Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr16

Mulualem T Kassa,Pierre R Fobert,Brent D Mccallum,Curt A Mccartney,James G Menzies,Andrew G Sharpe,John P Fellers,Colin W Hiebert,Nicole Rezac Harrison,D Gavin Humphreys,Frank M You,Curtis J Pozniak

doi:10.1186/s12870-017-0993-7

Abstract

BackgroundLr16 is a widely deployed leaf rust resistance gene in wheat (Triticum aestivum L.) that is highly effective against the North American Puccinia triticina population when pyramided with the gene Lr34. Lr16 is a seedling leaf rust resistance gene conditioning an incompatible interaction with a distinct necrotic ring surrounding the uredinium. Lr16 was previously mapped to the telomeric region of the short arm of wheat chromosome 2B. The goals of this study were to develop numerous single nucleotide polymorphism (SNP) markers for the Lr16 region and identify diagnostic gene-specific SNP marker assays for marker-assisted selection (MAS).ResultsForty-three SNP markers were developed and mapped on chromosome 2BS tightly linked with the resistance gene Lr16 across four mapping populations representing a total of 1528 gametes. Kompetitive Allele Specific PCR (KASP) assays were designed for all identified SNPs. Resistance gene analogs (RGAs) linked with the Lr16 locus were identified and RGA-based SNP markers were developed. The diagnostic potential of the SNPs co-segregating with Lr16 was evaluated in a diverse set of 133 cultivars and breeding lines. Six SNP markers were consistent with the Lr16 phenotype and are accurately predictive of Lr16 for all wheat lines/cultivars in the panel.ConclusionsLr16 was mapped relative to SNP markers in four populations. Six SNP markers exhibited high quality clustering in the KASP assay and are suitable for MAS of Lr16 in wheat breeding programs.

Highlights

Lr16 is a widely deployed leaf rust resistance gene in wheat (Triticum aestivum L.) that is highly effective against the North American Puccinia triticina population when pyramided with the gene Lr34
Marker development The sequence characterized amplified region (SCAR) marker pwm6 was developed from the Diversity Arrays Technology (DArT) marker wPt-5960 that mapped near Lr16, and the ConservedPrimer marker pwm16 was developed from the Wheat EST (wEST) BF483211 that was mapped on the distal end of chromosome 2BS
single nucleotide polymorphism (SNP) markers were identified from publicly available wheat genomic resources and SNP databases using sequences of previously mapped markers linked to the Lr16 locus on chromosome 2BS, syntenic genes of Brachypodium and rice genomes and from Resistance gene analog (RGA) identified from RNA sequences (RNA-seq) and in silico subtraction

Summary

Introduction

Lr16 is a widely deployed leaf rust resistance gene in wheat (Triticum aestivum L.) that is highly effective against the North American Puccinia triticina population when pyramided with the gene Lr34. Lr16 is a seedling leaf rust resistance gene conditioning an incompatible interaction with a distinct necrotic ring surrounding the uredinium. Wheat is grown on more than 215 million hectares and cultivated across more regions of the world than any other staple crop [1]. Wheat diseases caused by various pathogens cause significant yield loss across the world. The rust fungi cause serious diseases of wheat and pose significant constraints to wheat production. The three wheat rust diseases are stem, leaf, and stripe (or yellow) rust, caused by Puccinia graminis f. Henn., Puccinia triticina Eriks., and Puccinia striiformis Westend. Henn., Puccinia triticina Eriks., and Puccinia striiformis Westend. f.sp. tritici Erikss., respectively [2]

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