Accelerating domestication of perennial plants with genomics

Perennial crops are promising candidates for building climate resilient agricultural systems because they can sustain production in challenging environments and their deep roots mitigate soil erosion, nutrient leaching and preserve soil carbon. However, these plants are challenging to breed with classical approaches due to self-incompatibility, polyploidy, and large complex genomes. These factors have been a barrier to cultivar development, but with the advances in genomic technologies, this can change. The possibility of assembling genomes and generating molecular markers in a cost-effective way means that cultivars can be developed faster with marker-assisted selection similarly to major crops. Here, we describe a pathway to accelerate domestication, starting from the establishment of a diversity collection, assembly of a reference genome, the development of breeding populations, and use of sequencing to identify relevant alleles. We provide recommendations to successfully use genomics to accelerate domestication given an entirely new era of DNA sequencing technologies.