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synbreed specifications


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
methods, lattice, MASS, foreach, R(≥2.14), abind, igraph, doParallel, qtl, doBy, BGLR, regress(≥1.3-8), LDheatmap, synbreedData(≥1.5)
Maintained Yes




No version available



  • person_outline Chris-Carolin Schön

Publication for synbreed

synbreed citations


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

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 […]


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

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 […]


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

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 ( the pattern of ld decay over genetic distance was previously reported for this population (bajgain et al., ). we calculated the pairwise […]


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

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 ( 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 […]


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

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 […]


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

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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