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SNP panel
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The availability of high-density (HD) marker panels, genome wide variants and sequence data creates an unprecedented opportunity to dissect the genetic basis of complex traits, enhance genomic selection (GS) and identify causal variants of disease.
10p
vinarcissa
21-03-2023
5
1
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Diversity in crops is fundamental for plant breeding efforts. An accurate assessment of genetic diversity, using molecular markers, such as single nucleotide polymorphism (SNP), must be able to reveal the structure of the population under study
12p
vinarcissa
21-03-2023
8
1
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The efficiency of breeding programs partly relies on the accuracy of the estimated breeding values which decreases when pedigrees are incomplete. Two reproduction techniques are mainly used by sheep breeders to identify the sires of lambs: animal insemination and natural matings with a single ram per group of ewes.
11p
vinarcissa
21-03-2023
1
1
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Strategies for imputing genotypes from the Illumina-Bovine3K, Illumina-BovineLD (6K), BeefLD-GGP (8K), a non-commercial-15K and IndicusLD-GGP (20K) to either Illumina-BovineSNP50 (50K) or to Illumina-BovineHD (777K) SNP panel, as well as for imputing from 50K, GGP-IndicusHD (90iK) and GGP-BeefHD (90tK) to 777K were investigated.
15p
vinarcissa
21-03-2023
2
1
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The usefulness of such SNP panels for studying wheat evolution and domestication has not yet been fully explored and ascertainment bias issues can potentially affect their applicability when studying landraces and tetraploid ancestors of bread wheat.
13p
vinarcissa
21-03-2023
5
1
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Genomic selection (GS) has played an important role in cattle breeding programs. However, genotyping prices are still a challenge for implementation of GS in beef cattle and there is still a lack of information about the use of low-density Single Nucleotide Polymorphisms (SNP) chip panels for genomic predictions in breeds such as Brazilian Braford and Hereford.
14p
vinarcissa
21-03-2023
4
1
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SNPs are informative to estimate genomic breed composition (GBC) of individual animals, but selected SNPs for this purpose were not made available in the commercial bovine SNP chips prior to the present study. The primary objective of the present study was to select five common SNP panels for estimating GBC of individual animals initially involving 10 cattle breeds (two dairy breeds and eight beef breeds).
14p
vihagrid
30-01-2023
7
3
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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.
10p
vihagrid
30-01-2023
8
3
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Identifying functional non-coding variation is critical for defining the genetic contributions to human disease. While single-nucleotide polymorphisms (SNPs) within cis-acting transcriptional regulatory elements have been implicated in disease pathogenesis, not all cell types have been assessed and functional validations have been limited. In particular, the cells of the peripheral nervous system have been excluded from genome-wide efforts to link non-coding SNPs to altered gene function.
19p
vilarryellison
29-10-2021
11
0
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The aim of this study was to identify such regions and possibly identify causative variation affecting umbilical hernia in pigs. A case/control material consisting of 739 Norwegian Landrace pigs was collected and applied in a GWAS study with a genome-wide distributed panel of 60 K SNPs. Additionally candidate genes were sequenced to detect additional polymorphisms that were used for single SNP and haplotype association analyses in 453 of the pigs.
9p
vibeauty
23-10-2021
3
0
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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
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SNP panels that uniquely identify an individual are useful for genetic and forensic research. Previously recommended SNP panels are based on DNA profiles and mostly contain intragenic SNPs. With the increasing interest in RNA expression profiles, we aimed for establishing a SNP panel for both DNA and RNA-based genotyping.
12p
vibeauty
23-10-2021
11
1
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The LI was measured through the proviral load (PVL) set–point and white blood cells (WBC) counts. The goals of this work were to gain insight into the contribution of SNPs (bovine 50KSNP panel) on LI variability and to identify genomics regions underlying this trait.
15p
vibeauty
23-10-2021
7
0
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In this study we integrated the CNV (copy number variation) and WssGWAS (weighted single-step approach for genome-wide association) analyses to increase the knowledge about number of piglets born alive, an economically important reproductive trait with significant impact on production efficiency of pigs.
11p
visilicon2711
20-08-2021
11
1
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Single Nucleotide Polymorphism (SNP) in the genome has become crucial information for clinical use. For example, the targeted cancer therapy is primarily based on the information which clinically important SNPs are detectable from the tumor. Many hospitals have developed their own panels that include clinically important SNPs. The genome information exchange between the patient and the hospital has become more popular.
12p
visilicon2711
20-08-2021
4
1
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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
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Unravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS) using multi-locus models was conducted in a panel of 170 walnut accessions genotyped using the Axiom™ J. regia 700 K SNP array, with phenological data from 2018, 2019 and legacy data.
25p
vijeeni2711
24-07-2021
9
0
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Imputation accuracy among other things depends on the size of the reference panel, the marker’s minor allele frequency (MAF), and the correct placement of single nucleotide polymorphism (SNP) on the reference genome assembly.
12p
vijeeni2711
30-06-2021
6
2
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The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening.
16p
vilichoo2711
23-06-2021
11
1
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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
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