PhD Studentship: Genome editing and targeted sequence insertion with CrispR/Cas9 to elevate disease resistance in potato and tomato

University of East Anglia - School of Biological Sciences

Start Date:  1st October 2017

No. of positions available: 1

Supervisor: Prof. Jonathan Jones

Project description:

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 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.

The student will learn skills in molecular biology, Mendelian and somatic genetics, tissue culture, DNA and cDNA sequence capture and Resistance gene assembly (RenSeq) and associated bioinformatics, in GoldenGate cloning methods, and in genome editing using HR. A strong interest in genetics, in mechanisms of homologous recombination, in plant disease resistance and in crop improvement would be an advantage.

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

Person specification: Minimum entry 2:1

Funding notes: Full Studentships cover a stipend (RCUK rate: £14,296pa – 2016/7), research costs and tuition fees at UK/EU rate, and are available to UK and EU students who meet the UK residency requirements.

Students from EU countries who do not meet the UK residency requirements may be eligible for a fees-only award. Students in receipt of a fees-only award will be eligible for a maintenance stipend awarded by the NRPDTP Bioscience Doctoral Scholarships, which when combined will equal a full studentship. To be eligible students must meet the EU residency requirements.

Details on eligibility for funding on the BBSRC website: 

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