Plant & Animal Genome VI Conference

P95

EVALUATION OF AFLP IN SUGARBEET (Beta vulgaris L.)

1. Novartis Seeds AB, , Box 302, S-261 23 Landskrona, Sweden
2. Department of Genetics, Lund University, Sölvegatan 29, S-223 62 Lund, Sweden

AFLP markers were evaluated for their usefulness, reproducibility and robustness in analysis of sugarbeet and wild relatives. Accessions of ten different sugarbeet breeding lines and five wild beets were screened with 256 primer combinations. Of 11309 investigated loci, 96.4% were polymorphic among the accessions, with the number of polymorphisms per primer combination ranging from 10 to 111. A strong positive correlation was found between the number of polymorphisms and the AT content in the selective bases of the primer combination. Random subsets of primer combinations were used to produce genetic distance trees. Permutation tests showed that ten randomly selected primer combinations is sufficient to obtain the correct tree for wild beets with more than 95% probability. For the sugarbeet lines, 20 randomly selected primer combinations gave support values for the different branches ranging from 52% to 99%. The reproducibility of AFLP was investigated for seven primer combinations by repeated analysis of all steps from DNA isolation to data scoring. The overall reproducibility for 5088 comparisons was 97.6%. Re-evaluation of the non-consistent bands revealed 0.3% typing errors, 1.5% interpretation errors due to undistinguished band levels, and 0.5% errors intrinsic to the system, with clear band differences between replications. The robustness to genotyping errors was investigated by including an artificial 1:1 mixture of DNA from two sugarbeet lines in the screen for polymorphisms. For 3160 situations with a polymorphism between the two lines, 0.2% genotyping errors was found, where the expected band was absent in the mixture. These results show that AFLP is a powerful and robust marker system for most applications in sugarbeet.