Bridging the Genotype–Phenotype Gap for Precision Breeding in Rye
With release of two high-quality genome assemblies, rye has finally reached the genome era, enabling the integration and advancement of fundamental and applied breeding and research to understand how the genome builds, maintains, and operates rye. This chapter compiles a century of breeding research that aimed to describe and unravel the genetic diversity of rye. Systematic identification, management, and use of natural diversity became feasible in outbreeding rye with the establishment of hybrid breeding late in the twentieth century. Research conducted so far largely reflects target traits of rye improvement programs. We review progress achieved in the mapping of genes and QTL (quantitative trait loci) for agronomic traits, biotic and abiotic stress tolerance as well as grain quality. We describe how rye genome assemblies now enable association of the digital sequences of rye markers with locations in physical space, as an essential standard to conduct genome-based breeding and research in rye. Despite formidable achievements, major challenges in rye production remain, in particular concerning tailor-made grain qualities, to further advance rye from an all-rounder to an authentic high-performance crop with different and certified types of end-use. For this purpose, further progress in rye phenomics and functional genomics research is necessary to associate genome sequence information with phenotypes related to rye growth and development.