BMC Genet 2017 Dec 4;18(1):101. Epub 2017 Dec 4.
Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
: Breeding programs often rely on marker-assisted tests or variant calling of next generation sequence (NGS) data to identify regions of genomic introgression arising from the hybridization of two plant species. In this paper we present IntroMap, a bioinformatics pipeline for the screening of candidate plants through the application of signal processing techniques to NGS data, using alignment to a reference genome sequence (annotation is not required) that shares homology with the recurrent parental cultivar, and without the need for de novo assembly of the read data or variant calling.Results
: We show the accurate identification of introgressed genomic regions using both in silico simulated genomes, and a hybridized cultivar data set using our pipeline. Read More