Premium
Resistance gene enrichment sequencing ( R en S eq) enables reannotation of the NB ‐ LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations
Author(s) -
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,
Jones Jonathan D.G.
Publication year - 2013
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12307
Subject(s) - biology , phytophthora infestans , genetics , gene , genome , gene family , r gene , whole genome sequencing , computational biology , plant disease resistance
Summary 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 ‐ LRR s 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 ‐ LRR s 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 S olanum species S. berthaultii ( Rpi‐ber2 ) and S. ruiz‐ceballosii ( Rpi‐rzc1 ), we were able to apply R en S eq successfully to identify markers that co‐segregate with resistance towards the late blight pathogen P hytophthora infestans . These SNP identification workflows were designed as easy‐to‐adapt Galaxy pipelines.