Pioneer Hi-Bred International, Inc.
Calif. Inst. Biology Res.

Associations among inbred lines of maize using RFLP and DNA amplification technologies (AFLP and AP-PCR), and correlations with pedigree, F1 yield and heterosis
--Stephen Smith, Stella Luk, Bruno Sobral, Salah Muhawish, Johann Peleman and Marc Zabeau

Thirty-five and thirty-six of the thirty-seven inbred lines that previously have been reported upon (Smith et al., Theor. Appl. Genet. 80:833-840, 1990) for pedigree, F1 yield, heterosis and RFLP data were profiled using two DNA amplification procedures. These were Amplified Fragment Length Polymorphisms (AFLPs) or Selective Restriction Fragment Amplification (Zabeau and Vos, European Patent Application No. 0 534 858 A1, 1993) and Arbitrarily Primed Polymerase Chain Reaction (AP-PCR), (Welsh and McClelland, Nucl. Acids Res. 18:7213-7218, 1990).

Twenty AFLP primers were used to score 347 bands. Forty primers were used in AP-PCR and 258 bands were scored. Correlations for pairwise distances between inbreds from AFLP data and other data were r = 0.91 (F1 yield), r = 0.84 (heterosis), r = 0.90 (pedigree), r = 0.91 (RFLP) and r = 0.88 (AP-PCR). Correlations for pairwise distances between inbreds from AP-PCR data and other data were r = 0.92 (F1 yield), r = 0.84 (heterosis), r = 0.85 (pedigree) and r = 0.85 (RFLPs). As would be expected from the correlation data, cluster analyses of inbred lines using distance data from AFLP and AP-PCR resulted in associations of inbreds that were in close agreement with those generated from RFLP and pedigree distance (1 - Malecot Coefficient of Similarity) data.

AP-PCR and AFLP are different methods to sample DNA sequence diversity and they possibly differ in the regions of the genome that are targeted by RFLP probes made using methylation sensitive enzymes. Nevertheless, these data show that different perspectives on inbreds that have degrees of relatedness usually encountered in breeding programs are in concurrence. Therefore, data from these arbitrary primer DNA amplification methods further support that molecular marker data can provide useful information on inbred identities and relationships for the support of plant breeding. It will not be necessary to generate data from several marker technologies; technological choice can be made as suits the issues and circumstances (Ragot and Hoisington, DA, Theor. Appl. Genet. 86:975-984, 1993). 

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