Various methods are provided for determining progeny plant genotypes from a pooled sample. The methods include genotyping marker alleles in two or more progeny plants, each resulting from a different parental cross. The methods utilize in-silico deconvolution implementing Hidden Markov Modeling to determine a probability of each possible genotype for one or more marker loci in at least one progeny plant from the genetic signal generated from the pooled samples. The present methods provide for increased efficiency in genotyping progeny plants.