The availability of a high-quality, chromosome-level reference genome accelerates breeding programs. A reference genome assembled to large scaffolds or even full-length chromosomes reveals the genome architecture as well as locations of specific genes and markers. Insight into gene order allows QTL analyses to be performed without the need of a physical map. Additionally, questions involving structural variant detection can be answered, facilitating prediction of recombination frequencies along the genome. A high-quality reference genome is also a valuable addition to breeding programs involving commercial varieties that lack specific traits that are available in wild germplasm.

Haplotype discovery
Acceleration and cost reduction in plant breeding with improved genotype/phenotype relations, utilizing linked variants.