What use is a reference genome sequence . . . in applied tree breeding

• As a reference for re-sequencing elite individuals to identify
functional alleles or haplotypes, and consequently, to provide
superior estimates of kinship.
• As a physical map of marker locations, to guide imputation of
missing genotype data
• Essential for matrix-based methods of analysis
• Allows accurate imputation of progeny from structured
mating design based on known parental haplotypes
• As the fundamental framework for knowledge of conifer
genes and regulatory elements, to enable future advances in
MAS strategies as technology develops.

http://pinegenome.org/pinerefseq/files/Westerngulf_2013_Wheeler_Whetten.pdf