Hidden QTLs Revealed by Heterozygous de novo Assembly

Mapping of complex, commercially important traits is inefficient and error prone. One major cause of error is genotyping inaccuracy. Advanced, sequencing-based genotyping is commonly performed by comparing differences in DNA sequence between individual plants and a detailed reference genome of their species. However, commercial crop traits are also affected by highly polymorphic DNA segments that are masked when aligned to the reference genome.  Such polymorphisms include large InDels, repetitive elements and genomic rearrangements.

NRGENE's GenoMAGIC^TM genomic platform focuses on mapping complex commercial traits in breeding populations. We achieve an accurate representation of individual plant genomes by combining proprietary resequencing and de-novo assembly tools specifically designed to work on highly divergent, heterozygous genomes. We use these tools to reconstruct the sequence of haplotypes that are highly divergent from the reference and map them to the correct location in the genome of an individual plant.

NRGENE used the GenoMAGIC^TM genomic platform to analyze the genotype–phenotype relationships in a population of commercial rice hybrids and inbred lines. We demonstrate that our de-novo approach enables discovery of QTLs and trait-related genes, even in cases where their sequence is very different from that of the reference genome, Nipponbare (Oryza sativa var. Japonica).