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Fine mapping of Msv1, a major QTL for resistance to Maize Streak Virus leads to development of production markers for breeding pipelines

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Msv1 , the major QTL for MSV resistance was delimited to an interval of 0.87 cM on chromosome 1 at 87 Mb and production markers with high prediction accuracy were developed.

Abstract

Maize streak virus (MSV) disease is a devastating disease in the Sub-Saharan Africa (SSA), which causes significant yield loss in maize. Resistance to MSV has previously been mapped to a major QTL (Msv1) on chromosome 1 that is germplasm and environment independent and to several minor loci elsewhere in the genome. In this study, Msv1 was fine-mapped through QTL isogenic recombinant strategy using a large F 2 population of CML206 × CML312 to an interval of 0.87 cM on chromosome 1. Genome-wide association study was conducted in the DTMA (Drought Tolerant Maize for Africa)-Association mapping panel with 278 tropical/sub-tropical breeding lines from CIMMYT using the high-density genotyping-by-sequencing (GBS) markers. This study identified 19 SNPs in the region between 82 and 93 Mb on chromosome 1(B73 RefGen_V2) at a P < 1.00E-04, which coincided with the fine-mapped region of Msv1. Haplotype trend regression identified a haplotype block significantly associated with response to MSV. Three SNPs in this haplotype block at 87 Mb on chromosome 1 had an accuracy of 0.94 in predicting the disease reaction in a collection of breeding lines with known responses to MSV infection. In two biparental populations, selection for resistant Msv1 haplotype demonstrated a reduction of 1.03–1.39 units on a rating scale of 1–5, compared to the susceptible haplotype. High-throughput KASP assays have been developed for these three SNPs to enable routine marker screening in the breeding pipeline for MSV resistance.

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Acknowledgments

The authors gratefully acknowledge the financial support received from the Bill and Melinda Gates Foundation (BMGF) as part of the project, “Drought Tolerant Maize for Africa (DTMA)”. We thank CGIAR Research Program (CRP) on MAIZE for co-sponsoring this research work. The biparental populations and disease data from Kevin Pixley, CIMMYT and Jean-Marcel Ribaut, GCP, used in initial QTL mapping and validation study are thankfully acknowledged. Assistance for data analysis provided by Jyothsna Tejomurthula is appreciated. The authors would also like to thank the technical assistance from Carlos Martinez, Alberto Vergara and Jose Simon Marias of CIMMYT in carrying out this research work. The authors also gratefully acknowledge the two reviewers for their valuable comments that could improve the value of this manuscript.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The authors declare no ethical standards have been violated in the course of the study.

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Authors and Affiliations

  1. International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad, 502324, India

    Sudha K. Nair & Raman Babu

  2. International Maize and Wheat Improvement Center (CIMMYT), Mount Pleasant, MP163, Harare, Zimbabwe

    Cosmos Magorokosho

  3. International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, Nairobi, Kenya

    George Mahuku, Kassa Semagn, Yoseph Beyene, Biswanath Das, Dan Makumbi, Michael Olsen & Prasanna M. Boddupalli

  4. International Institute for Tropical Agriculture (IITA), Ibadan, PMB5320, Nigeria

    P. Lava Kumar

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  1. Sudha K. Nair
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  2. Raman Babu
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  3. Cosmos Magorokosho
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Correspondence to Sudha K. Nair.

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Communicated by M. Frisch.

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Nair, S.K., Babu, R., Magorokosho, C. et al. Fine mapping of Msv1, a major QTL for resistance to Maize Streak Virus leads to development of production markers for breeding pipelines. Theor Appl Genet 128, 1839–1854 (2015). https://doi.org/10.1007/s00122-015-2551-8

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  • DOI: https://doi.org/10.1007/s00122-015-2551-8

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