Theoretical and Applied Genetics

, Volume 128, Issue 9, pp 1839–1854

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

  • Sudha K. Nair
  • Raman Babu
  • Cosmos Magorokosho
  • George Mahuku
  • Kassa Semagn
  • Yoseph Beyene
  • Biswanath Das
  • Dan Makumbi
  • P. Lava Kumar
  • Michael Olsen
  • Prasanna M. Boddupalli
Original Paper

DOI: 10.1007/s00122-015-2551-8

Cite this article as:
Nair, S.K., Babu, R., Magorokosho, C. et al. Theor Appl Genet (2015) 128: 1839. doi:10.1007/s00122-015-2551-8

Abstract

Key message

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 F2 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.

Supplementary material

122_2015_2551_MOESM1_ESM.tif (1.7 mb)
Supplementary material 1 (TIFF 1717 kb)
122_2015_2551_MOESM2_ESM.pdf (237 kb)
Supplementary material 2 (PDF 237 kb)
122_2015_2551_MOESM3_ESM.pdf (334 kb)
Supplementary material 3 (PDF 333 kb)

Funding information

Funder NameGrant NumberFunding Note
BMGF
    MAIZE CRP

      Copyright information

      © Springer-Verlag Berlin Heidelberg 2015

      Authors and Affiliations

      • Sudha K. Nair
        • 1
      • Raman Babu
        • 1
      • Cosmos Magorokosho
        • 2
      • George Mahuku
        • 3
      • Kassa Semagn
        • 3
      • Yoseph Beyene
        • 3
      • Biswanath Das
        • 3
      • Dan Makumbi
        • 3
      • P. Lava Kumar
        • 4
      • Michael Olsen
        • 3
      • Prasanna M. Boddupalli
        • 3
      1. 1.International Maize and Wheat Improvement Center (CIMMYT), ICRISAT CampusGreater HyderabadIndia
      2. 2.International Maize and Wheat Improvement Center (CIMMYT)HarareZimbabwe
      3. 3.International Maize and Wheat Improvement Center (CIMMYT), ICRAF CampusNairobiKenya
      4. 4.International Institute for Tropical Agriculture (IITA)IbadanNigeria

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