ABSTRACT. The basic leucine zipper (bZIP) genes encode transcription factors involved in the regulation of various biological processes. Similar to WRKY, basic helix-loop-helix, and several other groups of proteins, the bZIP proteins form a superfamily of transcription factors that mediate plant stress responses. In this review, we present the roles of bZIP proteins in multiple biological processes that include pathogen defense; responses to abiotic stresses; seed development and germination; senescence; and responses to salicylic, jasmonic, and abscisic acids in rice. We also examined the characteristics of the bZIP proteins and their genetic composition. To ascertain the evolutionary changes in and functions of this supergene family, we performed an exhaustive comparison among the 89 rice bZIP genes that were previously described and those more recently listed in the MSU Rice Genome Annotation Project Database using a Hidden Markov Model. We excluded 3 genes from the list, resulting in a total of 86 bZIP genes in japonica rice.

ABSTRACT. Plant hormones play important roles in the crosstalk between biotic and abiotic stresses in rice throughout its entire growth period. However, these interactions are not completely understood. In this study, the physiological performance of rice seedlings under a single stress and a sequential combination of various stresses (intercross stress) was determined. We found that catalase, superoxide dismutase, and peroxidase activities and malondialdehyde were highly regulated by intercross stresses. Furthermore, the expression levels of pathogenesisrelated genes and drought stress-related genes under various treatments were analyzed. We demonstrated that under drought-disease intercross stress, the expression levels of the PR4, PAL, and Cht-1 genes were significantly upregulated, while under salt-disease intercross stress, the expression levels of the PR1a, PBZ1, Gns1, and Cht-1 genes underwent significant changes. Regardless of the type of intercross stress, the expression of LOX-RLL was significantly affected. We also showed that the expression of drought stress-related genes OsSKIPa, OsNADPH1, JRC0594, and OsGL1-2 was significantly regulated, suggesting that these genes play important roles in the interaction between biotic and abiotic stresses. We, therefore, conclude that the interactions between various types of biotic and abiotic stresses vary in a complex pattern and would require further in-depth investigation.

Genomic imprinting is an epigenetic phenomenon by which certain genes display monoallelic expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here we identified, with a high level of confidence, 208 imprinted candidates from rice. Imprinted genes of rice showed limited association to the transposable elements, which is contrast to the findings in Arabidopsis. Generally, imprinting of rice is conserved within species, but intraspecific variations were confirmed here. Imprinting between cultivated rice and wild rice are likely similar. The imprinted genes of rice do not show significant selective signatures overall, which suggests that domestication imposes limited evolutionary effects on genomic imprinting of rice. Though the conservation of imprinting in plants is limited, here we prove that some loci tend to be imprinted in different species. In addition, our results suggest that differential epigenetic regulation between parental alleles can be established either prior to or post-fertilization. The imprinted 24-nt small RNAs, but not the 21-nt ones, likely involve the regulation of imprinting in an opposite parental-allele targeting manner. Together, our findings suggest that regulation of imprinting can be very diverse, and genomic imprinting as well as imprinted genes have essential evolutionary and biological significance.