutation.

Results: The genetic segment for body weight on mouse chromosome 7 was investigated by newly created subcongenic znt7-KO mouse strains carrying different lengths of genomic segments of chromosome 7 from the 129P1 donor strain in the B6 background. We mapped the sub-QTL for body weight in the proximal region of the previously mapped QTL, ranging from 47. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-019-0715-2DOI Listing
February 2019
1 Read

Characterization of the extra copy of TPOX locus with tri-allelic pattern.

BMC Genet 2019 Feb 14;20(1):18. Epub 2019 Feb 14.

Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China.

Background: An STR locus with tri-allelic pattern is occasionally observed in routine forensic casework. The extra copy of TPOX locus with tri-allelic pattern in populations has been assumed to be inserted into an X chromosome, which took place forth before the Bantu expansion in Africa. Nonetheless, the exact location of the duplication and the form of rearrangement in the human genome has not been clarified yet. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-019-0723-2DOI Listing
February 2019

The epigenetic regulation of HsMar1, a human DNA transposon.

BMC Genet 2019 Feb 14;20(1):17. Epub 2019 Feb 14.

EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200, Tours, France.

Background: Both classes of transposable elements (DNA and RNA) are tightly regulated at the transcriptional level leading to the inactivation of transposition via epigenetic mechanisms. Due to the high copies number of these elements, the hypothesis has emerged that their regulation can coordinate a regulatory network of genes. Herein, we investigated whether transposition regulation of HsMar1, a human DNA transposon, differs in presence or absence of endogenous HsMar1 copies. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-019-0719-yDOI Listing
February 2019

Uncovering a multitude of human glucocorticoid receptor variants: an expansive survey of a single gene.

BMC Genet 2019 Feb 8;20(1):16. Epub 2019 Feb 8.

Shriners Hospitals for Children Northern California, Sacramento, California, USA.

Background: Glucocorticoids are commonly used in the clinical setting for their potent anti-inflammatory effects; however, significant variations in response to treatment have been demonstrated. Although the underlying mechanisms have yet to be fully understood, this variable response may be a result of alterations in human glucocorticoid receptor (hGR) expression and function. In addition to hGRα, the biologically active isoform, a screening of current databases and publications revealed five alternative splice isoforms and hundreds of variants that have been reported to date. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-019-0718-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368729PMC
February 2019

The main WAP isoform usually found in camel milk arises from the usage of an improbable intron cryptic splice site in the precursor to mRNA in which a GC-AG intron occurs.

BMC Genet 2019 Jan 29;20(1):14. Epub 2019 Jan 29.

INRA, UMR GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.

Background: Whey acidic protein (WAP) is a major protein identified in the milk of several mammalian species with cysteine-rich domains known as four-disulfide cores (4-DSC). The organization of the eutherian WAP genes is highly conserved through evolution. It has been proposed that WAP could play an important role in regulating the proliferation of mammary epithelial cells. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0704-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350295PMC
January 2019

Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle.

BMC Genet 2019 Jan 29;20(1):15. Epub 2019 Jan 29.

Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.

Background: Genome-wide association studies (GWAS) have been successfully implemented in cattle research and breeding. However, moving from the associations to identify the causal variants and reveal underlying mechanisms have proven complicated. In dairy cattle populations, we face a challenge due to long-range linkage disequilibrium (LD) arising from close familial relationships in the studied individuals. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-019-0717-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350337PMC
January 2019
2 Reads

Genetic diversity and structure in Arapaima gigas populations from Amazon and Araguaia-Tocantins river basins.

BMC Genet 2019 Jan 28;20(1):13. Epub 2019 Jan 28.

Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, Scotland, UK.

Background: Arapaima gigas (Schinz, 1822) is the largest freshwater scaled fish in the world, and an emerging species for tropical aquaculture development. Conservation of the species, and the expansion of aquaculture requires the development of genetic tools to study polymorphism, differentiation, and stock structure. This study aimed to investigate genomic polymorphism through ddRAD sequencing, in order to identify a panel of single nucleotide polymorphisms (SNPs) and to simultaneously assess genetic diversity and structure in wild (from rivers Amazon, Solimões, Tocantins and Araguaia) and captive populations. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0711-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6348655PMC
January 2019
6 Reads

Tissue expression profiles unveil the gene interaction of hepatopancreas, eyestalk, and ovary in the precocious female Chinese mitten crab, Eriocheir sinensis.

BMC Genet 2019 Jan 25;20(1):12. Epub 2019 Jan 25.

Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, 999, Hucheng huan Road, Lingang New City, Shanghai, 201306, China.

Background: Sexual precocity is a common biological phenomenon in animal species. A large number of precocity individuals were identified in Chinese mitten crab Eriocheir sinensis, which caused huge economic loss annually. However, the underlying genetic basis of precocity in E. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-019-0716-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347758PMC
January 2019
5 Reads

Dispersal route of the Asian house rat (Rattus tanezumi) on mainland China: insights from microsatellite and mitochondrial DNA.

BMC Genet 2019 Jan 22;20(1):11. Epub 2019 Jan 22.

State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.

Background: Rattus tanezumi is a common commensal rat and an important host animal of bubonic plague in South China and Southeast Asia. The northward dispersal of this species in mainland China has been reported in recent decades, along with more recent intercontinental expansion. Population genetics of R. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-019-0714-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341715PMC
January 2019
5 Reads
2.397 Impact Factor

p.E95K mutation in Indian hedgehog causing brachydactyly type A1 impairs IHH/Gli1 downstream transcriptional regulation.

BMC Genet 2019 Jan 16;20(1):10. Epub 2019 Jan 16.

Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, 209 Little White House, 1954 Hua Shan Road, Shanghai, 200030, People's Republic of China.

Background: Brachydactyly type A1 (BDA1, OMIM 112500) is a rare inherited malformation characterized primarily by shortness or absence of middle bones of fingers and toes. It is the first recorded disorder of the autosomal dominant Mendelian trait. Indian hedgehog (IHH) gene is closely associated with BDA1, which was firstly mapped and identified in Chinese families in 2000. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0697-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335781PMC
January 2019
2 Reads

Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle.

BMC Genet 2019 Jan 14;20(1). Epub 2019 Jan 14.

Animal Science Department, São Paulo State University (Unesp), Jaboticabal, SP, 144884-900, Brazil.

Background: Traditional single nucleotide polymorphism (SNP) genome-wide association analysis (GWAA) can be inefficient because single SNPs provide limited genetic information about genomic regions. On the other hand, using haplotypes in the statistical analysis may increase the extent of linkage disequilibrium (LD) between haplotypes and causal variants and may also potentially capture epistastic interactions between variants within a haplotyped locus, providing an increase in the power and robustness of the association studies. We performed GWAA (413,355 SNP markers) using haplotypes based on variable-sized sliding windows and compared the results to a single-SNP GWAA using Warner-Bratzler shear force measured in the longissimus thorasis muscle of 3161 Nelore bulls to ascertain the optimal window size for identifying the genomic regions that influence meat tenderness. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-019-0713-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6332854PMC
January 2019
2 Reads

Comparative transcriptome analysis of two selenium-accumulating genotypes of Aegilops tauschii Coss. in response to selenium.

BMC Genet 2019 Jan 14;20(1). Epub 2019 Jan 14.

Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 23# Xinning Lu, Xining, 810008, Qinghai, China.

Background: Selenium (Se), an essential micronutrient in both animals and humans, has various biological functions, and its deficiency can lead to various diseases. The most common method for increasing Se uptake is the consumption of Se-rich plants, which transform inorganic Se into organic forms. Wheat is eaten daily by many people. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0700-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6332533PMC
January 2019
1 Read
2.397 Impact Factor

Vps4b heterozygous mice do not develop tooth defects that replicate human dentin dysplasia I.

BMC Genet 2019 Jan 11;20(1). Epub 2019 Jan 11.

Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, No.1023, Shatai South Road, Guangzhou, 510515, People's Republic of China.

Background: Vacuolar protein sorting-associated protein 4B (VPS4B) is a member of the ATP enzyme AAA protein family, and is mainly involved in protein degradation and cell membrane fusion. Recently, a dominant mutation in this gene was identified in human dentin dysplasia type I (DD-I). Herein, we report the generation of Vps4b knockout (Vps4b KO) mice; however, the homozygous Vps4b KO mutation was embryonic lethal at the early stages of embryo development, and we therefore report the results of heterozygous mutant mice. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0699-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330468PMC
January 2019
4 Reads

A panel of 32 AIMs suitable for population stratification correction and global ancestry estimation in Mexican mestizos.

BMC Genet 2019 Jan 8;20(1). Epub 2019 Jan 8.

Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de Mexico, Mexico.

Background: Association studies are useful to unravel the genetic basis of common human diseases. However, the presence of undetected population structure can lead to both false positive results and failures to detect genuine associations. Even when most of the approaches to deal with population stratification require genome-wide data, the use of a well-selected panel of ancestry informative markers (AIMs) may appropriately correct for population stratification. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0707-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323778PMC
January 2019
5 Reads
2.397 Impact Factor

Genome-wide association study for response to vaccination in Angus calves.

BMC Genet 2019 Jan 8;20(1). Epub 2019 Jan 8.

Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.

Background: Bovine respiratory disease complex (BRDC) is one of the most important sources of loss within the beef cattle industry in the USA. Steps have been taken to reduce the incidence of BRDC through vaccination. Despite the effectiveness of vaccines, large proportions of cattle still experience morbidity and mortality. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0709-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325805PMC
January 2019
6 Reads

funbarRF: DNA barcode-based fungal species prediction using multiclass Random Forest supervised learning model.

BMC Genet 2019 Jan 7;20(1). Epub 2019 Jan 7.

Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.

Background: Identification of unknown fungal species aids to the conservation of fungal diversity. As many fungal species cannot be cultured, morphological identification of those species is almost impossible. But, DNA barcoding technique can be employed for identification of such species. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0710-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323839PMC
January 2019
2 Reads

Evidence for paternal DNA transmission to gynogenetic grass carp.

BMC Genet 2019 Jan 7;20(1). Epub 2019 Jan 7.

State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.

Background: Grass carp (Ctenopharyngodon idellus, GC), as the highest-output fish in China, is economically important. The production of gynogenetic grass carp (GGC) will provide important germplasm resource for producing improved GC. At present, knowledge regarding the heterologous sperm DNA in gynogenetic offspring is little. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0712-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323743PMC
January 2019
6 Reads

A genome wide association study for the number of animals born dead in domestic pigs.

BMC Genet 2019 Jan 7;20(1). Epub 2019 Jan 7.

College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.

Background: The number of animals born dead, which includes the number of mummified (NM) and stillborn (NS) animals, is the most important trait to directly quantify the reproductive loss in domestic pigs. In this study, 282 Landrace sows and 250 Large White sows were genotyped by sequencing (GBS). A total of 816 and 1068 litter records for NM and NS were collected from them. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0692-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324166PMC
January 2019
1 Read

Methylation of the first exon in the erythropoietin receptor gene does not correlate with its mRNA and protein level in cancer cells.

BMC Genet 2019 Jan 3;20(1). Epub 2019 Jan 3.

Department of Cell Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, SK-04154, Košice, Slovak Republic.

Background: Erythropoietin receptor (EPOR) is a functional membrane-bound cytokine receptor. Erythropoietin (EPO) represents an important hematopoietic factor for production, maturation and differentiation of erythroid progenitors. In non-hematopoietic tissue, EPO/EPOR signalization could also play cytoprotective and anti-apoptotic role. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0706-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318971PMC
January 2019
3 Reads

Characterization and functional analyses of the human HTR1A gene: 5' regulatory region modulates gene expression in vitro.

BMC Genet 2018 Dec 29;19(1):115. Epub 2018 Dec 29.

School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, China.

Background: The serotonin neurotransmitter (5-HT) and its receptors have important roles in neuropsychiatric disorders such as schizophrenia. The aim of this study was to investigate the functional sequences of the 5' regulation region of the human HTR1A gene to explore the effects on the expression of the 5-HT1A receptor.

Methods: Fourteen recombinant pGL3-basic vectors containing deletion fragments of the HTR1A gene regulatory region were transfected with HEK-293 and SK-N-SH cells. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0708-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311061PMC
December 2018
4 Reads

Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle.

BMC Genet 2018 Dec 20;19(1):114. Epub 2018 Dec 20.

Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.

Background: China exhibits a great diversity of ecosystems and abundant cattle resources, with nearly 30 million cattle from 53 indigenous breeds reared in specific geographic regions. To explore the genetic diversity and population structure of Chinese indigenous cattle, a population genetic analysis at both the individual and population levels was conducted and the admixture analysis was performed. We genotyped 572 samples from 20 Chinese indigenous cattle breeds using GeneSeek Genomic Profiler Bovine LD (GGP-LD, 30 K) and downloaded the published data of 77 samples from 4 worldwide commercial breeds genotyped with Illumina BovineSNP50 Beadchip (SNP50, 50 K). Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0705-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302425PMC
December 2018
7 Reads

Associations of sex hormone-binding globulin and testosterone with genome-wide DNA methylation.

BMC Genet 2018 Dec 14;19(1):113. Epub 2018 Dec 14.

Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.

Background: Levels of sex hormone-binding globulin (SHBG) and the androgen testosterone have been associated with risk of diseases throughout the lifecourse. Although both SHBG and testosterone have been shown to be highly heritable, only a fraction of that heritability has been explained by genetic studies. Epigenetic modifications such as DNA methylation may explain some of the missing heritability and could potentially inform biological knowledge of endocrine disease mechanisms involved in development of later life disease. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0703-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6295101PMC
December 2018
7 Reads

The transcription factor PRO44 and the histone chaperone ASF1 regulate distinct aspects of multicellular development in the filamentous fungus Sordaria macrospora.

BMC Genet 2018 Dec 13;19(1):112. Epub 2018 Dec 13.

Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780, Bochum, Germany.

Background: Fungal fruiting bodies are complex three-dimensional structures that are formed to protect and disperse the sexual spores. Their morphogenesis requires the concerted action of numerous genes; however, at the molecular level, the spatio-temporal sequence of events leading to the mature fruiting body is largely unknown. In previous studies, the transcription factor gene pro44 and the histone chaperone gene asf1 were shown to be essential for fruiting body formation in the ascomycete Sordaria macrospora. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0702-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6293562PMC
December 2018
1 Read

Retraction Note: Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle.

BMC Genet 2018 12 11;19(1):111. Epub 2018 Dec 11.

Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.

ᅟ. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0698-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288910PMC
December 2018
1 Read

Polymorphisms of HOMER1 gene are associated with piglet splay leg syndrome and one significant SNP can affect its intronic promoter activity in vitro.

BMC Genet 2018 Dec 7;19(1):110. Epub 2018 Dec 7.

Key Lab of Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.

Background: In our previous genome-wide association study (GWAS) on the piglet splay leg (PSL) syndrome, the homer scaffolding protein 1 (HOMER1) was detected as a candidate gene. The aim of this work was to further verify the candidate gene by sequencing the gene and find the significantly associated mutation. Then we preliminarily analyzed the effect of the significant SNP on intronic promoter activity. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0701-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6286600PMC
December 2018
2 Reads

A statistical measure for the skewness of X chromosome inactivation based on family trios.

BMC Genet 2018 Dec 5;19(1):109. Epub 2018 Dec 5.

State Key Laboratory of Organ Failure Research, Ministry of Education and Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China.

Background: X chromosome inactivation (XCI) is an important gene regulation mechanism in females to equalize the expression levels of X chromosome between two sexes. Generally, one of two X chromosomes in females is randomly chosen to be inactivated. Nonrandom XCI (XCI skewing) is also observed in females, which has been reported to play an important role in many X-linked diseases. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0694-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282303PMC
December 2018
11 Reads

Design of low density SNP chips for genotype imputation in layer chicken.

BMC Genet 2018 Dec 4;19(1):108. Epub 2018 Dec 4.

PEGASE, INRA, Agrocampus Ouest, 16 Le Clos, 35590, Saint-Gilles, France.

Background: The main goal of selection is to achieve genetic gain for a population by choosing the best breeders among a set of selection candidates. Since 2013, the use of a high density genotyping chip (600K Affymetrix® Axiom® HD genotyping array) for chicken has enabled the implementation of genomic selection in layer and broiler breeding, but the genotyping costs remain high for a routine use on a large number of selection candidates. It has thus been deemed interesting to develop a low density genotyping chip that would induce lower costs. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0695-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6278067PMC
December 2018
1 Read

Investigation of allele-specific expression of genes involved in adipogenesis and lipid metabolism suggests complex regulatory mechanisms of PPARGC1A expression in porcine fat tissues.

BMC Genet 2018 Nov 29;19(1):107. Epub 2018 Nov 29.

Chair of Livestock Biotechnology, Technical University of Munich, Liesel-Beckmannstr. 1, 85354, Freising, Germany.

Background: The expression of genes involved in regulating adipogenesis and lipid metabolism may affect economically important fatness traits in pigs. Allele-specific expression (ASE) reflects imbalance between allelic transcript levels and can be used to identify underlying cis-regulatory elements. ASE has not yet been intensively studied in pigs. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0696-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6267897PMC
November 2018
1 Read

Seedless mutant 'Wuzi Ougan' (Citrus suavissima Hort. ex Tanaka 'seedless') and the wild type were compared by iTRAQ-based quantitative proteomics and integratedly analyzed with transcriptome to improve understanding of male sterility.

BMC Genet 2018 Nov 20;19(1):106. Epub 2018 Nov 20.

State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, No.666, WuSu Street, Hangzhou, Zhejiang province, People's Republic of China, 311300.

Background: Bud mutation is a vital method of citrus. 'Wuzi Ougan' (mutant type, MT) as a bud variant of 'Ougan' (wild type, WT) was first found in 1996 and has become popular because of its male sterility and seedless character. Previous analysis of its cytological sections and transcriptome revealed that the abnormal microsporogenesis that occurs before the tetrad stage of anther development might be the result of down-regulated oxidation-reduction biological processes in MT. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0693-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6245639PMC
November 2018
16 Reads

Quantifying the genetic parameters of feed efficiency in juvenile Nile tilapia Oreochromis niloticus.

BMC Genet 2018 Nov 16;19(1):105. Epub 2018 Nov 16.

Worldfish, Jalan Batu Maung, 11960, Bayan Lepas, Penang, Malaysia.

Background: Improving feed efficiency in fish is crucial at the economic, social and environmental levels with respect to developing a more sustainable aquaculture. The important contribution of genetic improvement to achieve this goal has been hampered by the lack of accurate basic information on the genetic parameters of feed efficiency in fish. We used video assessment of feed intake on individual fish reared in groups to estimate the genetic parameters of six growth traits, feed intake, feed conversion ratio (FCR) and residual feed intake in 40 pedigreed families of the GIFT strain of Nile tilapia, Oreochromis niloticus. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0691-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240178PMC
November 2018
12 Reads

A preliminary integrated genetic map distinguishes every chromosome pair and locates essential genes related to abiotic adaptation of Crassostrea angulata/gigas.

BMC Genet 2018 Nov 15;19(1):104. Epub 2018 Nov 15.

Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain.

Background: The re-sequencing of C. angulata has revealed many polymorphisms in candidate genes related to adaptation to abiotic stress that are not present in C. gigas; these genes, therefore, are probably related to the ability of this oyster to retain high concentrations of toxic heavy metals. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0689-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6238303PMC
November 2018
3 Reads

Identification and validation of QTL and their associated genes for pre-emergent metribuzin tolerance in hexaploid wheat (Triticum aestivum L.).

BMC Genet 2018 Nov 12;19(1):102. Epub 2018 Nov 12.

UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6001, Australia.

Background: Herbicide tolerance is an important trait that allows effective weed management in wheat crops. Genetic knowledge of metribuzin tolerance in wheat is needed to develop new cultivars for the industry. Here, we evaluated metribuzin tolerance in a recombinant inbred line (RIL) mapping population derived from Synthetic W7984 and Opata 85 over two consecutive years to identify quantitative trait loci (QTL) contributing to the trait. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0690-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6233490PMC
November 2018
1 Read

SNP markers associated with body size and pelt length in American mink (Neovison vison).

BMC Genet 2018 Nov 12;19(1):103. Epub 2018 Nov 12.

Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.

Background: Identification of genes underlying production traits is a key aim of the mink research community. Recent availability of genomic tools have opened the possibility for faster genetic progress in mink breeding. Availability of mink genome assembly allows genome-wide association studies in mink. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0688-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6233529PMC
November 2018
11 Reads

Unexpected patterns of segregation distortion at a selfish supergene in the fire ant Solenopsis invicta.

BMC Genet 2018 Nov 7;19(1):101. Epub 2018 Nov 7.

Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA.

Background: The Sb supergene in the fire ant Solenopsis invicta determines the form of colony social organization, with colonies whose inhabitants bear the element containing multiple reproductive queens and colonies lacking it containing only a single queen. Several features of this supergene - including suppressed recombination, presence of deleterious mutations, association with a large centromere, and "green-beard" behavior - suggest that it may be a selfish genetic element that engages in transmission ratio distortion (TRD), defined as significant departures in progeny allele frequencies from Mendelian inheritance ratios. We tested this possibility by surveying segregation ratios in embryo progenies of 101 queens of the "polygyne" social form (3512 embryos) using three supergene-linked markers and twelve markers outside the supergene. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0685-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6223060PMC
November 2018
3 Reads

Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network construction.

BMC Genet 2018 Nov 6;19(1):100. Epub 2018 Nov 6.

Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.

Background: Identifying genetic variations that shape important complex traits is fundamental to the genetic improvement of important forest tree species, such as loblolly pine (Pinus taeda L.), which is one of the most commonly planted forest tree species in the southern U.S. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0687-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219081PMC
November 2018
9 Reads

Single-nucleotide polymorphisms(SNPs) in a sucrose synthase gene are associated with wood properties in Catalpa fargesii bur.

BMC Genet 2018 Nov 1;19(1):99. Epub 2018 Nov 1.

State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.

Background: Association study is a powerful means for identifying molecular markers, such as single-nucleotide polymorphisms (SNPs) associated with important traits in forest trees. Catalpa fargesii Bur is a valuable commercial tree in China and identifying SNPs that associate with wood property would make a foundation of the marker-assisted breeding in the future. However, related work has not been reported yet. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0686-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211571PMC
November 2018
7 Reads

An improved statistical model for taxonomic assignment of metagenomics.

BMC Genet 2018 Oct 29;19(1):98. Epub 2018 Oct 29.

Sergievsky Center, Taub Institute, and Departments of Epidemiology and Neurology, Columbia University, New York, NY, USA.

Background: With the advances in the next-generation sequencing technologies, researchers can now rapidly examine the composition of samples from humans and their surroundings. To enhance the accuracy of taxonomy assignments in metagenomic samples, we developed a method that allows multiple mismatch probabilities from different genomes.

Results: We extended the algorithm of taxonomic assignment of metagenomic sequence reads (TAMER) by developing an improved method that can set a different mismatch probability for each genome rather than imposing a single parameter for all genomes, thereby obtaining a greater degree of accuracy. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0680-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6206629PMC
October 2018
1 Read

Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae).

BMC Genet 2018 Oct 26;19(1):97. Epub 2018 Oct 26.

Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain.

Background: The whole repeat unit of 5S rDNA and the internal transcribed spacer (ITS) of four European Donax species were analysed. After amplifying, cloning and sequencing several 5S and ITS units, their basic features and their variation were described. The phylogenetic usefulness of 5S and ITS sequences in the inference of evolutionary relationships among these wedge clams was also investigated. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0684-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6204057PMC
October 2018
7 Reads

Correction to: Application of geographic population structure (GPS) algorithm for biogeographical analyses of populations with complex ancestries: a case study of South Asians from 1000 genomes project.

BMC Genet 2018 Oct 25;19(1):96. Epub 2018 Oct 25.

Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India.

Following publication of the original article [1], the authors flagged that acknowledgment of their equal contribution is omitted in the article [1]. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0683-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6201577PMC
October 2018
1 Read

A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland.

BMC Genet 2018 Oct 22;19(1):95. Epub 2018 Oct 22.

National Research Institute of Animal Production, Department of Horse Breeding, Krakowska 1, 32-083, Balice, Poland.

Background: Identification of selection signatures can provide a direct insight into the mechanism of artificial selection and allow further disclosure of the candidate genes related to the animals' phenotypic variation. Domestication and subsequent long-time selection have resulted in extensive phenotypic changes in domestic pigs, involving a number of traits, like behavior, body composition, disease resistance, reproduction and coat color. In this study, based on genotypes obtained from PorcineSNP60 Illumina assay we attempt to detect both diversifying and within-breed selection signatures in 530 pigs belonging to four breeds: Polish Landrace, Puławska, Złotnicka White and Złotnicka Spotted, of which the last three are a subject of conservative breeding and substantially represent the native populations. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0681-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198424PMC
October 2018
1 Read

Exome sequencing identifies gene variants and networks associated with extreme respiratory outcomes following preterm birth.

BMC Genet 2018 Oct 20;19(1):94. Epub 2018 Oct 20.

Department of Pediatrics, University of Rochester, Rochester, NY, USA.

Background: Previous studies have identified genetic variants associated with bronchopulmonary dysplasia (BPD) in extremely preterm infants. However, findings with genome-wide significance have been rare, and not replicated. We hypothesized that whole exome sequencing (WES) of premature subjects with extremely divergent phenotypic outcomes could facilitate the identification of genetic variants or gene networks contributing disease risk. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0679-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6195962PMC
October 2018
2 Reads

Genetic insight and mapping of the pod constriction trait in Virginia-type peanut.

BMC Genet 2018 Oct 19;19(1):93. Epub 2018 Oct 19.

Department of Field Crops, Institute of Plant Sciences, Agriculture research organization -the Volcani Center, HaMakkabbim Road, P. O. Box 15159, 7505101, Rishon LeZiyyon, Israel.

Background: Pod constriction is an important descriptive and agronomic trait of peanut. For the in-shell Virginia marketing-type, this trait has commercial importance as well, since deeply constricted pods have a tendency to break, which makes them unmarketable. Classical genetic studies have indicated that pod constriction in peanut is controlled by one to four genes, depending on the genetic background. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0674-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6195699PMC
October 2018
11 Reads

Genetic diversity and population structure analyses of Plectranthus edulis (Vatke) Agnew collections from diverse agro-ecologies in Ethiopia using newly developed EST-SSRs marker system.

BMC Genet 2018 Oct 11;19(1):92. Epub 2018 Oct 11.

Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden.

Background: Plectranthus edulis (Vatke) Agnew (locally known as Ethiopian dinich or Ethiopian potato) is one of the most economically important edible tuber crops indigenous to Ethiopia. Evaluating the extent of genetic diversity within and among populations is one of the first and most important steps in breeding and conservation measures. Hence, this study was aimed at evaluating the genetic diversity and population structure of this crop using collections from diverse agro-ecologies in Ethiopia. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0682-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182789PMC
October 2018
11 Reads

A recessive lethal chondrodysplasia in a miniature zebu family results from an insertion affecting the chondroitin sulfat domain of aggrecan.

BMC Genet 2018 Oct 11;19(1):91. Epub 2018 Oct 11.

Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559, Hannover, Germany.

Background: Congenital skeletal malformations represent a heterogeneous group of disorders affecting bone and cartilage development. In cattle, particular chondrodysplastic forms have been identified in several miniature breeds. In this study, a phenotypic characterization was performed of an affected Miniature Zebu calf using computed tomography, necropsy and histopathological examinations, whole genome sequencing of the case and its parents on an Illumina NextSeq 500 in 2 × 150 bp paired-end mode and validation using Sanger sequencing and a Kompetitive Allele Specific PCR assay. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0678-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180608PMC
October 2018
3 Reads

Assessment of shared alleles in drought-associated candidate genes among southern California white oak species (Quercus sect. Quercus).

BMC Genet 2018 Oct 1;19(1):88. Epub 2018 Oct 1.

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-7239, USA.

Background: Hybridization and introgression are common phenomena among oak species. These processes can be beneficial by introducing favorable genetic variants across species (adaptive introgression). Given that drought is an important stress, impacting physiological and morphological variation and limiting distributions, our goal was to identify drought-related genes that might exhibit patterns of introgression influenced by natural selection. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0677-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6167808PMC
October 2018
3 Reads

Combining controls can improve power in two-stage association studies.

Authors:
James Liley

BMC Genet 2018 Oct 3;19(1):89. Epub 2018 Oct 3.

Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.

Background: High dimensional case control studies are ubiquitous in the biological sciences, particularly genomics. To maximise power while constraining cost and to minimise type-1 error rates, researchers typically seek to replicate findings in a second experiment on independent cohorts before proceeding with further analyses. This can be an expensive procedure, particularly when control samples are difficult to recruit or ascertain; for example in inter-disease comparisons, or studies on degenerative diseases. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0675-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6171163PMC
October 2018
3 Reads

Investigating the frequency of triploid Atlantic salmon in wild Norwegian and Russian populations.

BMC Genet 2018 Oct 3;19(1):90. Epub 2018 Oct 3.

Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway.

Background: Fish may display variations in ploidy, including three sets of chromosomes, known as triploidy. A recent study revealed a frequency of ~ 2% spontaneous (i.e. Read More

View Article

Download full-text PDF

Source
https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
Publisher Site
http://dx.doi.org/10.1186/s12863-018-0676-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6171226PMC
October 2018
5 Reads

Detecting responses to treatment with fenofibrate in pedigrees.

BMC Genet 2018 Sep 17;19(Suppl 1):64. Epub 2018 Sep 17.

Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Dr. South, Los Angeles, CA, 90095, USA.

Background: Fenofibrate (Fb) is a known treatment for elevated triglyceride (TG) levels. The Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study was designed to investigate potential contributors to the effects of Fb on TG levels. Here, we summarize the analyses of 8 papers whose authors had access to the GOLDN data and were grouped together because they pursued investigations into Fb treatment responses as part of GAW20. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0652-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156837PMC
September 2018
2 Reads

The challenge of detecting genotype-by-methylation interaction: GAW20.

BMC Genet 2018 Sep 17;19(Suppl 1):81. Epub 2018 Sep 17.

Department of Statistics, Columbia University, 1255 Amsterdam Avenue, New York, NY, 10027, USA.

Background: GAW20 working group 5 brought together researchers who contributed 7 papers with the aim of evaluating methods to detect genetic by epigenetic interactions. GAW20 distributed real data from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study, including single-nucleotide polymorphism (SNP) markers, methylation (cytosine-phosphate-guanine [CpG]) markers, and phenotype information on up to 995 individuals. In addition, a simulated data set based on the real data was provided. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-018-0650-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157121PMC
September 2018
9 Reads