AUTHOR=Nsabiyera Vallence , Baranwal Deepak , Qureshi Naeela , Kay Pippa , Forrest Kerrie , Valárik Miroslav , Doležel Jaroslav , Hayden Matthew J. , Bariana Harbans S. , Bansal Urmil K. 

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

JOURNAL=Frontiers in Plant Science

VOLUME=10

YEAR=2020

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2019.01787

DOI=10.3389/fpls.2019.01787

ISSN=1664-462X

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