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The teosinte Zea nicaraguensis forms constitutive aerenchyma in the root cortex as observed in flooding tolerant wetland plants. We have previously identified a quantitative trait locus (QTL) controlling aerenchyma formation under non-flooding conditions on chromosome 1 (Qaer1.06) using 214 individuals of a maize Mi29 × Z. nicaraguensis BC2F1 population. The present studies objective was to increase the marker density around the Qaer1.06 locus, which is essential for the development of near-isogenic lines possessing the aerenchyma-forming gene with only a small region of the Z. nicaraguensis chromosome segment. A survey of 62 SSR and 38 insertion/deletion (INDEL) markers identified a total of 36 useful markers in the region of interest. These were selected for the construction of a linkage map in a 214 individual BC2F1 and a 123 individual BC4F1 population from a cross between Mi29 × Z. nicaraguensis. Using the BC4F1 population, we performed QTL mapping and the results indicated that a QTL for aerenchyma formation under non-flooding condition was located on chromosome 1 (bin 1.05) at a position that is near to Qaer1.06. The markers obtained here should be useful for the development of high quality near-isogenic lines possessing the Qaer1.05-6.

High-density linkage map around the root aerenchyma locus Qaer1.06 in the backcross populations of maize Mi29 * teosinte "Zea nicaraguensis"