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You searched for: Journal BMC genetics Remove constraint Journal: BMC genetics Publication Year 2018 Remove constraint Publication Year: 2018 Source 2018 v.19 no.1 Remove constraint Source: 2018 v.19 no.1
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1. A deeper view into the significance of simple sequence repeats in pre-miRNAs provides clues for its possible roles in determining the function of microRNAs

Author:
Joy, Nisha; Maimoonath Beevi, Y. P.; Soniya, E. V.
Source:
BMC genetics 2018 v.19 no.1 pp. 29
ISSN:
1471-2156
Subject:
Angiospermae; Chordata; alternative splicing; biogenesis; genes; genomics; microRNA; microsatellite repeats; regulatory sequences
Abstract:
... BACKGROUND: The central tenet of ‘genome content’ has been that the ‘non-coding’ parts are highly enriched with ‘microsatellites’ or ‘Simple Sequence Repeats’ (SSRs). We presume that the presence and change in number of repeat unit (n) of SSRs in different genomic locations may or may not become beneficial, depending on the position of SSRs in a gene. Very few studies have looked into the existenc ...
DOI:
10.1186/s12863-018-0615-x
PubMed:
29739315
PubMed Central:
PMC5941480

2. A genome-wide association study for harness racing success in the Norwegian-Swedish coldblooded trotter reveals genes for learning and energy metabolism

Author:
Velie, Brandon D.; Fegraeus, Kim Jäderkvist; Solé, Marina; Rosengren, Maria K.; Røed, Knut H.; Ihler, Carl-Fredrik; Strand, Eric; Lindgren, Gabriella
Source:
BMC genetics 2018 v.19 no.1 pp. 80
ISSN:
1471-2156
Subject:
energy metabolism; genes; genome-wide association study; genomics; genotyping; harness; immune response; industry; memory; quality control; racehorses; racing performance; single nucleotide polymorphism
Abstract:
... BACKGROUND: Although harness racing is of high economic importance to the global equine industry, significant genomic resources have yet to be applied to mapping harness racing success. To identify genomic regions associated with harness racing success, the current study performs genome-wide association analyses with three racing performance traits in the Norwegian-Swedish Coldblooded Trotter usin ...
DOI:
10.1186/s12863-018-0670-3
PubMed:
30157760
PubMed Central:
PMC6114527

3. A genome-wide association study identifies candidate loci associated to syringomyelia secondary to Chiari-like malformation in Cavalier King Charles Spaniels

Author:
Ancot, Frédéric; Lemay, Philippe; Knowler, Susan P.; Kennedy, Karen; Griffiths, Sandra; Cherubini, Giunio Bruto; Sykes, Jane; Mandigers, Paul J. J.; Rouleau, Guy A.; Rusbridge, Clare; Kibar, Zoha
Source:
BMC genetics 2018 v.19 no.1 pp. 16
ISSN:
1471-2156
Subject:
Cavalier King Charles Spaniel; abnormal development; brain; cell adhesion molecules; chromosome segregation; dogs; genes; genetic factors; genome-wide association study; genotyping; haplotypes; loci; magnetic resonance imaging; pain; penetrance; phenotype; sequence analysis; single nucleotide polymorphism; skull; spinal cord; syringomyelia; vertebrae
Abstract:
... BACKGROUND: Syringomyelia (SM) is a common condition affecting brachycephalic toy breed dogs and is characterized by the development of fluid-filled cavities within the spinal cord. It is often concurrent with a complex developmental malformation of the skull and craniocervical vertebrae called Chiari-like malformation (CM) characterized by a conformational change and overcrowding of the brain and ...
DOI:
10.1186/s12863-018-0605-z
PubMed:
29566674
PubMed Central:
PMC5865342

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

Author:
Gurgul, Artur; Jasielczuk, Igor; Ropka-Molik, Katarzyna; Semik-Gurgul, Ewelina; Pawlina-Tyszko, Klaudia; Szmatoła, Tomasz; Szyndler-Nędza, Magdalena; Bugno-Poniewierska, Monika; Blicharski, Tadeusz; Szulc, Karolina; Skrzypczak, Ewa; Krupiński, Jędrzej
Source:
BMC genetics 2018 v.19 no.1 pp. 95
ISSN:
1471-2156
Subject:
artificial selection; biochemical pathways; body composition; color; disease resistance; domestication; ears; genes; haplotypes; homozygosity; immune system; landraces; metabolism; neuropeptide Y; peroxisome proliferator-activated receptors; phenotype; phenotypic plasticity; statistical analysis; stress response; swine; swine breeds; Poland
Abstract:
... 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, dis ...
DOI:
10.1186/s12863-018-0681-0
PubMed:
30348079
PubMed Central:
PMC6198424

5. Analysis of coastal cod (Gadus morhua L.) sampled on spawning sites reveals a genetic gradient throughout Norway’s coastline

Author:
Dahle, Geir; Quintela, María; Johansen, Torild; Westgaard, Jon-Ivar; Besnier, François; Aglen, Asgeir; Jørstad, Knut E.; Glover, Kevin A.
Source:
BMC genetics 2018 v.19 no.1 pp. 42
ISSN:
1471-2156
Subject:
Gadus morhua; alleles; coasts; data collection; effective population size; fisheries; genetic markers; genetic variation; genomics; genotyping; heterozygosity; introgression; loci; marine fish; microsatellite repeats; otoliths; population genetics; population structure; spawning; Arctic region; Norway
Abstract:
... BACKGROUND: Atlantic cod (Gadus morhua L.) has formed the basis of many economically significant fisheries in the North Atlantic, and is one of the best studied marine fishes, but a legacy of overexploitation has depleted populations and collapsed fisheries in several regions. Previous studies have identified considerable population genetic structure for Atlantic cod. However, within Norway, which ...
DOI:
10.1186/s12863-018-0625-8
PubMed:
29986643
PubMed Central:
PMC6036686

6. An improved statistical model for taxonomic assignment of metagenomics

Author:
Yao, Yujing; Jin, Zhezhen; Lee, Joseph H
Source:
BMC genetics 2018 v.19 no.1 pp. 98
ISSN:
1471-2156
Subject:
algorithms; data collection; genome; high-throughput nucleotide sequencing; humans; metagenomics; probability; statistical models; taxonomy; variance
Abstract:
... 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 ...
DOI:
10.1186/s12863-018-0680-1
PubMed:
30373533
PubMed Central:
PMC6206629

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

Author:
Cross, Ismael; Portela-Bens, Silvia; García-Angulo, Aglaya; Merlo, Manuel A.; Rodríguez, María E.; Liehr, Thomas; Rebordinos, Laureana
Source:
BMC genetics 2018 v.19 no.1 pp. 104
ISSN:
1471-2156
Subject:
Crassostrea angulata; Crassostrea gigas; abiotic stress; bacterial artificial chromosomes; bioinformatics; clones; essential genes; fluorescence in situ hybridization; gene ontology; genomics; heavy metals; heterozygosity; histones; karyotyping; metacentric chromosomes; oysters; ribosomal DNA; toxicity
Abstract:
... 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. There is, in addition, an unresolved controversy as to whether or not C. angulata and C. gigas are the ...
DOI:
10.1186/s12863-018-0689-5
PubMed:
30442092
PubMed Central:
PMC6238303

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

Author:
Struck, Ann-Kathrin; Dierks, Claudia; Braun, Marina; Hellige, Maren; Wagner, Anna; Oelmaier, Bernd; Beineke, Andreas; Metzger, Julia; Distl, Ottmar
Source:
BMC genetics 2018 v.19 no.1 pp. 91
ISSN:
1471-2156
Subject:
abnormal development; alleles; calves; cartilage; cattle breeds; chondrocytes; chondroitin sulfate; computed tomography; dams (mothers); growth plate; head; herds; heterozygosity; high-throughput nucleotide sequencing; histopathology; homozygosity; miniature breeds; mutation; necropsy; nose; palate; phenotype; polymerase chain reaction; ribs; siblings; sires; vertebrae; zebu
Abstract:
... 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 ...
DOI:
10.1186/s12863-018-0678-8
PubMed:
30305023
PubMed Central:
PMC6180608

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

Author:
Oney-Birol, Signem; Fitz-Gibbon, Sorel; Chen, Jin-Ming; Gugger, Paul F.; Sork, Victoria L.
Source:
BMC genetics 2018 v.19 no.1 pp. 88
ISSN:
1471-2156
Subject:
Quercus alba; Quercus engelmannii; adaptive radiation; alleles; drought; gene frequency; genetic variation; glutathione; introgression; ligases; loci; natural selection; shrublands; stress response; transcriptome; California
Abstract:
... 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 o ...
DOI:
10.1186/s12863-018-0677-9
PubMed:
30285631
PubMed Central:
PMC6167808

10. Association between MKRN3 and LIN28B polymorphisms and precocious puberty

Author:
Yi, Bo Ram; Kim, Hyun Jeong; Park, Hye Sook; Cho, Yoon Jeong; Kim, Ju Young; Yee, Jeong; Chung, Jee Eun; Kim, Joo Hee; Lee, Kyung Eun; Gwak, Hye Sun
Source:
BMC genetics 2018 v.19 no.1 pp. 47
ISSN:
1471-2156
Subject:
Koreans; alleles; boys; children; cohort studies; databases; girls; models; puberty; regression analysis; risk; single nucleotide polymorphism; socioeconomic factors
Abstract:
... BACKGROUND: The present study aimed to investigate the association between MKRN3 and LIN28B gene polymorphisms and precocious puberty in Korean boys and girls. RESULTS: Children 7 to 9 years of age in 2011 to 2012 who were part of the Ewha Birth & Growth Cohort Study were recruited for this study. A total of 103 girls and 70 boys were included in the analyses. Seven girls and 26 boys were identifi ...
DOI:
10.1186/s12863-018-0658-z
PubMed:
30053798
PubMed Central:
PMC6062980

11. Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice

Author:
Jang, Su; Lee, Yunjoo; Lee, Gileung; Seo, Jeonghwan; Lee, Dongryung; Yu, Yoye; Chin, Joong Hyoun; Koh, Hee-Jong
Source:
BMC genetics 2018 v.19 no.1 pp. 5
ISSN:
1471-2156
Subject:
alleles; branches; breeding; breeding programs; cultivars; genetic markers; haplotypes; inflorescences; rice
Abstract:
... BACKGROUND: Balancing panicle-related traits such as panicle length and the numbers of primary and secondary branches per panicle, is key to improving the number of spikelets per panicle in rice. Identifying genetic information contributes to a broader understanding of the roles of gene and provides candidate alleles for use as DNA markers. Discovering relations between panicle-related traits and ...
DOI:
10.1186/s12863-017-0591-6
PubMed:
29334899
PubMed Central:
PMC5769279

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

Author:
Arathimos, Ryan; Sharp, Gemma C.; Granell, Raquel; Tilling, Kate; Relton, Caroline L.
Source:
BMC genetics 2018 v.19 no.1 pp. 113
ISSN:
1471-2156
Subject:
DNA methylation; adolescence; childhood; children; epigenetics; females; genes; genomics; heritability; longitudinal studies; males; parents; risk; sex hormone-binding globulin; testosterone
Abstract:
... 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 heritabil ...
DOI:
10.1186/s12863-018-0703-y
PubMed:
30547757
PubMed Central:
PMC6295101

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

Author:
Xu, Si-Qi; Zhang, Yu; Wang, Peng; Liu, Wei; Wu, Xian-Bo; Zhou, Ji-Yuan
Source:
BMC genetics 2018 v.19 no.1 pp. 109
ISSN:
1471-2156
Subject:
X chromosome; algorithms; alleles; confidence interval; females; genotype; loci; molecular genetics; population genetics; rheumatoid arthritis; statistical analysis; United States
Abstract:
... 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. However, there ...
DOI:
10.1186/s12863-018-0694-8
PubMed:
30518319
PubMed Central:
PMC6282303

14. Can metamorphosis survival during larval development in spiny lobster Sagmariasus verreauxi be improved through quantitative genetic inheritance?

Author:
Nguyen, Nguyen H.; Fitzgibbon, Quinn P.; Quinn, Jane; Smith, Greg; Battaglene, Stephen; Knibb, Wayne
Source:
BMC genetics 2018 v.19 no.1 pp. 27
ISSN:
1471-2156
Subject:
Sagmariasus verreauxi; analysis of variance; economic valuation; genetic correlation; genetic markers; genetic variance; hatcheries; heritability; inheritance (genetics); instars; larvae; larval development; lobster culture; lobsters; metamorphosis; molting; natural selection; parentage; phenotype; progeny; rearing; sires; statistical models; survival rate
Abstract:
... BACKGROUND: One of the major impediments to spiny lobster aquaculture is the high cost of hatchery production due to the long and complex larval cycle and poor survival during the many moult stages, especially at metamorphosis. We examined if the key trait of larval survival can be improved through selection by determining if genetic variance exists for this trait. Specifically, we report, for the ...
DOI:
10.1186/s12863-018-0621-z
PubMed:
29728054
PubMed Central:
PMC5936031

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

Author:
Wu, Xue; Xu, Feng-ling; Ding, Mei; Zhang, Jing-jing; Yao, Jun; Wang, Bao-jie
Source:
BMC genetics 2018 v.19 no.1 pp. 115
ISSN:
1471-2156
Subject:
cell lines; chemiluminescence; computer software; gene expression; humans; luciferase; neurotransmitters; prediction; protein synthesis; receptors; schizophrenia; serotonin; transcription factors; transcription initiation site
Abstract:
... 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 fragme ...
DOI:
10.1186/s12863-018-0708-6
PubMed:
30594152
PubMed Central:
PMC6311061

16. Characterization and functional analysis of GhWRKY42, a group IId WRKY gene, in upland cotton (Gossypium hirsutum L.)

Author:
Gu, Lijiao; Wei, Hengling; Wang, Hantao; Su, Junji; Yu, Shuxun
Source:
BMC genetics 2018 v.19 no.1 pp. 48
ISSN:
1471-2156
Subject:
Arabidopsis; Gossypium hirsutum; Nicotiana tabacum; abiotic stress; beta-glucuronidase; chlorophyll; cotton; gene expression; gene silencing; genes; leaves; models; phenotype; plant height; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; roots; stems; stress response; transactivators; transcriptional activation; transgenic plants; yeasts
Abstract:
... BACKGROUND: WRKY transcription factors (TFs) participate in various physiological processes of plants. Although WRKY genes have been well studied in model plants, knowledge of the functional roles of these genes is still extremely limited in cotton. RESULTS: In this study, a group IId WRKY gene from cotton, GhWRKY42, was isolated and characterized. Our data showed that GhWRKY42 localized to the nu ...
DOI:
10.1186/s12863-018-0653-4
PubMed:
30060731
PubMed Central:
PMC6065155

17. Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton

Author:
Magwanga, Richard Odongo; Lu, Pu; Kirungu, Joy Nyangasi; Lu, Hejun; Wang, Xingxing; Cai, Xiaoyan; Zhou, Zhongli; Zhang, Zhenmei; Salih, Haron; Wang, Kunbo; Liu, Fang
Source:
BMC genetics 2018 v.19 no.1 pp. 6
ISSN:
1471-2156
Subject:
drought tolerance; phylogeny; drought; hydrophobicity; Gossypium hirsutum; Gossypium tomentosum; hydrophilicity; water stress; gene expression; microRNA; genotype; embryogenesis; introns; crop production; cultivars; freshwater; chromosomes; gene ontology; textile industry; cash crops; cotton; proteins; stress response; gene duplication
Abstract:
... BACKGROUND: Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this research work was to characterize the late embryogenesis abundant (LEA) protein fam ...
DOI:
10.1186/s12863-017-0596-1
PubMed:
29334890
PubMed Central:
PMC5769447

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

Author:
Liley, James
Source:
BMC genetics 2018 v.19 no.1 pp. 89
ISSN:
1471-2156
Subject:
case-control studies; computer software; genetic techniques and protocols; genome-wide association study; genomics; mathematics and statistics
Abstract:
... 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 ...
DOI:
10.1186/s12863-018-0675-y
PubMed:
30285617
PubMed Central:
PMC6171163

19. Common variants in the hERG (KCNH2) voltage-gated potassium channel are associated with altered fasting and glucose-stimulated plasma incretin and glucagon responses

Author:
Engelbrechtsen, Line; Mahendran, Yuvaraj; Jonsson, Anna; Gjesing, Anette Prior; Weeke, Peter E.; Jørgensen, Marit E.; Færch, Kristine; Witte, Daniel R.; Holst, Jens J.; Jørgensen, Torben; Grarup, Niels; Pedersen, Oluf; Vestergaard, Henrik; Torekov, Signe; Kanters, Jørgen K.; Hansen, Torben
Source:
BMC genetics 2018 v.19 no.1 pp. 15
ISSN:
1471-2156
Subject:
alleles; arrhythmia; digestive system; ethics; fasting; gain-of-function mutation; gastric inhibitory polypeptide; glucagon; glucagon-like peptide 1; glucose; glucose tolerance tests; homeostasis; humans; hypoglycemia; insulin; patients; potassium channels; risk; secretin; secretion; Denmark
Abstract:
... BACKGROUND: Patients with long QT syndrome due to rare loss-of-function mutations in the human ether-á-go-go-related gene (hERG) have prolonged QT interval, risk of arrhythmias, increased secretion of insulin and incretins and impaired glucagon response to hypoglycemia. This is caused by a dysfunctional Kv11.1 voltage-gated potassium channel. Based on these findings in patients with rare variants ...
DOI:
10.1186/s12863-018-0602-2
PubMed:
29548277
PubMed Central:
PMC5857134

20. Comparative RNA-Seq analysis reveals a critical role for brassinosteroids in rose (Rosa hybrida) petal defense against Botrytis cinerea infection

Author:
Liu, Xintong; Cao, Xiaoqian; Shi, Shaochuan; Zhao, Na; Li, Dandan; Fang, Peihong; Chen, Xi; Qi, Weicong; Zhang, Zhao
Source:
BMC genetics 2018 v.19 no.1 pp. 62
ISSN:
1471-2156
Subject:
Botrytis cinerea; Rosa; biosynthesis; brassinosteroids; corolla; death; disease resistance; gene expression regulation; gene ontology; gene regulatory networks; genes; gray mold; host-pathogen relationships; hybrids; immunologic receptors; ornamental plants; plant hormones; plant pathogenic fungi; secondary metabolites; sequence analysis; signal transduction; transcription (genetics); transcription factors; transcriptome; transcriptomics
Abstract:
... BACKGROUND: One of the most popular ornamental plants worldwide, roses (Rosa sp.), are very susceptible to Botrytis gray mold disease. The necrotrophic infection of rose petals by B. cinerea causes the collapse and death of these tissues in both the growth and post-harvest stages, resulting in serious economic losses. To understand the molecular basis of rose resistance against B. cinerea, we prof ...
DOI:
10.1186/s12863-018-0668-x
PubMed:
30126371
PubMed Central:
PMC6102922