Genomic resources for crop wild relatives are critical for perennial fruit breeding and conservation.

Many perennial fruit crops are clonally propagated, resulting in uniform fruit quality but increasing vulnerability to pests, diseases, and climate change. In contrast, closely related crop wild relatives (CWRs) continue to evolve in response to these pressures and are a valuable source of adaptive traits. Despite their potential, CWRs are underutilized in perennial fruit breeding. Efficient and accurate introgression of traits from CWRs during perennial fruit breeding will require the use of genomics. Genomics-assisted breeding begins with genetic mapping, such as genome-wide association studies, to identify markers predictive of traits of interest. For diverse species such as CWRs, a pangenomic approach that incorporates multiple species as a reference is often necessary. Continued use of CWRs in fruit breeding also depends on their conservation, both in situ (in natural habitats) and ex situ (off-site). Ex situ collections can also be used for genetic mapping, further supporting genomics-assisted plant breeding efforts. Ultimately, breeding and conservation of perennial fruit crops are complementary goals that benefit from the development and application of genomic resources.