RAPD analysis of two pairs of sulse/su1Se near-isogenic lines for the identification of chromosomal regions affecting the sugary enhancer phenotype

Sweet corn with the sugary enhancer (se) phenotype is traditionally characterized by elevated sugar content, slow dry down of kernels, more wrinkled pericarp of mature dried seeds and lighter kernel color. The objective of our study was to identify chromosomal regions which affect these characteristics using RAPD analysis of near isogenic lines (NILs). Two independent pairs of near isogenic lines (IL678a and IL451b) were compared. The original su1se line IL677a was used as a reference. Three hundred and forty arbitrary, 10-mer primers were used to amplify genomic DNA extracted from the different genotypes. Three of the 340 primers generated amplification products which differed between the su1se genotypes and their su1Se isolines. The association between the RAPD discrete bands and the sugary enhancer phenotype was confirmed by analyzing 16 additional su1se and su1Se sweet corn inbreds. We mapped two of these markers to chromosome 6 and one of them to chromosome 3 by the analysis of their segregation in an sex Se F(2:3) population. The marked chromosome 3 region had been previously reported as being associated with kernel sugar content and taste while the chromosome 6 region was associated with both maltose concentration and kernel color. The results indicate that more than one locus may affect the sugary enhancer phenotype. The complications in phenotypic selection and the advantage of marker assisted breeding (MAB) for the se phenotype are demonstrated.