1,960 results match your criteria BMC genetics[Journal]


An integrative U method for joint analysis of multi-level omic data.

BMC Genet 2019 Apr 10;20(1):40. Epub 2019 Apr 10.

Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, 48824, USA.

Background: The advance of high-throughput technologies has made it cost-effective to collect diverse types of omic data in large-scale clinical and biological studies. While the collection of the vast amounts of multi-level omic data from these studies provides a great opportunity for genetic research, the high dimensionality of omic data and complex relationships among multi-level omic data bring tremendous analytic challenges.

Results: To address these challenges, we develop an integrative U (IU) method for the design and analysis of multi-level omic data. Read More

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https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
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http://dx.doi.org/10.1186/s12863-019-0742-zDOI Listing
April 2019
2 Reads

Genome-wide association study of four yield-related traits at the R6 stage in soybean.

BMC Genet 2019 Mar 29;20(1):39. Epub 2019 Mar 29.

National Center for Soybean Improvement/National Key laboratory of Crop Genetics and Germplasm enhancement, Key laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.

Background: The 100-pod fresh weight (PFW), 100-seed fresh weight (SFW), 100-seed dry weight (SDW) and moisture content of fresh seeds (MCFS) at the R6 stage are crucial factors for vegetable soybean yield. However, the genetic basis of yield at the R6 stage remains largely ambiguous in soybean.

Results: To better understand the molecular mechanism underlying yield, we investigated four yield-related traits of 133 soybean landraces in two consecutive years and conducted a genome-wide association study (GWAS) using 82,187 single nucleotide polymorphisms (SNPs). Read More

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http://dx.doi.org/10.1186/s12863-019-0737-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6440021PMC

Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces.

BMC Genet 2019 Mar 26;20(1):38. Epub 2019 Mar 26.

Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China.

Background: Stripe rust is a serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. Read More

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https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
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http://dx.doi.org/10.1186/s12863-019-0736-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434810PMC
March 2019
3 Reads
2.397 Impact Factor

Karyotypic and mtDNA based characterization of Malaysian water buffalo.

BMC Genet 2019 Mar 25;20(1):37. Epub 2019 Mar 25.

Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Malaysia.

Background: In Malaysia, the domestic water buffaloes (Bubalus bubalis) are classified into the swamp and the murrah buffaloes. Identification of these buffaloes is usually made via their phenotypic appearances. This study characterizes the subspecies of water buffaloes using karyotype, molecular and phylogenetic analyses. Read More

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http://dx.doi.org/10.1186/s12863-019-0741-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434848PMC

Genome-wide identification and expression analysis of HSP90 gene family in Nicotiana tabacum.

BMC Genet 2019 Mar 19;20(1):35. Epub 2019 Mar 19.

Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.

Background: Heat shock proteins 90 (HSP90s) are a highly conserved protein family of cellular chaperones widely found in plants; they play a fundamental role in response to biotic and abiotic stresses. The genome-wide analysis of HSP90 gene family has been completed for some species; however, it has been rarely reported for the tobacco HSP90 genes.

Results: In this study, we systematically conducted genome-wide identification and expression analysis of the tobacco HSP90 gene family, including gene structures, evolutionary relationships, chromosomal locations, conserved domains, and expression patterns. Read More

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http://dx.doi.org/10.1186/s12863-019-0738-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423791PMC
March 2019
1 Read

Identifying and exploiting gene-pathway interactions from RNA-seq data for binary phenotype.

BMC Genet 2019 Mar 19;20(1):36. Epub 2019 Mar 19.

Department of Biostatistics, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, Jiangsu, People's Republic of China.

Background: RNA sequencing (RNA-seq) technology has identified multiple differentially expressed (DE) genes associated to complex disease, however, these genes only explain a modest part of variance. Omnigenic model assumes that disease may be driven by genes with indirect relevance to disease and be propagated by functional pathways. Here, we focus on identifying the interactions between the external genes and functional pathways, referring to gene-pathway interactions (GPIs). Read More

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http://dx.doi.org/10.1186/s12863-019-0739-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423879PMC
March 2019
2.397 Impact Factor

Favorable alleles mining for gelatinization temperature, gel consistency and amylose content in Oryza sativa by association mapping.

BMC Genet 2019 Mar 19;20(1):34. Epub 2019 Mar 19.

Nanjing Agricultural University, Nanjing, 210095, China.

Background: Improving the gelatinization temperature (GT), gel consistency (GC) and amylose content (AC) for parental grain eating and cooking qualities (ECQs) are key factors for enhancing average grain ECQs for hybrid japonica rice.

Results: In this study, a genome-wide association mapping (GWAS) for ECQs was performed on a selected sample of 462 rice accessions in 5 environments using 262 simple sequence repeat markers. We identified 10 loci and 27 favorable alleles for GT, GC and AC, and some of these loci were overlapped with starch synthesis-related genes. Read More

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http://dx.doi.org/10.1186/s12863-019-0735-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423859PMC

Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations.

BMC Genet 2019 Mar 18;20(Suppl 1):26. Epub 2019 Mar 18.

The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia.

Background: Design of new highly productive livestock breeds, well-adapted to local climatic conditions is one of the aims of modern agriculture and breeding. The genetics underlying economically important traits in cattle are widely studied, whereas our knowledge of the genetic mechanisms of adaptation to local environments is still scarce. To address this issue for cold climates we used an integrated approach for detecting genomic intervals related to body temperature maintenance under acute cold stress. Read More

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http://dx.doi.org/10.1186/s12863-019-0725-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421640PMC
March 2019
1 Read

A toolset to study functions of Cytosolic non-specific dipeptidase 2 (CNDP2) using Drosophila as a model organism.

BMC Genet 2019 Mar 18;20(Suppl 1):31. Epub 2019 Mar 18.

Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.

Background: Expression of the CNDP2 gene is frequently up- or down-regulated in different types of human cancers. However, how the product of this gene is involved in cell growth and proliferation is poorly understood. Moreover, our knowledge of the functions of the CNDP2 orthologs in well-established model organisms is scarce. Read More

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http://dx.doi.org/10.1186/s12863-019-0726-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421639PMC

Computational models in genetics at BGRS-2018.

BMC Genet 2019 Mar 18;20(Suppl 1):28. Epub 2019 Mar 18.

Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia.

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http://dx.doi.org/10.1186/s12863-019-0724-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421937PMC

Organization and evolution of the chalcone synthase gene family in bread wheat and relative species.

BMC Genet 2019 Mar 18;20(Suppl 1):30. Epub 2019 Mar 18.

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.

Background: Flavonoid compounds are secondary plant metabolites, having a functional importance in plant development, protection from pathogens and unfavorable environmental factors. Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoids; it is involved in biosynthesis of all classes of flavonoid compounds. Nevertheless, the Chs gene family in bread wheat (Triticum aestivum L. Read More

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http://dx.doi.org/10.1186/s12863-019-0727-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421938PMC
March 2019
2 Reads

Genetic control of anthocyanin pigmentation of potato tissues.

BMC Genet 2019 Mar 18;20(Suppl 1):27. Epub 2019 Mar 18.

Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, Novosibirsk, 630090, Russia.

Background: The cultivated potato Solanum tuberosum L. is the fourth most important crop worldwide. Anthocyanins synthesis and accumulation in potato tissues are considered as one of important traits related to stress resistance and nutritional value. Read More

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http://dx.doi.org/10.1186/s12863-019-0728-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421638PMC

Starch phosphorylation associated SNPs found by genome-wide association studies in the potato (Solanum tuberosum L.).

BMC Genet 2019 Mar 18;20(Suppl 1):29. Epub 2019 Mar 18.

Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, Novosibirsk, 630090, Russia.

Background: The natural variation of starch phosphate content in potatoes has been previously reported. It is known that, in contrast to raw starch, commercially phosphorylated starch is more stable at high temperatures and shear rates and has higher water capacity. The genetic improvement of phosphate content in potato starch by selection or engineering would allow the production of phosphorylated starch in a natural, environmentally friendly way without chemicals. Read More

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http://dx.doi.org/10.1186/s12863-019-0729-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421637PMC

Identification of genomic regions and diagnostic markers for resistance to aflatoxin contamination in peanut (Arachis hypogaea L.).

BMC Genet 2019 Mar 12;20(1):32. Epub 2019 Mar 12.

Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China.

Background: Aflatoxin contamination caused by Aspergillus flavus is a major constraint to peanut industry worldwide due to its toxicological effects to human and animals. Developing peanut varieties with resistance to seed infection and/or aflatoxin accumulation is the most effective and economic strategy for reducing aflatoxin risk in food chain. Breeding for resistance to aflatoxin in peanut is a challenging task for breeders because the genetic basis is still poorly understood. Read More

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http://dx.doi.org/10.1186/s12863-019-0734-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417274PMC
March 2019
2.397 Impact Factor

Interspecific delimitation and relationships among four Ostrya species based on plastomes.

BMC Genet 2019 Mar 12;20(1):33. Epub 2019 Mar 12.

State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China.

Background: The genus Ostrya (Betulaceae) contains eight species and four of them are distributed in China. However, studies based on limited informative sites of several chloroplast markers failed to resolve interspecific delimitation and relationships among the four Chinese species. In this study, we aimed to use the whole chloroplast genomes to address these two issues. Read More

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http://dx.doi.org/10.1186/s12863-019-0733-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417023PMC
March 2019
7 Reads

Structural organization and functional divergence of high isoelectric point α-amylase genes in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.).

BMC Genet 2019 Mar 7;20(1):25. Epub 2019 Mar 7.

Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.

Background: High isoelectric point α-amylase genes (Amy1) play major roles during cereal seed germination, and are associated with unacceptable high residual α-amylase activities in ripe wheat grains. However, in wheat and barley, due to extremely high homology of duplicated copies, and large and complex genome background, the knowledge on this multigene family is limited.

Results: In the present work, we identified a total of 41 Amy1 genes among 13 investigated grasses. Read More

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http://dx.doi.org/10.1186/s12863-019-0732-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404323PMC

Inheritance of coat colour in the cane Corso Italiano dog.

BMC Genet 2019 Mar 4;20(1):24. Epub 2019 Mar 4.

Department of Genetics, ZOO Tábor, Dukelských hrdinů 19, 17000, Prague 7, Czech Republic.

Background: The inheritance of different coat colours in the Cane Corso Italiano dog has not been described thus far. We analysed data from 23,271 dogs and bitches using the Cane Corso Italiano Pedigree Database. We are describing for the first time the coat colour segregation ratios in Cane Corso Italiano offspring arising from crosses between parents of all possible coat colour combinations. Read More

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http://dx.doi.org/10.1186/s12863-019-0731-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6398231PMC

QTL for spike-layer uniformity and their influence on yield-related traits in wheat.

BMC Genet 2019 Feb 28;20(1):23. Epub 2019 Feb 28.

College of Agriculture, Ludong University, Yantai, 264025, Shandong, China.

Background: Common wheat (Triticum aestivum L.) is one of the most important food crops worldwide. Wheat spike-layer uniformity related traits (SLURTs) were complex traits that directly affect yield potential and appearance. Read More

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http://dx.doi.org/10.1186/s12863-019-0730-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396499PMC
February 2019
1 Read

Evaluation of fecal samples as a valid source of DNA by comparing paired blood and fecal samples from American bison (Bison bison).

BMC Genet 2019 Feb 26;20(1):22. Epub 2019 Feb 26.

Interdisciplinary Graduate Program of Genetics, Texas A&M University, College Station, TX, 77843, USA.

Background: The collection and analysis of fecal DNA is a common practice, especially when dealing with wildlife species that are difficult to track or capture. While fecal DNA is known to be lower quality than traditional sources of DNA, such as blood or other tissues, few investigations have verified fecal samples as a valid source of DNA by directly comparing the results to high quality DNA samples from the same individuals. Our goal was to compare DNA from fecal and blood samples from the same 50 American plains bison (Bison bison) from Yellowstone National Park, analyze 35 short tandem repeat (STR) loci for genotyping efficiency, and compare heterozygosity estimates. Read More

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http://dx.doi.org/10.1186/s12863-019-0722-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390568PMC
February 2019

Increasing accuracy of genomic selection in presence of high density marker panels through the prioritization of relevant polymorphisms.

BMC Genet 2019 Feb 22;20(1):21. Epub 2019 Feb 22.

Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA.

Background: It becomes clear that the increase in the density of marker panels and even the use of sequence data didn't result in any meaningful increase in the accuracy of genomic selection (GS) using either regression (RM) or variance component (VC) approaches. This is in part due to the limitations of current methods. Association model are well over-parameterized and suffer from severe co-linearity and lack of statistical power. Read More

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http://dx.doi.org/10.1186/s12863-019-0720-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6387489PMC
February 2019
2.397 Impact Factor

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

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http://dx.doi.org/10.1186/s12863-019-0721-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379953PMC
February 2019
5 Reads

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

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https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
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http://dx.doi.org/10.1186/s12863-019-0715-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6378724PMC
February 2019
4 Reads

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

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http://dx.doi.org/10.1186/s12863-019-0723-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376737PMC
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

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https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
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http://dx.doi.org/10.1186/s12863-019-0719-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375154PMC
February 2019
5 Reads

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

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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

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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

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https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
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http://dx.doi.org/10.1186/s12863-019-0717-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350337PMC
January 2019
4 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

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https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
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http://dx.doi.org/10.1186/s12863-018-0711-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6348655PMC
January 2019
13 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

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https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
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http://dx.doi.org/10.1186/s12863-019-0716-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347758PMC
January 2019
12 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

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https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-0
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http://dx.doi.org/10.1186/s12863-019-0714-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341715PMC
January 2019
10 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

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http://dx.doi.org/10.1186/s12863-018-0697-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335781PMC
January 2019
4 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

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http://dx.doi.org/10.1186/s12863-019-0713-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6332854PMC
January 2019
3 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

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http://dx.doi.org/10.1186/s12863-018-0700-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6332533PMC
January 2019
2 Reads
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

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http://dx.doi.org/10.1186/s12863-018-0699-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330468PMC
January 2019
8 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

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http://dx.doi.org/10.1186/s12863-018-0707-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323778PMC
January 2019
13 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

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http://dx.doi.org/10.1186/s12863-018-0709-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325805PMC
January 2019
10 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

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http://dx.doi.org/10.1186/s12863-018-0710-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323839PMC
January 2019
3 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

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http://dx.doi.org/10.1186/s12863-018-0712-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323743PMC
January 2019
17 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

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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

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http://dx.doi.org/10.1186/s12863-018-0706-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318971PMC
January 2019
4 Reads

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

BMC Genet 2018 12 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

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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 12 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

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http://dx.doi.org/10.1186/s12863-018-0705-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302425PMC
December 2018
17 Reads

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

BMC Genet 2018 12 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

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http://dx.doi.org/10.1186/s12863-018-0703-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6295101PMC
December 2018
13 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 12 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

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

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

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

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 12 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

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

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

BMC Genet 2018 12 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

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http://dx.doi.org/10.1186/s12863-018-0694-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282303PMC
December 2018
14 Reads

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

BMC Genet 2018 12 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

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

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 11 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

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

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 11 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

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