Perennial crops have large root systems that access deep water in the ground, reduce erosion, regenerate soil and provide multi-year harvests. These crops are highly advantageous for farmers. However, perennials often take longer to reach reproductive maturity than annuals, which slows the rate of crop improvement and domestication. Without knowing which plants will have agricultural advantages such as high yield, breeders must grow all seedlings to maturity, then select those with beneficial traits. To speed up this process and reduce resources spent on plants that ultimately will be discarded, breeders can genotype seeds—analyze individual plants’ DNA—and then select the desirable seeds to grow.
Genotyping thousands of seeds can be prohibitively expensive for many perennials that have large or complex genomes, making the process difficult. Preliminary research indicates that phenotyping plant seedlings—determining whether mature crops will have desired traits based on physical characteristics of the seedlings—is an alternate method of selecting superior plants for breeding.
Danforth Center researchers led by Dr. Allison Miller and Dr. Matthew Rubin, together with researcher partners at The Land Institute, Kansas State University and INIFAP, are studying phenotyping techniques to improve their accuracy and usefulness as a fast, economical alternative to genotyping. The researchers are comparing phenotyping and genotyping techniques by using these methods on the perennial crop intermediate wheatgrass. They are also comparing different phenotyping techniques to determine those that can produce data complex enough to rival genotyping.
Finally, the team is further expanding breeders’ phenotyping abilities by establishing which early-life traits in seedlings can reliably correspond to desired traits in mature plants, determining which other seedling traits not already used in phenotyping that can be helpful for predicting mature traits and identifying affordable robotics that can help phenotype on a large scale.