Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat

Abstract

Leaf rust, caused by <i>Puccinia triticina</i>, 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 <i>Lr49</i> was previously mapped on the long arm of chromosome 4B of cultivar VL404 and flanked by microsatellite markers <i>barc163</i> (8.1 cM) and <i>wmc349</i> (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 <i>Lr49</i> locus as a starting point to develop a diagnostic marker for use in breeding and to clone this gene. Marker <i>sunKASP_21</i> was mapped 0.4 cM proximal to <i>Lr49</i>, whereas a group of markers including <i>sunKASP_24</i> 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 <i>sunKASP</i>_<i>21</i> was most strongly associated with <i>Lr49</i>. Our results also show that the <i>Lr49</i> 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 <i>Lr49</i> cloning.