Abstract
Leaf rust, caused by Puccinia triticina, threatens global wheat production due to the constant evolution of virulent pathotypes that defeat commercially deployed all stage-resistance (ASR) genes in modern cultivars. Hence, the deployment of combinations of adult plant resistance (APR) and ASR genes in new wheat cultivars is desirable. Adult plant resistance gene Lr49 was previously mapped on the long arm of chromosome 4B of cultivar VL404 and flanked by microsatellite markers barc163 (8.1 cM) and wmc349 (10.1 cM), neither of which was sufficiently closely linked for efficient marker assisted selection. This study used high-density SNP genotyping and flow sorted chromosome sequencing to fine-map the Lr49 locus as a starting point to develop a diagnostic marker for use in breeding and to clone this gene. Marker sunKASP_21 was mapped 0.4 cM proximal to Lr49, whereas a group of markers including sunKASP_24 were placed 0.6 cM distal to this gene. Testing of the linked markers on 75 Australian and 90 European cultivars with diverse genetic backgrounds showed that sunKASP_21 was most strongly associated with Lr49. Our results also show that the Lr49 genomic region contains structural variation relative to the reference stock Chinese Spring, possibly an inverted genomic duplication, which introduces a new set of challenges for the Lr49 cloning.
Highlights
Leaf rust, caused by Puccinia triticina (Pt), is one of the most important diseases of wheat worldwide and can result in yield losses of up to 70% (Kolmer, 2005)
VL404 (Lr49) and WL711 exhibited infection type (IT) X and IT3+, respectively, when inoculated with Pt pathotype 76-1,3,5,10,12 at the 4th leaf stage under greenhouse conditions
Thirty-five thousand copies of chromosome 4B from each of VL404 and WL711 were sorted with 97% and 98% purity, respectively, and amplified by Multiple Displacement Amplified (MDA)
Summary
Leaf rust, caused by Puccinia triticina (Pt), is one of the most important diseases of wheat worldwide and can result in yield losses of up to 70% (Kolmer, 2005). Many leaf rust resistance genes have been identified and named in wheat (McIntosh et al, 1995; McIntosh et al, 2013; Bariana and Bansal, 2017). ASR genes exhibit hypersensitive reaction to condition a high level of resistance against avirulent pathogen isolates. They are prone to breakdown when the pathogen evolves to acquire virulence. While Lr48 and Lr49 were assigned by Saini et al (2002) to the hypersensitive category based on monocyclic flag leaf tests, Bariana and Bansal (unpublished results) observed these genes to be slow rusting under polycyclic infection conditions in the field
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