Dramatically reduced costs for DNA sequencing have opened the way to better understanding the relationship between a plant's DNA makeup and its field performance, in what is known as genotype-phenotype correlation analysis, or trait mapping. To provide useful outcomes, such analyses must be very precise when applied to closely related individuals, with relatively low DNA polymorphism. NRGENE's MAESTROTM platform is designed for precise identification of the specific genomic DNA sequences that contribute the final trait value. Currently, NRGENE is focused on rice (Oryza sativa L.), a major staple food for half of the world's population. Rice has a relatively small and well-characterized genome which makes it an ideal model organism for trait-mapping analyses. NRGENE is aimed at discovering the genomic basis for the phenomenon of heterosis, which is widely used by the industry to develop high-yielding hybrid rice varieties. NRGENE analysis determined the full genomic sequence of rice's leading hybrids from South-East Asia. Such germplasms have genomic DNA introgressions originated from Japonica and introduced into the Indica background. Our analysis detects structural variation of different lengths, this allows us to differentiates between genomic changes that are not detectable by SNP genotyping. Following the bioinformatics analysis, segregating populations were created to evaluate the phenotypic effect of each Japonica insertion, in both the Japonica/Indica heterozygous state and the Japonica/Japonica homozygous state. The overall results will enable us to better understand the basis of the interspecies heterosis revealed in rice.