Reconstruction of pedigrees in clonal plant populations.
We present a Bayesian method for the reconstruction of pedigrees in clonal populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). The accuracy of the algorithm is demonstrated for simulated data. We show that the joint estimation of parameters of interest such as the rate of self-fertilization is possible with high accuracy even with marker panels of moderate power. Classical methods can only assign a very limited number of statistically significant parentages in this case and would therefore fail. Statistical confidence is estimated by Markov Chain Monte Carlo (MCMC) sampling. The method is implemented in a fast and easy to use open source software that scales to large datasets with many thousand individuals.
Riester
Markus
M
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany. markus@bioinf.uni-leipzig.de
Stadler
Peter F
PF
Klemm
Konstantin
K
D001499:Bayes Theorem; D019976:Cloning, Organism / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D005819:Genetic Markers; D016013:Likelihood Functions; D008390:Markov Chains; D018895:Microsatellite Repeats; D008957:Models, Genetic; D009010:Monte Carlo Method; D010375:Pedigree; D010944:Plants / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D057945:Self-Fertilization / Q000235:genetics
D005819:Genetic Markers