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synbreed specifications

Information


Unique identifier OMICS_14509
Name synbreed
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.12-9
Stability Stable
Requirements
methods, lattice, MASS, foreach, R(≥2.14), abind, igraph, doParallel, qtl, doBy, BGLR, regress(≥1.3-8), LDheatmap, synbreedData(≥1.5)
Maintained Yes

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  • person_outline Chris-Carolin Schön

Publication for synbreed

synbreed citations

 (62)
library_books

Genomic heritability estimates in sweet cherry reveal non additive genetic variance is relevant for industry prioritized traits

2018
BMC Genet
PMCID: 5894190
PMID: 29636022
DOI: 10.1186/s12863-018-0609-8

[…] using the rosbreed cherry 6 k snp array v1 (an illumina infinium® ii array) []. the snp curation pipeline was described in cai et al. []. missing data were imputed with beagle as implemented in synbreed [, ] using the hidden markov model and a minor allele frequency of 0.05. individuals or snps missing more than 25% data were removed from analysis. in total, a genome-wide set of 1615 snps […]

library_books

Investigating Drought Tolerance in Chickpea Using Genome Wide Association Mapping and Genomic Selection Based on Whole Genome Resequencing Data

2018
Front Plant Sci
PMCID: 5825913
PMID: 29515606
DOI: 10.3389/fpls.2018.00190

[…] feature of both variables selection and shrinkage, whereas brr only shrinks variables. the detailed similarities and differences between genomic prediction models are reviewed by . the r package synbreed was used to fit the three models ()., a fivefold cross-validation was performed to evaluate the prediction performance of the three models. the whole dataset was randomly divided into five […]

library_books

A Genome Wide Association Study of Field and Seedling Response to Individual Stem Rust Pathogen Races Reveals Combinations of Race Specific Genes in North American Spring Wheat

2018
Front Plant Sci
PMCID: 5797647
PMID: 29441083
DOI: 10.3389/fpls.2018.00052

[…] algorithm (money et al., ) in tassel 5 (bradbury et al., )., intra-chromosomal ld between all possible pairwise comparisons of snps was calculated as squared allele frequency correlation (r2) in synbreed r package (http://synbreed.r-forge.r-project.org/). the pattern of ld decay over genetic distance was previously reported for this population (bajgain et al., ). we calculated the pairwise […]

library_books

Efficiency of different strategies to mitigate ascertainment bias when using SNP panels in diversity studies

2018
BMC Genomics
PMCID: 5756397
PMID: 29304727
DOI: 10.1186/s12864-017-4416-9

[…] available. a list of the 42 populations with their abbreviations and population sizes as used in the study is provided in table . samples used in this study were collected under the umbrella of the synbreed project (www.synbreed.tum.de) from chicken fancy breeds in germany between 2010 and 2012. the collection was completed by samples of two red jungle fowl populations, gallus gallus gallus […]

library_books

Genomic Prediction and Association Mapping of Curd Related Traits in Gene Bank Accessions of Cauliflower

2017
PMCID: 5919744
PMID: 29255118
DOI: 10.1534/g3.117.300199

[…] β is an n × 1 vector of random effects, and x is the marker matrix. the residuals follow a normal distribution e∼n(0,iσ2), where i is the identity matrix. the gblup and rrblup implementations of the synbreed r package () were used., additionally, a bayesb () model as implemented in the bglr r package () was used to estimate marker effects and to calculate prediction ability. bayesb uses […]

library_books

Genetic Architecture of Charcoal Rot (Macrophomina phaseolina) Resistance in Soybean Revealed Using a Diverse Panel

2017
Front Plant Sci
PMCID: 5613161
PMID: 28983305
DOI: 10.3389/fpls.2017.01626

[…] distance and chromosome-wide densities. pairwise linkage disequilibrium (ld) between markers was measured using the squared correlation coefficient (r2) between alleles with the r package, synbreed (wimmer et al., ). the r2 was calculated separately for euchromatic and heterochromatic regions due to the variability of recombination. only significant r2 values (p < 0.001), calculated […]


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synbreed institution(s)
Plant Breeding, Technische Universität München, Freising, Germany
synbreed funding source(s)
This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).

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