Molecular variation and F1 performance among strains of the sweet corn inbred P39

Some maize (Zea mays L.) inbreds produce morphological variants at unexpectedly high frequencies. In some cases, heterosis has been observed in crosses between variants and the progenitor inbred. Causes of such variants and resulting heterosis are unclear. Unique materials for addressing these questions me strains of the sweet corn inbred P39, Several morphologically distinct strains of P39 have been identified. Molecular variation of P39 strains was analyzed by means of three types of molecular markers, including four probes that hybridize to multiple sequences, 78 single copy restriction fragment length polymorphisms (RFLP), and 671 amplified fragment length polymorphisms (AFLP). All crosses were made among seven P39 strains. Ear weight and plant and ear height of the crosses were measured in 2 yr with one location and eight replications per year. Ten-ear weight ranged from 0.49 to 0.84 kg. Significant levels of molecular variation were observed among the strains. Summing polymorphisms per inbred pair over the multiple sequence probes resulted in a range among pairwise comparisons of 0 to 18. RFLPs ranged from 6 (7%) to 28 (35%) polymorphisms per inbred pair. AFLPs between inbred pairs ranged from 3 (0.5%) to 145 (22%). Ten-ear weight was correlated with the number of polymorphisms between pairs of strains for the multiple copy probes. RFLP variation was correlated with plant height (r = 0.75**) and ear height (r = 0.91**) but not ear weight. AFLP variation was correlated with ear weight (r = 0.82**). While initial isolation of some of the P39 strains was due to a mutation at a single gene, the amount of molecular variation was unexpectedly high. The molecular variation and changes in combining ability indicates the occurrence of alterations throughout the genome.