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本研究以耐黄萎病的海岛棉品种“新海17号”为材料,采用RNA-Seq分析了接种黄萎病菌0、8h、24 h后叶器官和根器官.结果发现与接菌前相比,在接菌8h和24 h的叶器官中分别有779个和9 240个差异表达基因,根器官中有11 051个和14 465个差异表达基因,2个器官在接菌前,8h和24 h时差异表达基因分别为10 019、17 497和16 549个.通过对差异表达基因的分布分析,发现接菌前后叶器官中共278个共同表达的基因,根器官中有2 598个共同表达的基因.通过进一步的GO功能注释,主要注释到37项功能,其中生物过程主要有18项;细胞组分主要有9项,分子功能主要10项功能.KEGG代谢路径分析鉴定到了129条通路,其中信号传导途径、植物与病原菌之间的互作、黄酮类等生物碱合成、ABC转运体、抗坏血酸和藻酸盐代谢、次生代谢产物合成等相关路径,这些通路都与棉花的抗黄萎病菌相关.本研究为进一步从耐黄萎病的海岛棉中发掘并利用抗病基因提供了分子基础.“,”The expression profile of leaves and roots of “Xinhai 17” one kind of Gossypium barb ade nse L.with strong Verticillium wilt resistance was used as a resource under verticillium wilt stress 0,8 h,and 24 h by RNA-Seq.The result showed that,compared with no infection,779 and 9 420 DEGs (differentially expressed genes)were identified in leaves after 8 h and 24 h hours infection;while 11 051 and 14 465 DEGs were identified in cotton roots after 8 h and 24 h respectively.Compared with leaves,there were 10 019,17 497,and 16 549 DEGs in root tissue at 0,8 h and 24 h respectively.There were 278 and 2 598 common differential expression genes at different stress time in leaves and roots respectively.Functional categorization of these DEGs was further annotated onto mainly 37 categories according to Gene Ontology.There are 18 for biological process 9 for cellular component and 10 for molecular function.By pathway analysis,a total of 129 pathways were identified including plant hormone signal transduction plant-pathogen interaction ascorbate and aldarate metabolism flavonoid biosynthesis and biosynthesis of secondary metabolites which are all metabolic pathways of disease resistance or pathogen infection.We proposed that our results provide novel insights into the molecular mechanism of cotton Verticillium wilt resistance and laid the foundation for further study of disease resistance genes as well as molecular makers.