Abstract：Soybean cyst nematode (SCN)(Heterodera glycines) is the most devastating pathogen of soybean (Glycine max) in the world. To complete the life cycle, SCN enters into host roots and causes dramatic morphological and physiological changes in host cells. At the same time, the gene's expression changed in host roots. In this paper, Illumina HiSeqTM 2500 technique was used to sequence the genes expression of the soybean, which was resistance to race 4 of SCN, after SCN infection 9 and 17 d. These time points were chosen to contrast with plant gene expression without inoculated cyst nematode. The previous time point was identified because it was the development transition period of second-stage juvenile (J2) to third-stage juvenile (J3). Similarly, the later time point was the development period of third-stage juvenile (J3) to the fourth-stage juvenile (J4). Finally, a total of 1.96×1010 bp bases were obtained. There were 2 180 and 4 210 genes with altered expression in roots at 9 day and 17 day after SCN infection, respectively, and a total of 840 common genes were expressed between 2 periods. Gene ontology (GO) significant enrichment analysis displayed 1 898 and 3 627 differentially expressed genes (DEG) which could be divided into cellular component, molecular function and biological processes of these 3 ontology. And there was relatively more DEG classified to extracellular region, antioxidant activity, nutrient reservoir activity and cell killing. Differentially expressed genes were classified into 25 categories using Cluster of Orthologous Groups of proteins (COG) annotation, and a total of 880 and 1 751 DEG annotated to this database at those 2 periods respectively. The function of COG was more comprehensive, the general function prediction only had the largest proportion, and the second is the transcription. In addition, gene expression patterns were integrated with biochemical pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG). Part of DEG may be involved 83 and 105 different metabolic pathway based on KEGG database at 9 day and 17 day after SCN infection, respectively. Genes encoding enzymes involved in phenylalanine metabolism, energy metabolism and plant hormone signal transduction were altered. This result will be useful to clarify the mechanism of disease resistance. In a word, these data provide some support for screening the key resistant gene and vivificating the function.
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