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Genetic diversity analysis of elite European maize (Zea mays L.) inbred lines using AFLP, SSR, and SNP markers reveals ascertainment bias for a subset of SNPs

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Abstract

Recent advances in high-throughput sequencing technologies have triggered a shift toward single-nucleotide polymorphism (SNP) markers. A systematic bias can be introduced if SNPs are ascertained in a small panel of genotypes and then used for characterizing a larger population (ascertainment bias). With the objective of evaluating a potential ascertainment bias of the Illumina MaizeSNP50 array with respect to elite European maize dent and flint inbred lines, we compared the genetic diversity among these materials based on 731 amplified fragment length polymorphisms (AFLPs), 186 simple sequence repeats (SSRs), 41,434 SNPs of the MaizeSNP50 array (SNP-A), and two subsets of it, i.e., 30,068 Panzea (SNP-P) and 11,366 Syngenta markers (SNP-S). We evaluated the bias effects on major allele frequency, allele number, gene diversity, modified Roger’s distance (MRD), and on molecular variance (AMOVA). We revealed ascertainment bias in SNP-A, compared to AFLPs and SSRs. It affected especially European flint lines analyzed with markers (SNP-S) specifically developed to maximize differences among North American dent germplasm. The bias affected all genetic parameters, but did not substantially alter the relative distances between inbred lines within groups. For these reasons, we conclude that the SNP markers of the MaizeSNP50 array can be employed for breeding purposes in the investigated material. However, attention should be paid in case of comparisons between genotypes belonging to different heterotic groups. In this case, it is advisable to prefer a marker subset with potentially low ascertainment bias, like in our case the SNP-P marker set.

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Acknowledgments

We thank H.-P. Piepho and K. J. Schmid for their useful comments and discussion and the two anonymous reviewers for their valuable suggestions. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed—Synergistic plant and animal breeding (FKZ: 0315528d). E. Frascaroli was supported by the Deutscher Akademischer Austauschdienst (DAAD) grant A/11/04103.

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Authors and Affiliations

  1. Department of Agroenvironmental Sciences and Technologies, University of Bologna, Viale Fanin 44, 40127, Bologna, Italy

    Elisabetta Frascaroli

  2. Institute of Plant Breeding, Seed Science, Population Genetics, University of Hohenheim, 70593, Stuttgart, Germany

    Tobias A. Schrag & Albrecht E. Melchinger

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  1. Elisabetta Frascaroli
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  2. Tobias A. Schrag
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  3. Albrecht E. Melchinger
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Correspondence to Albrecht E. Melchinger.

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Communicated by M. Xu.

Elisabetta Frascaroli and Tobias A. Schrag contributed equally to this work.

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Frascaroli, E., Schrag, T.A. & Melchinger, A.E. Genetic diversity analysis of elite European maize (Zea mays L.) inbred lines using AFLP, SSR, and SNP markers reveals ascertainment bias for a subset of SNPs. Theor Appl Genet 126, 133–141 (2013). https://doi.org/10.1007/s00122-012-1968-6

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