Near-isogenic lines (NILs) were applied for the first time to microarray analysis of 8,987 randomly selected expressed sequence tags (ESTs) aiming at screening rice genes associated with seed callus proliferation. Callus proliferation of the variety Koshihikari is poor, since its callus tends to become brown with time. We developed ten NILs that each had a chromosomal segment of the variety Kasalath on chromosome 1 in a Koshihikari background, to cover a region that contains two QTLs for subcultured callus color, qSc1-1 and qSc1-2. The existence of QTLs was verified through tissue culture of the seed calli of these NILs. mRNAs from the calli of three NILs that had the Kasalath allele in qSc1-1 and/or qSc1-2 were applied to microarray analysis. A comparison of expression profiles between Koshihikari and each NIL followed by Northern hybridization showed that 22 unique genes were induced and 15 unique genes were repressed in the calli of these Kasalath allele-containing NILs on chromosome 1. The results of a cis-element search using 500 bp of genomic sequence upstream of each gene suggested that the expression profiles of GA- and/or sugar-responsive genes were different between each NIL and Koshihikari, and that defense-related genes and genes that act negatively in metabolism were repressed in the NILs compared with Koshihikari.