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Genotype simulation
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QTL mapping through genome-wide association studies (GWAS) is challenging, especially in the case of low heritability complex traits and when few animals possess genotypic and phenotypic information.
9p
vinarcissa
21-03-2023
1
1
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Population-wide genotypic and phenotypic data is frequently used to predict the disease risk or genetic/phenotypic values, or to localize genetic variations responsible for complex traits. GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures.
6p
vinarcissa
21-03-2023
2
1
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In this paper, we propose a methodological prospect of mixed linear models to analyze genotype by environment interaction effects using association mapping designs. First, we simulated datasets to assess the power of linear mixed models to detect interaction effects.
12p
vinarcissa
21-03-2023
5
1
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Genetic variance that is not captured by single nucleotide polymorphisms (SNPs) is due to imperfect linkage disequilibrium (LD) between SNPs and quantitative trait loci (QTLs), and the extent of LD between SNPs and QTLs depends on different minor allele frequencies (MAF) between them.
14p
vinarcissa
21-03-2023
4
1
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The main goal of selection is to achieve genetic gain for a population by choosing the best breeders among a set of selection candidates. In this perspective, various simulation studies have been conducted to find the best way to select a set of SNPs for low density genotyping of two laying hen lines.
14p
vihagrid
30-01-2023
4
3
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Genomic prediction (GP) is used in animal and plant breeding to help identify the best genotypes for selection. One of the most important measures of the effectiveness and reliability of GP in plant breeding is predictive accuracy. An accurate estimate of this measure is thus central to GP.
18p
vijeeni2711
24-07-2021
12
0
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The Present study was carried out in the wire-netting house of the Krishi Vigyan Kendra, Kalahandi during Rabi 2014-15.The objective of the present endeavour was to screen 6 number of Paddy varieties (early group,75-85 days) for higher photosynthetic efficiency with higher productivity under simulated moisture stress conditions. The experiment was laid out in a factorial CRD with three stress treatments and three replications.
11p
cothumenhmong9
18-01-2021
12
2
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Forward-time population genetic simulations play a central role in deriving and testing evolutionary hypotheses. Such simulations may be data-intensive, depending on the settings to the various parameters controlling them. In particular, for certain settings, the data footprint may quickly exceed the memory of a single compute node.
12p
viwyoming2711
16-12-2020
13
2
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The correlations of genotypic and phenotypic tests with treatment, clinical history and the significance of mutations in viruses of HIV-infected patients are used to establish resistance mutations to protease inhibitors (PIs).
17p
vikentucky2711
26-11-2020
5
0
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Advances in genotyping and phenotyping techniques have enabled the acquisition of a great amount of data. Consequently, there is an interest in multivariate statistical analyses that identify genomic regions likely to contain causal mutations affecting multiple traits (i.e., pleiotropy).
10p
vikentucky2711
24-11-2020
11
1
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To evaluate statistical methods for genome-wide genetic analyses, one needs to be able to simulate realistic genotypes. We here describe a method, applicable to a broad range of association study designs, that can simulate autosome-wide single-nucleotide polymorphism data with realistic linkage disequilibrium and with spiked in, user-specified, single or multi-SNP causal effects.
10p
viconnecticut2711
29-10-2020
9
1
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Drought seriously curtails growth, physiology and productivity in rapeseed (Brassica napus). Although drought tolerance is a complex trait, efficient phenotyping and genotyping has led to the identification of novel marker-trait associations underlying drought tolerance. A diverse panel of 228 Brassica accessions was phenotyped under normal (without stress) and water-stress conditions, simulated by polyethylene glycol (PEG-6000) (15% PEG stress) at the seedling stage; stress tolerance index (STI) and stress susceptibility index (SSI) values were acquired.
15p
covid19
14-06-2020
42
0
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The ability of a plant to overcome animal-induced damage is referred to as compensation or tolerance and ranges from undercompensation (decreased fitness when damaged) to overcompensation (increased fitness when damaged).
12p
vihashirama2711
21-05-2020
18
1
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