AFLP–SSR maps of maize × teosinte and maize × maize: comparison of map length and segregation distortion

Two genetic linkage maps of Zea mays were constructed: one population comprised 94 F2 individuals of a dent ‘B64’ × teosinte (Z. mays ssp. huehuetenangensis) cross while the second consisted of 94 F2 individuals of a ‘B64’ × Caribbean flint ‘Na4’ cross. The level of polymorphism was higher in the ‘B64’ × teosinte combination than the ‘B64’ × ‘Na4’ combination. In the ‘B64’ × teosinte cross, a total of 338 amplified fragment length polymorphism (AFLP) and 75 simple sequence repeat (SSR) markers were mapped to 10 chromosomes, which covered 1402.4 cM. In the ‘B64’ × ‘Na4’ cross, a total of 340 AFLP and 97 SSR markers were mapped to 10 chromosomes, covering 1662.8 cM. Segregation distortion regions were found on chromosomes 4, 5 and 8 in the ‘B64’ × teosinte cross and on chromosome 9 in the ‘B64’ × ‘Na4’ cross. Comparison of the two maps revealed that the maize × teosinte map was 11.5% shorter than the maize × maize map. The maps generated in this study may be useful to identify genes controlling flooding tolerance.