Expression Profiling Of Genes For Cold Tolerance In Cassava(Manihot Esculenta Crantz)

Cassava(Manihot esculenta Crantz), a species in Euphorbiaceae, the third potato in the world as well as rank the sixth staple food crop in the world, and it already became an important source of biofuel and industrial starch in China. Cold tolerance of cassava varieties is a special constraints to commercial plantation in higher latitude region of China. Up to now, there were a few reports on cold tolerance of cassava although there were many researches on cold stress mechanism in other crops. Expression profiling based on next-generation sequencing technology known as a powerful tool, here, we choice a cold tolerant variety SC124to take cold treatment in chamber with12samples. Expression profiling sequencing was used for screen of genes response to cold. Another transcriptome sequence data from mixture sample was added into the analysis. All tags and their expression richness of transcripts have been revealed by3'-end sequencing, and combining to RNA-seq annotation we performed the functional annotation of the genes for cold response. The essential results shown as the following:SC124, which has the better ability to cold stress, was cold injury induced, then, lobus cardiacus, function leaves and roots was sampling separately at6h,24h,48h. Also the lobus cardiacus, function leaves and roots without low temperature treatment was sampling. Every sample has a tag library which was sequenced with Solexa method separately. Every tag from each tag library was analyzed. We assembled the mixed samples'tag and got the transcripts that was annotated later. The statistic analysis result shows that there is difference not only in numbers but also in species between samples with low temperature treatment and those without. A large different expression exists in each part at different time. We select some genes that has high expression level in low temperature treatment, and these genes are related to cold stress.Through the bioinformatics analysis, we got conclusions as follow:(1) Throgh sequencing of the gene expression profile of12samples, including SC124in low temperature treatments and the control, distinct tagas were found between102804and189320, among which there are4.45%high expression level tags which copy number is above100,3.84%tags which copy number is between51and100,8.08%tags which copy number is21and50, around9,43%tags which copy number is between11and20, around14.12%tags which copy number is between5and10. Those tags which copy number is below5are very rich in species and represents60.05%of the total mRNA.(2) Compare the differential expression genes of tip leaves,function leaves and tuber roots at different time under cold stress, we found that506-715genes of tip leaves were up regulated at the three times, while812-1425were down regulated.500-746genes of function leaves were up regulated at the three times, while553-1043were down regulated.439-806were up regulated at the three times, while500-862were down regulated at the three times.That means when cassava is under cold stress, some genes that are in high expression level play a important role in cold stress.(3) Expression pattern analysis showed the expression pattern of clustering results of young leaves, function leaves and roots and the trend expression of important genes. By comparion of the expression clust result in three different parts of cassava, it is found that there are more down regulated expression in young leaves while more up regulated expression in function leaves(4) GO analysis of light absorption in photosynthesis, photosynthesis, light harvesting, chlorophyll biosynthetic process, pigment biosynthetic process, pigment metabolic process, regulation of catalytic activity, response to osmotic stress, response to oxidative stress, response to auxin stimulus, lipid biosynthetic process, lipid metabolic process, oxidative phosphorylation.(5) Genes that has different expression level in cold stress and low temperature stress were analyzed by pathway method and the significant metabolic pathways are Photosynthesis-antenna protein, porphyrins and chlorophyll metabolism, photosynthesis, metabolic pathway, the oxidation mainly in the mitochondria in photosynthetic organisms phosphorylation, solid carbon, plant hormones biosynthesis, carotenoids synthesis of alpha linolenic acid metabolism, ABC transshipment..(6) We got a series of differential expression genes that can express in cold stress and low temperature stress. They are in rich Glycine protein, gibberellic acid control protein, UDP-glycosyl transferase, calcium ions transporter, CIPK homologous gene, half of lactose shift enzyme, zinc ion and copper ions transporter, plasma membrane H+-ATPase, APX2.