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In order to understand molecular basis of cross-fertilized kel advantage and heterosis, improved differential display of mRNA was used in this study to analyze alterations in gene expression between cross-fertilized and self-fertilized kels at 2, 4, 6, 8, 10 and 12 days after pollination (DAP) by using 3 wheat hybrids with different level of heterosis. Four patts of differential expression were observed: (i) bands observed in cross-fertilized kels but not in self-fertilized kels (BCnS); (ii) bands occurring in only self-fertilized kels but not in cross-fertilized kels (BSnC); (iii) cDNA over-expressed in cross-fertilized kels compared to self-fertilized kels (OEC);(iv) cDNA under-expressed in cross-fertilized kels compared to self-fertilized kels (UEC). Further analysis showed that BCnS is positively correlated with heterosis, but BSnC is negatively correlated with heterosis. Four differentially expressed cDNA fragments were verified by reverse-north blot and sequence homology search in GenBank showed that one of them was new sequences; the other exhibited higher similarity to NBS-LRR type resistance protein, 1;6-bisphosphatase and photosystem Ⅱ chlorophyll a-binding protein psbB, respectively, which indicated diverse pathways may be involved in heterosis formation.