Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations

Jupe, Florian, Witek, Kamil, Verweij, Walter, Śliwka, Jadwiga, Pritchard, Leighton, Etherington, Graham J., Maclean, Dan, Cock, Peter J., Leggett, Richard M., Bryan, Glenn J., Cardle, Linda, Hein, Ingo and Jones, Jonathan D.g. (2013) Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. The Plant Journal, 76 (3). pp. 530-544. ISSN 0960-7412

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Abstract

RenSeq is a NB-LRR (nucleotide binding-site leucine-rich repeat) gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB-LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB-LRRs and can be accessed through a genome browser that we provide. We compared these NB-LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ~80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum ‘Heinz 1706’ extended the NB-LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi-ber2) and S. ruiz-ceballosii (Rpi-rzc1), we were able to apply RenSeq successfully to identify markers that co-segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy-to-adapt Galaxy pipelines.

Item Type:	Article
Additional Information:	Funded by: RESAS/BBSRC CRF. Grant Number: SCR/929/11; JHI SEEDCORN; BBSRC. Grant Numbers: BB/H019820/1, BB/G02197X/1; Gatsby Foundation The Plant Journal © 2013 John Wiley & Sons LtdThis is an open access article under the terms of the Creative Commons Attribution License,which permits use, distribution and reproduction in any medium, provided the original work is properly cited
Uncontrolled Keywords:	nb-lrr;,pathogen resistance,solanaceae,target enrichment,next-generation sequencing,solanum ruiz-ceballosii ,solanum berthaultii ,solanum lycopersicum,technical advance
Faculty \ School:	Faculty of Science > The Sainsbury Laboratory Faculty of Science > School of Chemistry Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Plant Sciences
Depositing User:	Pure Connector
Date Deposited:	27 Jan 2014 15:06
Last Modified:	24 Oct 2022 05:59
URI:	https://ueaeprints.uea.ac.uk/id/eprint/47308
DOI:	10.1111/tpj.2013.76.issue-3

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