Utilization of heterosis has greatly increased the productivity of many crops worldwide. Although tremendous progress has been made in characterizing the genetic basis of heterosis using genomic technologies, molecular mechanisms underlying the genetic components are much less understood. Allele-specific expression (ASE), or imbalance between the expression levels of two parental alleles in the hybrid, has been suggested as a mechanism of heterosis. Here, we performed a genome-wide analysis of ASE by comparing the read ratios of the parental alleles in RNA-sequencing data of an elite rice hybrid and its parents using three tissues from plants grown under four conditions. The analysis identified a total of 3,270 genes showing ASE (ASEGs) in various ways, which can be classified into two patterns: consistent ASEGs such that the ASE was biased toward one parental allele in all tissues/conditions, and inconsistent ASEGs such that ASE was found in some but not all tissues/conditions, including direction-shifting ASEGs in which the ASE was biased toward one parental allele in some tissues/conditions while toward the other parental allele in other tissues/conditions. The results suggested that these patterns may have distinct implications in the genetic basis of heterosis: The consistent ASEGs may cause partial to full dominance effects on the traits that they regulate, and direction-shifting ASEGs may cause overdominance. We also showed that ASEGs were significantly enriched in genomic regions that were differentially selected during rice breeding. These ASEGs provide an index of the genes for future pursuit of the genetic and molecular mechanism of heterosis.

Hybrid sterility frequently occurs in crosses between indica and japonica subspecies of Asian cultivated rice. In this study, we investigated the cytological processes involved in formation and development of male and female gametes as well as their interactions in fertilization, using an indica/japonica hybrid in comparison with an indica/indica hybrid. It was found that more than 50% of the microspores generated in the indica/ japonica hybrid could not develop into functional pollen. The abortion rate of microspores in the indica/japonica hybrid was much higher than that in the indica/indica hybrid. Abortive embryo sacs made up roughly 70% of the embryo sacs examined in the indica/japonica hybrid, which was also much higher than that detected in the indica/indica hybrid. Moreover, the amount of pollen adherence on stigmas of the indica variety upon handpollination with pollen from the japonica variety was much lower than the indica/indica pollination, and the number of pollen adhered on the stigmas by natural selfpollination was much greater in the indica/indica hybrid than in the indica/japonica hybrid. The indica/japonica hybrid also encountered difficulties in pollen tube growth after pollination, and the fertilization rate of the indica/ japonica hybrid was much lower than that of the indica/ indica hybrid. These results clearly illustrate the complexity of the mechanisms underlying inter-subspecific hybrid sterility in rice involving both pre-and post-zygotic reproductive isolation mechanisms.

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