Genome editing and targeted sequence insertion with CrispR/Cas9 to elevate disease resistance in potato and tomato (JONES_S17DTP)

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Programmable nucleases such as CrispR/Cas9 are revolutionizing biology by enabling specific genome sequences to be targeted for mutation, or for homologous recombination (HR). Such New Breeding Technologies (NBTs) can result in loss-of-function mutations, or enable precise replacement (Knock-In Exchange, or KIE) of useful genes from one plant via HR into the corresponding chromosomal position of another plant. We work with Resistance to Phytophthora infestans (Rpi) genes from wild potato and tomato relatives. The main goal of this project is to use CrispR/Cas9 (and test also the related Cpf1 programmable nuclease) to replace non-functional Rpi gene homologs in tomato and potato diploid inbred lines, with functional Rpi gene alleles. We work with inbred potato lines from www.solynta.com. Prior to targeting with KIE, resistance gene repertoires of Solanum genotypes of interest will be characterized using RenSeq with long PacBio reads (Witek et al 2016). The student will generate KIE events that (depending on NBT regulation) could be brought to market in F1 hybrids, and will interact with private and public sector breeders.Cermak T (2015) High-frequency, precise modification of the tomato genome Genome Biology 16:232 DOI 10.1186/s13059-015-0796-9 Witek (2016) Rpi gene cloning using Renseq and sMrt sequencing Nat Biot 34:656-660 www.ncbi.nlm.nih.gov/pubmed/27111721