Large Scale Crop Housekeeping Genes And Wheat Seed-specific Genes Mining

Molecular hybridization experiments showed that in the cells, only a few of gene expression (5-10%). Expression of gene in the genome is divided into two categories:(1) class of cells is to maintain basic life activities necessary, said housekeeping gene, such as various kinds of histone gene.; 2) Another kind is to guide the synthesis of tissue specificity protein gene, have important effects on differentiation, said luxury gene.Housekeeping genes were constitutive expression in almost all cells and tissue-specific genes expressed in specific tissues. These genes specifically expressed or not will control the cell growth, differentiation, cell cycle regulation and homeostasis, cell aging, programmed cell death. The study on cell in different type and different differentiating phase could get important information of whole cell life process. Housekeeping genes maintenance of basic cellular functions, therefore they played a very important role in biology and physiology. They almost ubiquitously, stably and high expressed in all tissue/cell and had shorter introns, untranslated regions and coding sequences. There was little research achievement of graminaceous crop HK genes and few HK genes list at present.In this work, we collected 362 chips of 30 wheat experiments,409 chips of 79 rice experiments,250 chips of 37 maize experiments,440 chips of 45 barley experiments from PLEXdb (Plant Expression Database), large expressed sequence tags (ESTs) and Unigene classified database from NCBI (National Center for Biotechnology Information) of rice, wheat, maize, and barley. RMA (Robust multi-array average) treatment means format data of chips were used to screen stable expression by our method and classified ESTs were mapped and validated the candidate housekeeping genes.5% of all probes were selected as the most stably expression genes. ESTs-rich contigs validated the candidate HK gene. We get 3065 stably expressed probes from wheat chips and 3041 probe sequence. In EST enrichment,1097 sequence were significantly enriched (>20 hits); at the same time, there were 16 sequence didn’t find any EST. In tissue enrichment,2307 sequence had tissue annotation include 2143 non-redundant sequence and 1670 sequence were function annotated at last 734 sequence couldn’t find any annotation in protein database. The same analysis in barley,1124 sequence were detected from all chips,447 sequence had significantly EST enriched.1005 non-redundant sequence aligned protein targets and 928 sequence had tissue classification.Compare to wheat and barley, rice and maize had much higher mapping rate. There were only 1 sequence didn’t find EST hits. Sequence structure, distribution on chromosome, Gene Ontology (GO) annotation were analyzed to find the general character of the candidate HK gene. That the candidate HK genes (stably expression and ESTs-rich) has compacted gene structure:short exons and introns. Most HK genes have more than one multi-copy and short distance to centromere. The same time, a pipeline for reverse genetics to mining tissue-specific genes were provided, some interest gene were found for our research. As conclusion, we provide a sample and effective method to screen HK genes and tissue-specific genes by gene chips data produced from different laboratory. And the pipeline of this study could be applied to screen genome-wide function gene for other plants and animals. Graminaceous crop HK genes from this study will be useful for other genome-wide analyses in future research.