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Statistically unbiased prediction enables accurate denoising of voltage imaging data
Here we report SUPPORT (statistically unbiased prediction utilizing spatiotemporal information in imaging data), a self-supervised learning method...
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Impact and utility of shallow pedigree using single-step genomic BLUP for prediction of unbiased genomic breeding values
In unstructured dairy programs, pedigree is usually shallow, which leads to biased prediction of breeding values using best linear unbiased...
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Metabolomic-genomic prediction can improve prediction accuracy of breeding values for malting quality traits in barley
BackgroundMetabolomics measures an intermediate stage between genotype and phenotype, and may therefore be useful for breeding. Our objectives were...
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Comparison of linear and semi-parametric models incorporating genomic, pedigree, and associated loci information for the prediction of resistance to stripe rust in an Austrian winter wheat breeding program
Key messageWe used a historical dataset on stripe rust resistance across 11 years in an Austrian winter wheat breeding program to evaluate genomic...
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Factor analysis applied in genomic prediction considering different density marker panels in rice
The study objective was to evaluate the application of factor analysis (FA) on genomic prediction considering different density marker panels. The FA...
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An unbiased kinship estimation method for genetic data analysis
Accurate estimate of relatedness is important for genetic data analyses, such as heritability estimation and association map** based on data...
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Choosing the right tool: Leveraging of plant genetic resources in wheat (Triticum aestivum L.) benefits from selection of a suitable genomic prediction model
Key messageGenomic prediction of genebank accessions benefits from the consideration of additive-by-additive epistasis and subpopulation-specific...
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LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA
Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical...
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The impact of genoty** strategies and statistical models on accuracy of genomic prediction for survival in pigs
BackgroundSurvival from birth to slaughter is an important economic trait in commercial pig productions. Increasing survival can improve both...
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First Genomic Prediction of Single-Step Models in Large Yellow Croaker
Genome selection is mainly used in disease-resistant traits of aquatic species; however, its implementation is hindered by a high cost of genotype...
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Using residual regressions to quantify and map signal leakage in genomic prediction
BackgroundMost genomic prediction applications in animal breeding use genotypes with tens of thousands of single nucleotide polymorphisms (SNPs)....
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Weighted single-step genomic best linear unbiased prediction integrating variants selected from sequencing data by association and bioinformatics analyses
BackgroundSequencing data enable the detection of causal loci or single nucleotide polymorphisms (SNPs) highly linked to causal loci to improve...
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Accuracy of genomic prediction using multiple Atlantic salmon populations
BackgroundThe accuracy of genomic prediction is partly determined by the size of the reference population. In Atlantic salmon breeding programs, four...
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Effects of marker density on genomic prediction for yield traits in sweet corn
By accounting for many traits, phenoty** sweet corn is a costly practice, making complementary strategies necessary. Thus, predictive methods...
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deepGBLUP: joint deep learning networks and GBLUP framework for accurate genomic prediction of complex traits in Korean native cattle
BackgroundGenomic prediction has become widespread as a valuable tool to estimate genetic merit in animal and plant breeding. Here we develop a novel...
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Sparse testing using genomic prediction improves selection for breeding targets in elite spring wheat
Key messageSparse testing using genomic prediction can be efficiently used to increase the number of testing environments while maintaining selection...
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Tomato genomic prediction for good performance under high-temperature and identification of loci involved in thermotolerance response
Many studies showed that few degrees above tomato optimum growth temperature threshold can lead to serious loss in production. Therefore, the...
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Linear Mixed Models
The linear mixed model framework is explained in detail in this chapter. We explore three methods of parameter estimation (maximum likelihood, EM...
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Genomic dissection of additive and non-additive genetic effects and genomic prediction in an open-pollinated family test of Japanese larch
Genomic dissection of genetic effects on desirable traits and the subsequent use of genomic selection hold great promise for accelerating the rate of...
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Genomic prediction in pigs using data from a commercial crossbred population: insights from the Duroc x (Landrace x Yorkshire) three-way crossbreeding system
BackgroundGenomic selection is widely applied for genetic improvement in livestock crossbreeding systems to select excellent nucleus purebred (PB)...
