Molecular Breeding

, Volume 31, Issue 1, pp 233–237 | Cite as

Development and validation of a breeder-friendly KASPar marker for wheat leaf rust resistance locus Lr21

  • Kumari Neelam
  • Gina Brown-Guedira
  • Li Huang
Short communication


Development and utilization of genetic markers play a pivotal role in marker-assisted breeding of wheat cultivars with pyramids of disease resistance genes. The objective of this study was to develop a closed-tube, gel-free assay for high-throughput genotyping of leaf rust resistance locus Lr21. Polymorphism identified from re-sequencing of a 2.4-kb fragment covering the functional region of the Lr21 gene from the second to the fourth indels was targeted for assay development. The generated sequence data revealed the 88- or 105-bp indel in the first intron of the Lr21 gene in the selected resistant cultivars compared to susceptible US spring and winter wheat cultivars. Allele-specific primers for a KASPar assay were designed around the junction of the indel at position 1,346 bp. The marker was tested on a panel of 384 US wheat lines and found to be effective in differentiating resistant and susceptible genotypes.


Leaf rust KASPar assay SNP genotyping Puccinia triticina Eriks. 



The contribution of Mr. Jared Smith and Mrs. Sharon Williamson (USDA-ARS Eastern Regional Small Grains Genotyping, Laboratory) in designing KASPar assays and assay setup is acknowledged with thanks. This work was supported in part by funds provided by the USDA T-CAP AFRI grant number 2011-68002-30029.

Supplementary material

11032_2012_9773_MOESM1_ESM.docx (24 kb)
Supplementary material 1 (DOCX 24 kb)


  1. Chen W, Mingus J, Mammadov J, Backlund JE, Greene T, Thompson S, Kumpatla S (2010) KASPar: a simple and cost-effective system for SNP genotyping. In: Proceedings of plant and animal genomes XVIII conference. San Diego, p 94Google Scholar
  2. Fu YB, Peterson GW, McCallum BD, Huang L (2010) Population based resequencing analysis of improved wheat germplasm at wheat leaf rust resistance locus Lr21. Theor Appl Genet 121:271–281PubMedCrossRefGoogle Scholar
  3. Huang L, Brooks SA, Li W, Fellers J, Trick HN, Gill B (2003) Map based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of breed wheat. Genetics 164:655–664PubMedGoogle Scholar
  4. Kolmer JA, Anderson JA (2011) First detection in North America of virulence in wheat leaf rust (Puccinia triticina) to seedling plants of wheat with Lr21. Plant Dis 95:1032CrossRefGoogle Scholar
  5. Kumpatla SP, Buyyarapu R, Abdurakhmonov IY, Mammadov JA (2012) Genomics-assisted plant breeding in the 21st century: technological advances and progress. In: Abdurakhmonov IY (ed) Plant breeding, pp 131–183, InTech publishers

Copyright information

© Springer Science+Business Media B.V. (outside the USA) 2012

Authors and Affiliations

  1. 1.Department of Crop ScienceNorth Carolina State UniversityRaleighUSA
  2. 2.USDA-ARS Plant Science ResearchRaleighUSA
  3. 3.Department of Plant Sciences and Plant PathologyMontana State UniversityBozemanUSA

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