Pathak Rajesh Kumar, Baunthiyal Mamta, Pandey Dinesh, Kumar Anil
Department of Biotechnology, Govind Ballabh Pant Institute of Engineering & Technology, Pauri Garhwal, Uttarakhand, 246194, India.
Department of Molecular Biology & Genetic Engineering, College of Basic Sciences & Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, 263145, India.
J Genet Eng Biotechnol. 2020 Jul 1;18(1):17. doi: 10.1186/s43141-020-00032-y.
Alternaria blight, a recalcitrant disease caused by Alternaria brassicae and Alternaria brassicicola, has been recognized for significant losses of oilseed crops especially rapeseed-mustard throughout the world. Till date, no resistance source is available against the disease; hence, plant breeding methods cannot be used to develop disease-resistant varieties. Therefore, in the present study, efforts have been made to identify resistance and defense-related genes as well as key components of JA-SA-ET-mediated pathway involved in resistance against Alternaria brasscicola through computational analysis of microarray data and network biology approach. Microarray profiling data from wild type and mutant Arabidopsis plants challenged with Alternaria brassicicola along with control plant were obtained from the Gene Expression Omnibus (GEO) database. The data analysis, including DEGs extraction, functional enrichment, annotation, and network analysis, was used to identify genes associated with disease resistance and defense response.
A total of 2854 genes were differentially expressed in WT9C9; among them, 1327 genes were upregulated and 1527 genes were downregulated. A total of 1159 genes were differentially expressed in JAM9C9; among them, 809 were upregulated and 350 were downregulated. A total of 2516 genes were differentially expressed in SAM9C9; among them, 1355 were upregulated and 1161 were downregulated. A total of 1567 genes were differentially expressed in ETM9C9; among them, 917 were upregulated and 650 were downregulated. Besides, a total of 2965 genes were differentially expressed in contrast WT24C24; among them, 1510 genes were upregulated and 1455 genes were downregulated. A total of 4598 genes were differentially expressed in JAM24C24; among them, 2201 were upregulated and 2397 were downregulated. A total of 3803 genes were differentially expressed in SAM24C24; among them, 1819 were upregulated and 1984 were downregulated. A total of 4164 genes were differentially expressed in ETM24C24; among them, 1895 were upregulated and 2269 were downregulated. The upregulated genes of Arabidopsis thaliana were mapped and annotated with CDS sequences of Brassica rapa obtained from PlantGDB database. Additionally, PPI network of these genes were constructed to investigate the key components of hormone-mediated pathway involved in resistance during pathogenesis.
The obtained information from present study can be used to engineer resistance to Alternaria blight caused by Alternaria brasscicola through molecular breeding or genetic manipulation-based approaches for improving Brassica oilseed productivity.
链格孢叶枯病是由芸苔链格孢和甘蓝链格孢引起的一种顽固性病害，已被公认为会给世界各地的油料作物尤其是油菜籽造成重大损失。迄今为止，尚未发现针对该病害的抗性资源；因此，无法利用植物育种方法培育抗病品种。因此，在本研究中，通过对微阵列数据进行计算分析和网络生物学方法，努力鉴定与抗性和防御相关的基因以及茉莉酸 - 水杨酸 - 乙烯介导途径中参与抗甘蓝链格孢的关键成分。从基因表达综合数据库（GEO）获取了野生型和突变拟南芥植株在接种甘蓝链格孢后以及对照植株的微阵列分析数据。数据分析包括差异表达基因（DEGs）提取、功能富集、注释和网络分析，用于鉴定与抗病性和防御反应相关的基因。
在WT9C9中共有2854个基因差异表达；其中，1327个基因上调，1527个基因下调。在JAM9C9中有1159个基因差异表达；其中，809个上调，350个下调。在SAM9C9中有2516个基因差异表达；其中，1355个上调，1161个下调。在ETM9C9中有1567个基因差异表达；其中，917个上调，650个下调。此外，在对照WT24C24中有2965个基因差异表达；其中，1510个基因上调，1455个基因下调。在JAM24C24中有4598个基因差异表达；其中，2201个上调，2397个下调。在SAM24C24中有3803个基因差异表达；其中，1819个上调，1984个下调。在ETM24C24中有4164个基因差异表达；其中，1895个上调，2269个下调。将拟南芥上调基因与从植物基因组数据库（PlantGDB）获得的白菜CDS序列进行比对和注释。此外，构建了这些基因的蛋白质 - 蛋白质相互作用（PPI）网络，以研究发病过程中激素介导途径参与抗性的关键成分。
本研究获得的信息可用于通过分子育种或基于基因操作的方法培育对甘蓝链格孢引起的链格孢叶枯病的抗性，从而提高油菜籽产量。
