Genome mock to predict single-crosses

Even though there are several genotyping platforms for obtaining single nucleotide polymorphism (SNP) markers, lacking comparative information on how these platforms affect hybrid prediction or the inclusion of non-additive effects. Moreover, SNP discovery techniques are commonly based on a unique reference genome, which can introduce an ascertainment bias when tested germplasms are distant from reference.

We employed a tropical maize single-crosses panel and genomic data from two genotyping platforms: array and genotyping-by-sequencing, both based on the B73 genome (temperate). Also, we used a pipeline to build a mock reference genome for SNP discovery aiming to capture unique SNP markers within the tropical maize population, independent from an external reference genome. Our results indicate that mock reference genomes deliver reliable estimates for genetic diversity and population structure assessment.