Improving fruit and wine: what does genomics have to offer?

Will we still be drinking wines made from Pinot Noir and eating McIntosh apples in the 23rd century? Elite grape and apple cultivars, vegetatively propagated for centuries, are highly susceptible to evolving pathogens. In response, growers continually expand their agrochemical weaponry at enormous environmental costs. By contrast, breeders are seeking disease-resistant, tastier alternatives to the handful of dominant cultivars by exploring genetic diversity in these fruits. However, this is a formidable task because consumers cling to ancient cultivars, and breeding long-lived woody perennials is laborious and expensive. Although genomics tools may not solve the former sociocultural dilemma, they can help overcome the latter practical obstacles. Screening seedlings for desirable genetic profiles using molecular techniques reduces the time and high costs associated with growing plants to maturity and evaluating fruit. Such screening is currently in its infancy in apples and grapes, but the adoption of modern DNA sequencing technologies and statistical approaches promises to accelerate cultivar improvement significantly. Here, I describe standard approaches for molecular breeding in apples and grapes, and some of the challenges associated with the collection and analysis of next-generation DNA sequence data. In addition, I urge breeders to establish populations specifically designed for a future of inexpensive genome sequencing.