Combined linkage and association mapping identifies a major QTL (qRtsc8-1), conferring tar spot complex resistance in maize
- 12 March 2016
- journal article
- research article
- Published by Springer Science and Business Media LLC in Theoretical and Applied Genetics
- Vol. 129 (6), 1217-1229
- https://doi.org/10.1007/s00122-016-2698-y
Abstract
Key message A major QTL ( qRtsc8 - 1 ) conditioning resistance to tar spot complex of maize and occurring at a frequency of 3.5 % across 890 maize inbred lines. Abstract Tar spot complex (TSC) is a highly destructive disease of maize found in some countries in America. Identification of TSC resistant germplasm and elucidating the genetic mechanism of resistance is crucial for the use of host resistance to manage this disease. We evaluated 890 elite maize inbred lines in multiple environments and used genome wide association analysis (GWAS) with genotypic data from Illumina MaizeSNP50 BeadChip containing 56 K SNPs to dissect the genetics of TSC resistance. GWAS results were validated through linkage analysis in three bi-parental populations derived from different resistant and susceptible parents. Through GWAS, three TSC resistance loci were identified on chromosome 2, 7 and 8 (−log10 (p) > 5.99). A major quantitative resistance locus (QTL) designated qRtsc8-1, was detected on maize chromosome bin 8.03. qRtsc8-1, was confirmed in three independent bi-parental populations and it accounted for 18–43 % of the observed phenotypic variation for TSC. A rare haplotype within the qRtsc8-1 region, occurring at a frequency of 3.5 % increased TSC resistance by 14 %. Candidate gene analysis revealed that a leucine-rich repeat receptor-like protein (LRR-RLKs) gene family maybe the candidate gene for qRtsc8-1. Identification and localization of a major locus conditioning TSC resistance provides the foundation for fine mapping qRtsc8-1 and developing functional markers for improving TSC resistance in maize breeding programs. To the best of our knowledge, this is the first report of a major QTL for TSC resistance.Keywords
Funding Information
- Regional Fund for Agricultural Technology (FTG-8028-08)
- Bill and Melinda Gates Foundation
- CGIAR Research Program (CRP) on MAIZE
This publication has 44 references indexed in Scilit:
- Combined linkage and association mapping reveals candidates for Scmv1, a major locus involved in resistance to sugarcane mosaic virus (SCMV) in maizeBMC Plant Biology, 2013
- Genome-wide identification, characterization and expression analysis of populusleucine-rich repeat receptor-like protein kinase genesBMC Genomics, 2013
- Lessons from Dwarf8 on the Strengths and Weaknesses of Structured Association MappingPLoS Genetics, 2013
- Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markersBMC Genomics, 2012
- The Arabidopsis Leucine-Rich Repeat Receptor–Like Kinases BAK1/SERK3 and BKK1/SERK4 Are Required for Innate Immunity to Hemibiotrophic and Biotrophic PathogensTHE PLANT CELL ONLINE, 2011
- Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maizeProceedings of the National Academy of Sciences of the United States of America, 2011
- Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maizeProceedings of the National Academy of Sciences of the United States of America, 2010
- Association Mapping: Critical Considerations Shift from Genotyping to Experimental DesignTHE PLANT CELL ONLINE, 2009
- PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage AnalysesAmerican Journal of Human Genetics, 2007
- A unified mixed-model method for association mapping that accounts for multiple levels of relatednessNature Genetics, 2005