TONG Yuexia,HU Xiaoxuan,CHENG Zongming,et al.Expression of apple NBS-encoding genes in response to the infection of Alternaria blotch pathogen[J].Journal of Nanjing Agricultural University,2019,42(2):253-260.[doi:10.7685/jnau.201806006]





Expression of apple NBS-encoding genes in response to the infection of Alternaria blotch pathogen
童月霞 胡晓璇 程宗明 仲岩
南京农业大学园艺学院, 江苏 南京 210095
TONG Yuexia HU Xiaoxuan CHENG Zongming ZHONG Yan
College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
apple Alternaria blotchNBS-encoding geneexpression patternselection pressureco-expression network
[目的] 本文旨在分析苹果差异表达NBS-encoding基因的特征,挖掘在苹果斑点落叶病菌侵染过程中的潜在响应基因。[方法] 通过苹果斑点落叶病菌侵染‘红星’后的RNA-seq数据筛选出差异表达的NBS-encoding基因,并利用ProtParam、Pfam、SMART等网站分析了其理化性质;利用R studio软件构建表达热图并分析其表达模式;利用FastTree 2软件构建苹果NBS-encoding基因家族的系统进化树,并利用MEGA 6.0软件计算差异表达的NBS-encoding基因所在系统进化支的Ka/Ks值,研究NBS-encoding基因在进化过程中受到的选择压力;利用Cytoscape 3.0软件构建共表达网络图,分析NBS-encoding基因之间的关联性。[结果] 共筛选得到了19个差异表达NBS-encoding基因。表达模式分析表明,有3个基因(登录号为MDP0000259862、MDP0000304378和MDP0000292810)可能在响应苹果斑点落叶病的过程中起了关键作用。19个差异表达基因分布在系统进化树的15个进化支中,其中进化支10、12、14、15的平均Ka/Ks值均大于1,说明这些进化支中的基因受到正选择压力的作用,尤其是登录号为MDP0000210357、MDP0000751628、MDP0000147704和MDP0000372663的基因;而其余15个NBS-encoding基因的平均Ka/Ks值均小于1,说明它们受到纯化选择的作用。此外,有16个基因处于同一个共表达网络中,登录号为MDP0000210357、MDP0000240537和MDP0000291205的基因扮演着重要的角色。[结论] 19个苹果NBS-encoding基因参与苹果斑点落叶病菌侵染后的响应过程,其中登录号为MDP0000259862、MDP0000304378、MDP0000292810、MDP0000210357、MDP0000240537和MDP0000291205的基因可作为候选基因进行苹果抗病品种选育。
[Objectives] This paper aimed to analyze the characters of differentially expressed NBS-encoding genes in ‘Starking’ and to explore the potential functional genes in the process of apple Alternaria blotch pathogen infection.[Methods] In this report,the differentially expressed NBS-encoding genes were obtained by screening RNA-seq data of ‘Starking’ infected by apple Alternaria blotch pathogen. In addition,the physico-chemical properties of these genes were analyzed using the websites of ProtParam,Pfam,SMART,etc.. The expression heat map was built by R studio software to analyze their expression patterns. The phylogenetic tree of apple NBS-encoding gene family was constructed by FastTree 2 software. The Ka/Ks ratios of these NBS-encoding genes were calculated by using MEGA 6.0 to study the selection pressure during the evolution process. At the same time,the co-expression network of the NBS-encoding genes was constructed by Cytoscape software.[Results] A total of 19 differentially expressed NBS-encoding genes were obtained based on the RNA-seq data. According to the expression profiles of these genes,we found that three genes(GenBank accession No. MDP0000259862,MDP0000304378 and MDP0000292810) might play a crucial role in response to the infection of apple Alternaria blotch pathogen. In addition,it was also found that the 19 NBS-encoding genes were distributed in 15 clades in the phylogenetic tree of all NBS-encoding genes. The average Ka/Ks ratios of clade 10,12,14,and 15 were all greater than 1,indicating that the genes of these clades were subjected to positive selection,especially genes of accession No. MDP0000210357,MDP0000751628,MDP0000147704 and MDP0000372663. However,the other 15 NBS-encoding genes with Ka/Ks values less than 1 were under purifying selection. Besides,there were 16 NBS-encoding genes in the same one co-expression network,in which genes of accession No. MDP0000210357,MDP0000240537 and MDP0000291205 played important parts in the co-expression network.[Conclusions] There were 19 apple NBS-encoding genes involved in response to the infection of apple Alternaria blotch pathogen,in which genes of accession No.MDP0000259862,MDP0000304378,MDP0000292810,MDP0000210357,MDP0000240537 and MDP0000291205 could be used as candidate genes in apple breeding resistant varieties.


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更新日期/Last Update: 1900-01-01