E3 ubiquitin ligase plays a central role in determining specificity of the ubiquitination system by selecting appropriate candidate proteins. Compared with other eukaryotic species there are significantly more U-box protein-encoding genes in plant genome. The rice genome contain 77 U-box-type E3 encoding genes. The 77 members of the rice plant U-box (PUB) E3 family can be placed into 8 major groups based on their domain organizations. In this study, we generate and analyze phylogenomic data integrating anatomical expression patterns consisting of anatomical and stress responsive expression patterns base on 1150 affymetrix arrays to the phylogenic tree of rice plant U-box E3 family. Then, we highlighted 8 genes in subfamilies II (5) and VII (3) of E3 ligases showing significant upregulation in water stress conditions such as drought and high concentration of salt stress. We further developed functional gene network meditated by E3 ligases and refined the components in network by integrating gene expression patterns in response to drought and salt stresses. We expect that our analysis will be a useful platform to facilitate the functional identification for each of U-box E3 family.

Cryopreservation has been known as an efficient method for long-term preservation of clonally propagated plants, and several cryopreservation methods have been developed. Among them, a droplet-vitrification method for potato using axillary shoot tips in vitro has been established previously. In this study, we have optimized the procedure in which explants were submitted to a step-wise pre-culture in liquid sucrose-enriched medium (0.3 and 0.7 M for 7 and 17 h, respectively). The pre-cultured explants were dehydrated with PVS3 (w/v, 50% glycerol + 50% sucrose) for 90 min or modified PVS2 vitrification solution (w/v, 37.5% glycerol + 15% DMSO + 15.0% ethylene glycol + 22.5% sucrose) for 30 min. This two dehydration solutions produced post-cryopreservation regeneration percentages of 57.2% and 80.9%, respectively. We also compared a new post-culture medium (0.1 mg L ･ -1 GA3, 0.1 mg L ･ -1 kinetin) with the conventional one (0.15 mg L ･ -1 IAA, 0.2 mg L ･ -1 zeatin, 0.05 mg L ･ -1 GA3); the shooting initiation rates were 80.9% and 43.5%, respectively. The results suggest that the modified droplet-vitrification protocol described in this study is more effective, easier to implement, and more economical than the droplet-vitrification protocols currently used for potato.

TILLING (Targeting Induced Local Lesions IN Genomes) is broadly regarded as an excellent methodology for reverse genetics applications. Approximately 15,000 M3 TILLING lines have been developed via the application of gamma-ray irradiation to rice seeds (cv. Donganbyeo), followed by subsequent selections. In an effort to evaluate the genetic diversity of the TILLING population, we have employed the AFLP multiple dominant marker technique. A total of 96 (0.64%) TILLING lines as well as Donganbyeo were selected randomly and their genetic diversity was assessed based on AFLP marker polymorphisms using 5 primer combinations. An average of 100.4 loci in a range of 97 to 106 was detected using these primer combinations, yielding a total of 158 (31.4%) polymorphic loci between Donganbyeo and each of the 96 lines. A broad range of similarity from 80% to 96% with an average of 89.4% between Donganbyeo and each of the 96 lines was also observed, reflecting the genetic diversity of the TILLING population. Approximately 28 polymorphic loci have been cloned and their sequences were BLAST-searched against rice whole genome sequences, resulting in 20 matches to each of the gene bodies including exon, intron, 1 kb upstream and 1 kb downstream regions. Six polymorphic loci evidenced changes in the coding regions of genes as compared to the rice pseudomolecules, 4 loci of which exhibited missense mutations and 2 loci of which exhibited silent mutations. Therefore, the results of our study show that the TILLING rice population should prove to be a useful genetic material pool for functional genomics as well as mutation breeding applications.