Single Nucleotide Polymorphism arrays
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We evaluated the performance of single-nucleotide polymorphism (SNP) genotyping arrays OncoScan (Thermo Fisher Scientific, San Diego, CA) and Infinium CytoSNP-850K (CytoSNP; Illumina, Waltham, MA) for assessing homologous recombination deficiency (HRD) genomic instability.
9p vileonardodavinci 23-12-2023 4 3 Download
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Copy number variation (CNV) is an important source of genetic variability associated with phenotypic variation and disease susceptibility. Comprehensive genome-wide CNV maps provide valuable information for genetic and functional studies.
9p vinarcissa 21-03-2023 4 1 Download
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The soil borne, obligate biotrophic fungus Synchytrium endobioticum causes tumor-like tissue proliferation (wart) in potato tubers and thereby considerable crop damage. Chemical control is not effective and unfriendly to the environment. S. endobioticum is therefore a quarantined pathogen. The emergence of new pathotypes of the fungus aggravate this agricultural problem.
16p vinarcissa 21-03-2023 5 1 Download
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Toll-like receptors play a key role in innate immunity by recognizing pathogens and activating appropriate responses. Pathogens express several signal molecules (pathogen-associated molecular patterns, PAMPs) essential for survival and pathogenicity. Recognition of PAMPs triggers an array of anti-microbial immune responses through the induction of various inflammatory cytokines.
8p vinarcissa 21-03-2023 4 1 Download
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Two individuals with a first-degree relationship share about 50 percent of their alleles. Parent–offspring relationships cannot be homozygous for alternative alleles (genetic exclusion). Methods: Applying the concept of genetic exclusion to HD arrays typed in animals for experimental purposes or genomic selection allows estimation of the rate of rejection of first-degree relationships as the rate at which two individuals typed for a large number of Single Nucleotide Polymorphisms (SNPs) do not share at least one allele.
12p vihagrid 30-01-2023 8 3 Download
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Single nucleotide polymorphism (SNP) panels have been widely used to study genomic variations within and between populations. Methods of SNP discovery have been a matter of debate for their potential of introducing ascertainment bias, and genetic diversity results obtained from the SNP genotype data can be misleading. We used a total of 42 chicken populations where both individual genotyped array data and pool whole genome resequencing (WGS) data were available.
16p vibeauty 23-10-2021 9 1 Download
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Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species.
13p viseulgi2711 31-08-2021 10 1 Download
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Genomic selection accuracy increases with the use of high SNP (single nucleotide polymorphism) coverage. However, such gains in coverage come at high costs, preventing their prompt operational implementation by breeders.
16p visilicon2711 20-08-2021 9 1 Download
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Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs.
13p viansan2711 30-07-2021 12 1 Download
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Improving fiber quality and yield are the primary research objectives in cotton breeding for enhancing the economic viability and sustainability of Upland cotton production. Identifying the quantitative trait loci (QTL) for fiber quality and yield traits using the high-density SNP-based genetic maps allows for bridging genomics with cotton breeding through marker assisted and genomic selection.
26p viansan2711 30-07-2021 19 1 Download
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In forest trees, genetic markers have been used to understand the genetic architecture of natural populations, identify quantitative trait loci, infer gene function, and enhance tree breeding.
17p vijeeni2711 24-07-2021 3 0 Download
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Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen.
18p vilichoo2711 23-06-2021 14 0 Download
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Population genetic studies based on genotyped single nucleotide polymorphisms (SNPs) are influenced by a non-random selection of the SNPs included in the used genotyping arrays.
13p vilichoo2711 23-06-2021 11 2 Download
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Identifying the loci and dissecting the genetic architecture underlying wheat yield- and qualityrelated traits are essential for wheat breeding. A genome-wide association study was conducted using a highdensity 90 K SNP array to analyze the yield- and quality-related traits of 543 bread wheat varieties.
11p vijichea2711 28-05-2021 6 1 Download
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Stripe rust (yellow rust) is a significant disease for bread wheat (Triticum aestivum L.) worldwide. A genome-wide association study was conducted on 240 Chinese wheat cultivars and elite lines genotyped with the wheat 90 K single nucleotide polymorphism (SNP) arrays to decipher the genetic architecture of stripe rust resistance in Chinese germplasm.
13p vijichea2711 28-05-2021 6 1 Download
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Along with the improvement of high throughput sequencing technologies, the genetics community is showing marked interest for the rare variants/common diseases hypothesis. While sequencing can still be prohibitive for large studies, commercially available genotyping arrays targeting rare variants prove to be a reasonable alternative.
12p vikentucky2711 26-11-2020 9 1 Download
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Copy Number Variations (CNVs) are usually inferred from Single Nucleotide Polymorphism (SNP) arrays by use of some software packages based on given algorithms. However, there is no clear understanding of the performance of these software packages; it is therefore difficult to select one or several software packages for CNV detection based on the SNP array platform.
9p vikentucky2711 26-11-2020 18 0 Download
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Breast Cancer (BC) is associated with inherited gene mutations. High throughput genotyping of BC samples has led to the identification and characterization of biomarkers for the diagnosis of BC. The most common genetic variants studied are SNPs (Single Nucleotide Polymorphisms) that determine susceptibility to an array of diseases thus serving as a potential tool for identifying the underlying causes of breast carcinogenesis.
8p viamsterdam 18-09-2020 6 0 Download
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Landraces are an important source of genetic diversity in common wheat, but archival collections of Afghan wheat landraces remain poorly characterised. The recent development of array based marker systems, particularly single nucleotide polymorphism (SNP) markers, provide an excellent tool for examining the genetic diversity of local populations.
11p viminato2711 22-05-2020 15 1 Download
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Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) carries many outstanding agronomic traits, therefore is a valuable resource for wheat genetic improvement. Wheat–P. huashanica translocation lines are important intermediate materials for wheat breeding and studying the functions of alien chromosomes.
13p viuchiha2711 21-04-2020 7 1 Download