Transcriptome Comparison Of Cold Tolerance Traits In Weedy Rice And Cultivated Rice And Annotation On Cold Tolerance Gene

Rice is the third largest food crop worldwide after maize and wheat,of which cold damage has a serious impact on the growth and development of rice.In this study,we analyzed the transcriptomics and expression of differential genes of different cold tolerance weedy rice and cultivated riceunder cold stress through RNA-Seq technology.Besides,we performed real-time fluorescence quantitative PCR and semi-quantitative RT-PCR of different genes,and investigated the relationship between conductivity and cold tolerance of the four rice crops as above.The main research results are as follows:1.The relative electrical conductivity(REC)of the weedy rice 03-35,weedy rice 03-26,cultivated rice 131 and cultivated rice 9311 were determined after cold treatment.The result was that:REC(cultivated rice 131)<REC(weedy rice 03-35)<REC(weedy rice 03-26)<REC(cultivated rice 9311).2.Using Illumina HiSeqTM2000,we illuminated the different cold-response related genes from the four rice crops.14213 differential expression genes were obtained fromcold-resistant weedy-rice 03-35,including 7315 up-regulated genes and 6898 down-regulated genes.720 differential expression genes were obtained from cold-sensitive weedy-rice 03-26,including 554 up-regulated genes and 166 down-regulated genes.14730 differential expression genes were obtained from cold-resistant cultured rice 131,including 7918 up-regulated genes and 6812 down-regulated genes.9219 differential expression genes were obtained from cold-sensitive cultured rice 9311,including 5160 up-regulated genes and 4059 down-regulated genes.The result of GO function statistical analysis of the differential expression genes are as follows.Differential expression genes were significantly enriched in different GO items of biological processes,cellular components and molecular functions in weedy-rice 03-35.Cellular metabolic process,cell and structural molecule activity were the three GO items containing the most differential expression genes in three function group,respectively.Differential expression genes were enriched in different GO items of biological processes,and molecular functions in weedy-rice 03-26.Biosynthetic process and ammonia-lyase activity were the two GO items containing the most differential expression genes in two function group,respectively.Differential expression genes were significantly enriched in different GO items of biological processes,cellular components and molecular functions in cultured rice 131.Cellular process,cell and nucleic acid binding were the three GO items containing the most differential expression genes in three function group,respectively.Differential expression genes were significantly enriched in different GO items of biological processes,cellular components and molecular functions in cultured rice 9311.Biosynthetic process,nucleus and nucleic-acid binding transcription factor activity were the three GO items containing the most differential expression genes in three function group,respectively.The comparison result of the of differential expression genes with KEGG database showed that differential expression genes were significantly enriched in the only one pathway,the Biosynthesis of amino acids pathway,in weedy rice 03-35.The differential expression genes were significantly enriched in 8 pathways in weedy rice 03-26,among which the Plant-pathogen interaction pathway and the Plant hormone signal pathway contained the most differential expression genes.The differential expression genes were significantly enriched in the only one pathway,the Plant-pathogen interaction pathway,in cultivated rice 131.The differential expression genes were significantly enriched in 7 pathways in cultivated rice 9311,among which Biosynthesis of secondary metabolites pathway contained the most differential expression genes.3.12 differential expression genes were selected randomly for semi quantitative RT-PCR and real-time fluorescent quantitative PCR validation from weedy-rice 03-35,weedy-rice 03-26,cultured rice 131 and cultured rice 9311.The result indicated that both the semi quantitative RT-PCR and the real-time fluorescent quantitative PCR were nearly identical to the transcriptome sequencing.