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Signatures of selection

Tìm thấy 12+ kết quả cho từ khóa "Signatures of selection"

Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

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First, we detect the se- lection signatures within Jiaxian Red cattle using two different statistics, the nucleotide diversity (θπ) and the composite likelihood ratio (CLR) [52]. Empirical P values were calculated for π and CLR windows, and the overlap of the top 1% windows of each method were considered as candidate signatures of selection..

Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

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Two OB key ancestor bulls born in 1967 and 1974 (ENA SRA sample accession numbers SAMEA4827662 and SAMEA4827664) were heterozygous carriers of a single base pair deletion (BTA24:g.21222030delC) in the MOCOS gene (OMIA that causes xanthi- nuria in the homozygous state in Tyrolean grey cattle [19]. Signatures of selection. Top candidate signatures of selection.

Selection signatures of Fuzhong Buffalo based on whole-genome sequences

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Identification of variants associated with divergent feed efficiency groups using multiple RNA-sequencing datasets from dairy and beef cattle. A genome-wide association study suggests several novel candidate genes for. Discovery of novel genetic networks associated with 19 economically important traits in beef cattle. Strong signatures of selection in the domestic pig genome. Recent and ongoing selection in the human genome

Contrasting genetic variation and positive selection followed the divergence of NBSencoding genes in Asian and European pears

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The resulting SNPs were used to calculate the π and F ST with a 1000 bp sliding window and a step size of 500 bp across the linear sequence of all 338 NBS-encoding genes. To identify signatures of selection, we calculated the Ka/Ks ratio of all orthologous NBS-encoding gene pairs to identify signatures of positive selection on them. Genome-wide expression analysis of the NBS-encoding genes. To investigate the expression changes of the NBS-encoding genes after inoculation with A..

Episodes of gene flow and selection during the evolutionary history of domesticated barley

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Identification of adaptive genes without prior know- ledge of the phenotypes they confer is possible with a bottom-up approach that begins with population genetic screening to detect signatures of selection [17].

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

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When the sequence vari- ant calling of the 175 samples was performed together with the 70 key ancestor animals using the multi-sample approach implemented in the GATK, all concordance metrics were considerably worse. 3 Signatures of selection detected in the sire and dam line of the SLW breed. Signatures of selection detected in the sire and dam line of the SLW breed using CLR (a) and iHS (b) Dotted lines indicate the empirical 0.5 (CLR) and 0.1% (iHS) thresholds.

Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using wholegenome re-sequencing data

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Overlapping of the putative sweep regions identified from the top 1% of the cross-population DCMS statistic with candidate regions under positive selection previously reported in other cattle populations.. of the within-population DCMS statistic with the candidate regions under positive selection previously reported in other cattle populations.. of the cross-population DCMS statistic with the candidate regions under positive selection previously reported in other cattle populations..

Identifying the unique characteristics of the Chinese indigenous pig breeds in the Yangtze River Delta region for precise conservation

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A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds

Breeding history and candidate genes responsible for black skin of Xichuan blackbone chicken

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Advances in research of the origin and domestication of domestic animals. Transcriptome analysis of the pectoral muscles of local chickens and commercial broilers using Ribo-Zero ribonucleic acid sequencing. Novel analysis of the Harderian gland transcriptome response to Newcastle disease virus in two inbred chicken lines. Strong signatures of selection in the domestic pig genome.

Assessing breed integrity of Göttingen Minipigs

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Structure-function of the multifunctional Ca2+/. Piórkowska K, Ż ukowski K, Tyra M, Szyndler-N ę dza M, Szulc K, Skrzypczak E, et al. Recent insights into the role and molecular mechanisms of the autoimmune regulator (AIRE) gene in autoimmunity. Rubin C-J, Megens HJ, Martinez Barrio A, Maqbool K, Sayyab S, Schwochow D, et al. Strong signatures of selection in the domestic pig genome. Fang X, Mou Y, Huang Z, Li Y, Han L, Zhang Y, et al.

Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

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Table 2 Results of the gene-set enrichment analysis (GSEA) testing for differences in expression of color-associated gene sets between color phenotypes. 3 Signatures of selection on single-nucleotide polymorphisms (SNPs) in the transcriptome of Oophaga pumilio. A) Graphical results of the BayeScan analysis, the plot shows, for each of the 398,910 bi-allelic SNPs tested, the Fst between the three color phenotypes and their corresponding q-values (SNPs under diversifying selection, q <.

Copy number variation in human genomes from three major ethno-linguistic groups in Africa

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Given the association of HLADQB1 and KIR in pre- eclampsia and infectious disease which may impact infant birth and survival, they may be the actual targets of positive selection, resulting in the signatures of selection which have been seen in these loci. We found that CNV distinguish major continental popu- lations, when we included Asians, South Asians, Ameri- cans, Europeans and Africans from the 1000 Genomes in the same PCA plot.

Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale

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Genetic signatures of Salmonella adaptation to animal sources. enterica serovars associated by microbial GWAS with animal sources (i.e.

Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids

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Significant differ- ences in the number of orthogroups under relaxed or intensified selection were quantified using Fisher’s Exact Tests in R. If Arctic charr Salvelinus alpinus is ‘ the most diverse vertebrate. Positive and negative selection in the DAZ gene family. Signatures of relaxed selection in the CYP8B1 gene of birds and mammals. Selection in the evolution of gene duplications

Analysis of the brain transcriptome in lines of laying hens divergently selected for feather pecking

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Variation in neighbouring genes of the dopaminergic and serotonergic systems affects feather pecking behaviour of laying hens. https://doi.org/10.1111/j x.. Genomewide Mapping of Selection Signatures and Genes for Extreme Feather Pecking in Two Divergently Selected Laying Hen Lines. https://doi.org/10.3390/ani10020262.. https://doi.org/10.1007/s . https://doi.org/10.3390/ani6010003..

Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral

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This finding suggests that our set of reference sequences is able to detect signatures of positive selection in re- gions where the query is longer than the actual func- tional element under selection, and in particular across most of the size range of known regulatory elements and open chromatin regions in the human genome..

Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae

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Effects of positive selection can be investigated by analyzing nucleotide sequences of the loci of interest. The objectives of this work were to study the nucleotide sequence diversity of exon 2 of the MHC class II DRB and DQB loci in the family Equidae, and to assess signatures of positive and nega- tive selection on this functionally important domain of the antigen-presenting MHC class II molecules.

Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing

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The role of the insulin-like growth factor 1 (IGF-1) in skeletal muscle physiology. Mapping signatures of positive selection in the genome of livestock. Supramolecular organization of the subsarcolemmal cytoskeleton of adult skeletal muscle fibers. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape..

Protein changes as robust signatures of fish chronic stress: A proteomics approach to fish welfare research

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(ii) a de- crease of the cortisol levels to basal levels within. This will be crucial to form a robust welfare as- sessment and to allow, in the future, the development of targeted recommendations and legislation. Despite the limi- tations to the use of these technologies in the aquacul- ture field [29], several studies prove already the huge potential of proteomics for the identification of stress signatures [30–34]..

The global gene expression outline of the bovine blastocyst: Reflector of environmental conditions and predictor of developmental capacity

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The results of the present study unravelled that Table 8 Molecular signatures of in vivo and in vitro derived embryos correlated with developmental capacity. CVO: Competent in vivo blastocysts that resulted in pregnancy;. CVT: Competent in in vitro blastocysts that resulted in pregnancy.