Transcriptome analysis for the identification of spot blotch responsive genes and miRNAs in wheat

Spot blotch caused by Bipolaris sorokiniana is one of the most devastating foliar diseases of wheat particularly in South Asian countries including India, Nepal, Bangladesh etc. In the present study, using whole genome transcriptome sequencing data from two contrasting genotypes for spot blotch disease (one resistant and the other susceptible), at three time points after inoculation, we identified a large number of differentially expressed genes (DEGs) and many micro RNAs (miRNAs) with their target genes (in silico). The mean reads in six libraries were 39.8 millions with a range of 32.1 to 44.9 million reads per library. The DEGs included 5294 upregulated and 4383 downregulated genes. Functional annotation and enrichment analysis showed that the main pathways enriched for the DEGs included photosynthesis-antenna proteins, MAPK signaling pathways, plant-pathogen interactions, circadian rhythm-plant, etc. These DEGs mainly encoded proteins with leucine rich repeat (LRR) domain, F-box-like domain, non-specific serine/threonine-protein kinases, wall-associated receptor kinases (WAKs), etc. Many DEGs also belonged to the following families of transcription factors (TFs): AP2/ERF, NAC, WRKY, GRAS, MYB etc.

由平脐蠕孢菌（Bipolaris sorokiniana）引发的小麦斑点病是最为严重的小麦叶部病害之一，在印度、尼泊尔、孟加拉国等南亚国家尤为高发。本研究以两个对斑点病抗性表型差异显著的小麦基因型（分别为抗病型与感病型）为材料，采集其接种病原菌后三个时间点的全基因组转录组测序数据，通过生物信息学预测（in silico）手段鉴定出大量差异表达基因（differentially expressed genes, DEGs）以及众多micro RNAs（miRNAs）及其靶基因。六个测序文库的平均读段数为39.8百万，单文库读段数范围为32.1至44.9百万。本次鉴定到的差异表达基因中，包含5294个上调基因与4383个下调基因。功能注释与富集分析结果显示，差异表达基因显著富集的通路主要包括光合天线蛋白、MAPK信号通路、植物-病原体互作、植物昼夜节律等。这些差异表达基因主要编码富含亮氨酸重复序列（leucine rich repeat, LRR）结构域蛋白、F-box样结构域蛋白、非特异性丝氨酸/苏氨酸蛋白激酶以及细胞壁相关受体激酶（wall-associated receptor kinases, WAKs）等类型的蛋白质。此外，大量差异表达基因还属于AP2/ERF、NAC、WRKY、GRAS、MYB等转录因子家族。