Genetic similarities among winter wheat cultivars determined on the basis of RFLPs, AFLPs, and SSRs and their use for predicting progeny variance

The efficiency of breeding programs could be increased by predicting the prospects of crosses for line development before producing and testing lines derived from them. In this study, we (i) assessed the level of genetic diversity among German and Austrian winter wheat (Triticum aestivum L.) cultivars using 117 restriction fragment length polymorphism (RFLP) probes, 16 amplified fragment length polymorphism (AFLP) primer combinations, and 21 simple sequence repeat (SSR) primer pairs, (ii) investigated the correlation between coancestry (f) and genetic similarity (GS) estimated from molecular markers, and (iii) evaluated the use of f and GS for predicting the genetic variance (σ(g)/²) within sets of 22 F(4:n) (n = 7 or 8) lines derived from 30 crosses between these winter wheat cultivars. The average polymorphic information content (PIC) for polymorphic bands was not significantly different between the three marker systems (0.30 ≤ PIC ≤ 0.33), whereas the marker index was low for RFLPs and SSRs but high for AFLPs. Estimates of f between all 55 cultivar combinations ranged from 0.01 to 0.53. GS-values varied between 0.52 and 0.89 for RFLPs, between 0.40 and 0.83 for AFLPs, and between 0.16 and 0.91 for SSRs. The Mantel Z test statistic revealed no common pattern between the four dendrograms obtained by cluster analyses. Significant (P < 0.05) correlations among f, GS-RFLP, GS-AFLP, and GS-SSR were detected only for related parent combinations (f ≥ 0.10). For all seven traits analyzed, estimates of σ(g)/² were not significantly associated with any measure of GS between parents. On the basis of these results, we recommend AFLPs for fingerprinting wheat cultivars. However, predicting the progeny variance σ(g)/² remains an unsolved problem.