In addition to those involved in starch and redox homeostasis that have been reference 4 detailed above, genes involved in additional biological processes such as cell rescue defense, hormone response, and protein bio synthesis and degradation are also differentially expressed between CSSL50 1 and Asominori. It is note worthy that most genes involved in these pathways did not change significantly in terms of fold changes. Such a result, however, is similar to a previous cDNA array study of grain chalkiness under high temperature. The subtle change in gene expression and the significant consequence in endosperm chalkiness formation seems to suggest that rice grain filling is a fine tuned process which can be easily affected by genetic variations as well as fluctuations in environmental conditions.

We there fore depicted a possible gene network according to the microarray data. As shown in Figure 6, in addition to the enhanced carbohydrate metabolisms for starch and suppressed non starch polysaccharides and an elevated ROS homeostasis, changes of gene expression levels in four additional pathways may also play roles in chalki ness formation of rice grains, genes that are known to be involved in biotic and abiotic stress responses, encoding those such as the NB ARC domain contain ing proteins, the leucine rich repeat family proteins and harpin induced proteins, as well as heavy metal binding proteins and proteins involved in wound, senescence, light, UV and other stress responses, Genes involved in ROS signaling such as phospholipase D, phosphatases, Ca2 Ca2 binding protein, G pro teins, and Ras proteins, Hormone biosynthesis and signaling related genes, such as auxin, BR, GA, ethylene and cytokinin, Genes involved in protein synth esis, such as those encoding ribosomal S3, S9, S11, L10a 1 and L18 subunits and alanyl, aspartyl, lysyl, phenylalanyl tRNA synthetases and degradation, such as those encoding F box, protease, peptidase, oligopeptidase, carboxy peptidase, C terminal hydrolase and transamidase.

Therefore, the formation of grain chalkiness likely involves alterations in multiple biolo gical processes and multiple genetic pathways. For confirmation, 21 transcripts were randomly cho sen for semi quantitative RT PCR analysis. The RT PCR results correlate well with the microarray data, thus validating our microarray data.

Discussion CSSL50 GSK-3 1 is an ideal material for exploring the molecular basis of rice grain chalkiness Grain endosperm chalkiness is a complex quantitative genetic trait and is controlled by multiple factors. Pre vious studies showed that there are as many as 42 QTLs that may contribute to the percentages of grains with chalkiness and degrees of endosperm chalkiness. These genes spread among 10 rice chromosomes as being located using seven different genetic populations.