Small RNA profiling reveal regulation of microRNAs in field peanut pod rot pathogen infection
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ORIGINAL ARTICLE
Small RNA profiling reveal regulation of microRNAs in field peanut pod rot pathogen infection Mian Wang 1 & Chao-xin Zhang 2 & Li-juan Pan 1 & Tong Wang 1 & Na Chen 1 & Ming-na Chen 1 & Zhen Yang 1 & Xin-gang Guo 3 & Shan-lin Yu 1 & Xiao-yuan Chi 1 Received: 7 October 2019 / Accepted: 26 March 2020 # Institute of Molecular Biology, Slovak Academy of Sciences 2020
Abstract In recent years, the prevalence of peanut pod rot in northern China has increased, thereby severely threatening peanut yield and quality. The purpose of this study is to identify and analysis miRNAs during the process of peanut responding to pod rot, providing theoretical basis for improving the disease resistance of peanut by genetic engineering. The DNA libraries were diluted and quantified for sequencing through the Small RNA sequencing technology using Illumina HiSeq 2000. The raw reads were clean after quality trimming. The expression profiles of miRNAs were constructed and its target genes were analysis by quantitative real time PCR. The validation of miR156 targets were conducted by the 5’ RACE PCR. The present study identified 334 peanut miRNAs, of which 97 were down regulated and 27 were up regulated. The expression of 15 miRNAs was performed by qRT-PCR. Target gene prediction shown 1,998 target genes and 2,646 target loci were predicted for 303 miRNAs. A total of 152 target genes were predicted for the 119 differentially expressed miRNAs. Correlation analysis of transcriptome sequencing results identified 14 genes, which are regulated by 10 miRNAs. Negative regulatory relationships were observed between four miRNAs and their respective putative target genes. Many different miRNAs were involved in the molecular regulation of peanut responding to pod rot by negatively regulating target genes. These miRNAs showed different expression trends, the same miRNA might target multiple genes and have multiple target sites. Keywords Peanut . Pod rot . microRNA sequencing . Correlation analysis
Abbreviations miRNAS microRNAs qRT-PCR Quantitative real time polymerase chain reaction TIR1 Transport inhibitor response 1 AFB2 Auxin signaling F-box 2 Electronic supplementary material The online version of this article (https://doi.org/10.2478/s11756-020-00485-z) contains supplementary material, which is available to authorized users. * Li-juan Pan [email protected] * Xiao-yuan Chi [email protected] 1
Shandong Peanut Research Institute, Qingdao 266100, People’s Republic of China
2
Qingdao Appearance and Environmental sanitation Center, Qingdao 266100, People’s Republic of China
3
Zouping Comprehensive Inspection and Testing Center, BinZhou, Shandong 256200, People’s Republic of China
AFB3 PAGE CDS FC FDR GO
Auxin signaling F-box 3 Denatured polyacrylamide gel electrophoresis Coding sequence Fold Change False discovery rate Gene Ontology
Introduction Peanut pod rot has become a major disease in peanut production, posing a serious threat to the yield and quality of peanut. Unfortunately, it appears that all commercial culti
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