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BMC Genetics

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https://www.readbyqxmd.com/read/30547757/associations-of-sex-hormone-binding-globulin-and-testosterone-with-genome-wide-dna-methylation
#1
Ryan Arathimos, Gemma C Sharp, Raquel Granell, Kate Tilling, Caroline L Relton
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...
December 14, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30545291/the-transcription-factor-pro44-and-the-histone-chaperone-asf1-regulate-distinct-aspects-of-multicellular-development-in-the-filamentous-fungus-sordaria-macrospora
#2
David Immanuel Schumacher, Ramona Lütkenhaus, Florian Altegoer, Ines Teichert, Ulrich Kück, Minou Nowrousian
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...
December 13, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30537928/retraction-note-dissecting-closely-linked-association-signals-in-combination-with-the-mammalian-phenotype-database-can-identify-candidate-genes-in-dairy-cattle
#3
https://www.readbyqxmd.com/read/30526478/polymorphisms-of-homer1-gene-are-associated-with-piglet-splay-leg-syndrome-and-one-significant-snp-can-affect-its-intronic-promoter-activity-in-vitro
#4
Sutong Xu, Xingjie Hao, Min Zhang, Kai Wang, Shuaifeng Li, Xing Chen, Liaohan Yang, Lin Hu, Shujun Zhang
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. This research provided a reference for further investigation of the pathogenesis of PSL...
December 7, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30518319/a-statistical-measure-for-the-skewness-of-x-chromosome-inactivation-based-on-family-trios
#5
Si-Qi Xu, Yu Zhang, Peng Wang, Wei Liu, Xian-Bo Wu, Ji-Yuan Zhou
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 is no statistical measure available for the degree of the XCI skewing based on family data in population genetics...
December 5, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30514201/design-of-low-density-snp-chips-for-genotype-imputation-in-layer-chicken
#6
Florian Herry, Frédéric Hérault, David Picard Druet, Amandine Varenne, Thierry Burlot, Pascale Le Roy, Sophie Allais
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...
December 4, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30497374/investigation-of-allele-specific-expression-of-genes-involved-in-adipogenesis-and-lipid-metabolism-suggests-complex-regulatory-mechanisms-of-ppargc1a-expression-in-porcine-fat-tissues
#7
Monika Stachowiak, Izabela Szczerbal, Krzysztof Flisikowski
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. The aim of this investigation was to analyze the differential allelic expression of four genes, PPARA, PPARG, SREBF1, and PPARGC1A, which are involved in the regulation of fat deposition in porcine subcutaneous and visceral fat and longissimus dorsi muscle...
November 29, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30458706/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
#8
Chi Zhang, Dihu Yu, Fuzhi Ke, Mimi Zhu, Jianguo Xu, Min Zhang
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. To reveal the mechanism behind the male sterility in MT at the post-transcriptional stage, proteome profiling and integrative analysis on previously obtained transcriptome and proteome data were performed in two strains...
November 20, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30445908/quantifying-the-genetic-parameters-of-feed-efficiency-in-juvenile-nile-tilapia-oreochromis-niloticus
#9
Hugues de Verdal, Marc Vandeputte, Wagdy Mekkawy, Béatrice Chatain, John A H Benzie
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...
November 16, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30442092/a-preliminary-integrated-genetic-map-distinguishes-every-chromosome-pair-and-locates-essential-genes-related-to-abiotic-adaptation-of-crassostrea-angulata-gigas
#10
Ismael Cross, Silvia Portela-Bens, Aglaya García-Angulo, Manuel A Merlo, María E Rodríguez, Thomas Liehr, Laureana Rebordinos
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 same species or subspecies. Both oysters have 20 metacentric chromosomes of similar size that are morphologically indistinguishable...
November 15, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30419811/identification-and-validation-of-qtl-and-their-associated-genes-for-pre-emergent-metribuzin-tolerance-in-hexaploid-wheat-triticum-aestivum-l
#11
Roopali Bhoite, Ifeyinwa Onyemaobi, Ping Si, Kadambot H M Siddique, Guijun Yan
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. Herbicide tolerance was measured by two chlorophyll traits, SPAD chlorophyll content index (CCI) and visual senescence score (SNS)...
November 12, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30419805/snp-markers-associated-with-body-size-and-pelt-length-in-american-mink-neovison-vison
#12
Zexi Cai, Trine Michelle Villumsen, Torben Asp, Bernt Guldbrandtsen, Goutam Sahana, Mogens Sandø Lund
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. RESULTS: In this study, we used genotyping-by-sequencing to obtain single nucleotide polymorphism (SNP) genotypes of 2496 mink. After multiple rounds of filtering, we retained 28,336 high quality SNPs and 2352 individuals for a genome-wide association study (GWAS)...
November 12, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30404617/unexpected-patterns-of-segregation-distortion-at-a-selfish-supergene-in-the-fire-ant-solenopsis-invicta
#13
Kenneth G Ross, DeWayne Shoemaker
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...
November 7, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30400815/exploring-the-genetic-basis-of-gene-transcript-abundance-and-metabolite-levels-in-loblolly-pine-pinus-taeda-l-using-association-mapping-and-network-construction
#14
Mengmeng Lu, Candace M Seeve, Carol A Loopstra, Konstantin V Krutovsky
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. Gene transcripts and metabolites are important regulatory intermediates that link genetic variations to higher-order complex traits such as wood development and drought response. A few prior studies have associated intermediate phenotypes including mRNA expression and metabolite levels with a limited number of molecular markers, but the identification of genetic variations that regulate intermediate phenotypes needs further investigation...
November 6, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30384853/single-nucleotide-polymorphisms-snps-in-a-sucrose-synthase-gene-are-associated-with-wood-properties-in-catalpa-fargesii-bur
#15
Nan Lu, Fang Mei, Zhi Wang, Nan Wang, Yao Xiao, Lisheng Kong, Guanzheng Qu, Wenjun Ma, Junhui Wang
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. RESULTS: We cloned a 2887 bp long sucrose synthase (SUS) gene from the genome of C...
November 1, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30373533/an-improved-statistical-model-for-taxonomic-assignment-of-metagenomics
#16
Yujing Yao, Zhezhen Jin, Joseph H Lee
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...
October 29, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30367592/sequence-characterization-of-the-5s-ribosomal-dna-and-the-internal-transcribed-spacer-its-region-in-four-european-donax-species-bivalvia-donacidae
#17
Jenyfer Fernández-Pérez, Ana Nantón, Josefina Méndez
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. RESULTS: The length of the 5S repeat presented little variation among species, except D...
October 26, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30359224/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
#18
Ranajit Das, Priyanka Upadhyai
Following publication of the original article [1], the authors flagged that acknowledgment of their equal contribution is omitted in the article [1].
October 25, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30348079/a-genome-wide-detection-of-selection-signatures-in-conserved-and-commercial-pig-breeds-maintained-in-poland
#19
Artur Gurgul, Igor Jasielczuk, Katarzyna Ropka-Molik, Ewelina Semik-Gurgul, Klaudia Pawlina-Tyszko, Tomasz Szmatoła, Magdalena Szyndler-Nędza, Monika Bugno-Poniewierska, Tadeusz Blicharski, Karolina Szulc, Ewa Skrzypczak, Jędrzej Krupiński
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...
October 22, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30342483/exome-sequencing-identifies-gene-variants-and-networks-associated-with-extreme-respiratory-outcomes-following-preterm-birth
#20
Aaron Hamvas, Rui Feng, Yingtao Bi, Fan Wang, Soumyaroop Bhattacharya, Jared Mereness, Madhurima Kaushal, C Michael Cotten, Philip L Ballard, Thomas J Mariani
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. RESULTS: The Prematurity and Respiratory Outcomes Program (PROP) recruited a cohort of > 765 extremely preterm infants for the identification of markers of respiratory morbidity...
October 20, 2018: BMC Genetics
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