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Combined linkage and association mapping identifies a major QTL (qRtsc8-1), conferring tar spot complex resistance in maize

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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.

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Acknowledgments

The authors gratefully acknowledge the financial support from the Regional fund for agricultural technology (FONTAGRO) project FTG-8028, the Bill and Melinda Gates Foundation (BMGF) as part of the project, “Drought Tolerant Maize for Africa (DTMA)”, and the CGIAR research program (CRP) on maize for co-sponsoring this research work. We are grateful to CIMMYT technicians in Mexico and Colombia for managing the trials and contributing to phenotypic evaluation.

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  1. George Mahuku

    Present address: International Institute of Tropical Agriculture (IITA), P.O.Box, 34443, Dar es Salaam, Tanzania

Authors and Affiliations

  1. International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, PO Box 1041-00621, Nairobi, Kenya

    George Mahuku

  2. International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico

    Jiafa Chen & Rosemary Shrestha

  3. International Maize and Wheat Improvement Center (CIMMYT), Apdo. Aereo 67-13, Cali, Colombia

    Luis A. Narro, Karen Viviana Osorio Guerrero & Alba Lucia Arcos

  4. International Maize and Wheat Improvement Center (CIMMYT) and Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Yunbi Xu

  5. College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China

    Jiafa Chen

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Communicated by A. Augusto Franco Garcia.

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122_2016_2698_MOESM1_ESM.jpg

Supplementary Figure S1. The symptoms and development of tar spot complex (TSC) on maize leaves and cobs in Mexico. a-c) Development of the TSC symptoms on young to mature maize leaves; d-g) Impacts of TSC on maize plants and kernel development; h-i) TSC resistant and susceptible maize plants hybrids

122_2016_2698_MOESM2_ESM.tif

Supplementary Figure S2. The most significant SNP markers associated with tar spot complex (TSC) resistance and identified through GWAS for each environment. Manhattan plots, plotted with the individual SNPs on the X-axis and –log10 P value of each SNP derived from the association study on the Y-axis

122_2016_2698_MOESM3_ESM.tif

Supplementary Figure S3. Linkage map generated for a bi-parental population (Pop1). Genetic linkage map generated using 166 SNP markers from the doubled haploid population (Pop1, n = 201) derived from the parental lines CML495 and LaPostaSEQ.C7F64-2-6-2-2-B*3. Each marker name and marker position interval (cM) are shown on the right and left of each chromosome, respectively. QTL detected for different environments and combined environments are shown on the map

122_2016_2698_MOESM4_ESM.tif

Supplementary Figure S4. Linkage map generated for bi-parental population (Pop2). Genetic linkage map generated using 253 SNP markers from the doubled haploid population (Pop2, n = 116) derived from the parental lines CML451 and DTPYC9-F46-1-2-1-2-B*3. Each marker name and marker position interval (cM) are shown on the right and left of each chromosome, respectively. Detected QTL are shown on the map

122_2016_2698_MOESM5_ESM.tif

Supplementary Figure S5. LD decay in qRtsc8-1 region. The x-axis indicates the physical distance between SNPs within the qRtsc8-1 region, y-axis indicates the parameter r2 of LD and the fitting curve (red line) illustrates the LD decay

122_2016_2698_MOESM6_ESM.docx

Supplementary Table S1. Best-bet tar spot complex (TSC) resistance donors and respective haplotype at the qRtsc8-1 region

122_2016_2698_MOESM7_ESM.docx

Supplementary Table S2. Significant SNP markers associated with tar spot complex (TSC) resistance identified through GWAS. Marker indicates the name of the SNP

122_2016_2698_MOESM8_ESM.docx

Supplementary Table S3. QTL for tar spot complex (TSC) resistance determined by ICIM for doubled haploid maize populations evaluated in in Agua Fria in 2012 and 2013

Supplementary Table S4. QTL for tar spot complex (TSC) resistance detected using single marker analysis in Pop3

Supplementary Table S5. Candidate genes linked to SNPS associated with TSC resistance in the qRtsc8-1 region

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Mahuku, G., Chen, J., Shrestha, R. et al. Combined linkage and association mapping identifies a major QTL (qRtsc8-1), conferring tar spot complex resistance in maize. Theor Appl Genet 129, 1217–1229 (2016). https://doi.org/10.1007/s00122-016-2698-y

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