Identification of essentially derived varieties obtained from biparental crosses of homozygous lines: I. Simple sequence repeat data from maize inbreds

Genetic distances (GDs) based on molecular markers such as simple sequence repeats (SSRs) have been proposed as an appropriate tool to assess the genetic conformity between putative essentially derived varieties (EDVs) and their initial varieties (IVs). However, for maize (Zea mays L.) and other crops, no consensus has been reached regarding GD thresholds for identification of EDVs, mainly because reliable benchmark data are lacking. Our objectives were to (i) determine the variation in the parental contribution (p) to the genome of homozygous progeny lines derived in recycling breeding programs; (ii) investigate the power of SSR-based GD estimates for discriminating between progeny lines derived from F₂, BC₁, and BC₂ populations (BC = backcross); (iii) compare theoretical and simulated results of a companion study to our experimental data; and (iv) draw conclusions with regard to various EDV thresholds suggested hitherto. A total of 220 European and U.S. maize inbred lines comprising 163 triplets were genotyped with 100 uniformly distributed SSRs. A triplet consisted of one F₂-, or BC₁-derived progeny line and both parental lines. The SSR-based estimates of p varied from 0.25 to 0.74 for F₂-derived lines with a mean (0.49) close to the expectation (0.50), and ranged from 0.51 to 0.80 for BC₁-derived lines with a mean (0.66) significantly smaller than the expectation (0.75). Relative to the variation in p, the GD between progeny lines and parents was little influenced by the variation in the GD between the parents, particularly for BC₁-derived lines. Suggested GD thresholds for EDVs resulted in different Type I (α) and Type II (β) errors, depending on the germplasm pool. Considerable overlaps in the GD frequency distributions of F₂-, BC₁-, and BC₂-derived lines indicate that the resolution to discriminate these types of progeny is poor unless a much larger number or a set of extremely polymorphic markers is used.