Using Extremely High-Density Genetic Maps for Efficient QTL Detection in Breeding Populations

Characterizing the exact genotype of individual plants in diverse F2 populations is crucial for efficient mapping of the genetic basis of most commercially important traits. The use of a fixed set of DNA markers, such as that printed in a generic SNP microarray, may be misleading. Such a microarray may provide uneven genome coverage of polymorphic markers, leading to inaccurate and partial genotype data.

NRGENE’s GenoMAGIC^TM system utilizes next generation sequencing (NGS) methods, together with proprietary algorithms, to create tailor-made extremely high-density (EHD) genetic maps for each independent mapping population. Those EHD maps are later used for broad genotyping of each individual plant within a mapping population, resulting in a full genomic characterization of alleles, haplotypes and their zygosity state.

NRGENE has used GenoMAGIC^TM to analyze an F2 population of a leading commercial rice hybrid. Phenotypes for various commercially important traits and the corresponding EHD maps were created in a set of 188 F2 plants. Our analysis revealed the epistatic effect of numerous QTLs previously mapped to heterozygous loci in the hybrid. In addition, we detected novel QTLs and QTL combinations for traits such as grain dimension, heading date and male sterility.