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Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat
Vallence Nsabiyera1, Deepak Baranwal1, Naeela Qureshi1,2
1Faculty of Science, School of Life Sciences and Environment, The University of Sydney Plant Breeding Institute, Cobbitty, NSW, Australia.
Frontiers in Plant Science
|March 3, 2020
Summary
Leaf rust resistance gene Lr49 in wheat was fine-mapped using SNP genotyping. A closely linked marker, sunKASP_21, was identified for breeding applications, though genomic variations pose cloning challenges.
Area of Science:
- Plant Pathology
- Wheat Genetics
- Molecular Breeding
Background:
- Leaf rust, caused by *Puccinia triticina*, poses a significant threat to global wheat production.
- Virulent pathotypes continuously evolve, overcoming commercially deployed all-stage resistance (ASR) genes in wheat cultivars.
- Combining adult plant resistance (APR) with ASR genes is crucial for durable wheat resistance.
Purpose of the Study:
- To fine-map the *Lr49* adult plant resistance locus in wheat.
- To develop a diagnostic marker for *Lr49* to aid in wheat breeding programs.
- To initiate the cloning of the *Lr49* gene.
Main Methods:
- High-density SNP genotyping was employed to fine-map the *Lr49* locus.
- Flow sorted chromosome sequencing was utilized for high-resolution mapping.
- Marker-trait association analysis was performed on diverse Australian and European wheat cultivars.
Main Results:
- The *Lr49* locus was fine-mapped on chromosome 4B, with marker *sunKASP_21* located 0.4 cM proximally and *sunKASP_24* 0.6 cM distally.
- *sunKASP_21* showed the strongest association with *Lr49* across diverse wheat germplasm.
- Structural variations, including a potential inverted genomic duplication, were identified in the *Lr49* region compared to the reference genome.
Conclusions:
- Fine-mapping of *Lr49* has identified closely linked markers suitable for marker-assisted selection in wheat breeding.
- The identified marker *sunKASP_21* can facilitate the deployment of *Lr49* in new wheat cultivars for improved leaf rust resistance.
- Genomic structural variations present challenges for the efficient cloning of the *Lr49* gene.
