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Analysis of effectiveness of R1-nj anthocyanin marker for in vivo haploid identification in maize and molecular markers for predicting the inhibition of R1-nj expression

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R1-nj anthocyanin marker inhibition is highly frequent in tropical maize germplasm considerably affecting efficiency of haploid identification. Molecular markers reliably differentiating germplasm with anthocyanin color inhibitor have been identified in this study.

Abstract

The R1-Navajo (R1-nj) color marker facilitates easy and quick identification of haploid kernels at the seed stage during in vivo haploid induction process in maize. However, the Navajo phenotype can be completely suppressed or poorly expressed in some germplasm, making it impossible or inefficient to identify haploids at the seed stage. In this study, we characterized the expression of R1-nj marker in a large array of tropical/subtropical inbred lines, breeding populations and landraces by crossing with the R1-nj-based tropicalized haploid inducer. There was a high frequency of inhibition of the Navajo phenotype in the maize inbred lines, which are used in tropical breeding programs. Genome-wide association mapping showed that the C1 anthocyanin regulatory locus is the most significant genetic factor influencing inhibition of the Navajo phenotype. Molecular marker assays were designed based on polymorphism in the C1 vs C1-I alleles. Analysis of a set of 714 inbred lines demonstrated that a combination of two gene-specific markers—8 bp C1-I InDel and C1-I SNP—could predict with high accuracy the presence of anthocyanin color inhibition in the germplasm analyzed. Information generated in this study aids in making informed decisions on the constitution of source populations for doubled haploid (DH) line development in tropical germplasm, particularly those derived from elite maize lines from CIMMYT. The C1-I gene-specific molecular markers identified and validated will facilitate high-throughput and cost-effective evaluation of a large pool of germplasm for the presence of the dominant color inhibitor in maize germplasm.

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Acknowledgments

The authors gratefully acknowledge the financial support received from the CGIAR Research Program (CRP) MAIZE, Limagrain, and the MASAGRO project funded by the Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA). The R1-nj-based tropical haploid inducers used in this study were the products of collaborative research efforts between CIMMYT and the University of Hohenheim, Germany. The assistance provided by Juan Burgueno for data analysis, and Miguel Mellado for the preparation of figures, is gratefully acknowledged.

Conflict of interest

The authors declare that no competing interests exist.

Ethical standards

The authors declare that the experiments comply with the laws of Mexico.

Author information

Authors and Affiliations

  1. International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico D.F, Mexico

    Vijay Chaikam, Leocadio Martinez & Jyothsna Tejomurtula

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

    Sudha K. Nair & Raman Babu

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

    Prasanna M. Boddupalli

Authors
  1. Vijay Chaikam
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  2. Sudha K. Nair
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  3. Raman Babu
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  4. Leocadio Martinez
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  5. Jyothsna Tejomurtula
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  6. Prasanna M. Boddupalli
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Corresponding author

Correspondence to Prasanna M. Boddupalli.

Additional information

Communicated by Xianchun Xia.

Electronic supplementary material

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Supplementary Table 1 Data on R1-nj marker expression in endosperm and embryo in the progenies of tropical inbreds crossed with a R1-nj-based inducer

Supplementary Table 2 List of inbred lines with complete anthocyanin color inhibition and the corresponding C1-I marker genotypes

Supplementary Fig. 1 Genome-wide association study (GWAS) based on ~410 K GBS-SNPs in 897 lines for (a) endosperm color intensity; (b) endosperm area marked; (c) embryo inhibition; and (d) embryo color intensity established C1 as the major gene controlling color expression. The most significant SNP (S9_9741377) on chromosome 9 was localized within the C1 locus.

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Supplementary material 3 (PDF 162 kb)

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Chaikam, V., Nair, S.K., Babu, R. et al. Analysis of effectiveness of R1-nj anthocyanin marker for in vivo haploid identification in maize and molecular markers for predicting the inhibition of R1-nj expression. Theor Appl Genet 128, 159–171 (2015). https://doi.org/10.1007/s00122-014-2419-3

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  • DOI: https://doi.org/10.1007/s00122-014-2419-3

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