Genome-Wide Identification and Characterization of Potato Long Non-coding RNAs Associated With Phytophthora infestans Resistance.

Weilin Cao,Shumei Zhou,Xuechen Zhao,Liming Gan,Mingyu Zhang,Chenchen Wang,Jinwen Du,Changxiang Zhu

doi:10.3389/fpls.2021.619062

Abstract

Long non-coding RNA (lncRNA) is a crucial regulatory mechanism in the plant response to biotic and abiotic stress. However, their roles in potato (Solanum tuberosum L.) resistance to Phytophthora infestans (P. infestans) largely remain unknown. In this study, we identify 2857 lncRNAs and 33,150 mRNAs of the potato from large-scale published RNA sequencing data. Characteristic analysis indicates a similar distribution pattern of lncRNAs and mRNAs on the potato chromosomes, and the mRNAs were longer and had more exons than lncRNAs. Identification of alternative splicing (AS) shows that there were a total of 2491 lncRNAs generated from AS and the highest frequency (46.49%) of alternative acceptors (AA). We performed R package TCseq to cluster 133 specific differentially expressed lncRNAs from resistance lines and found that the lncRNAs of cluster 2 were upregulated. The lncRNA targets were subject to KEGG pathway enrichment analysis, and the interactive network between lncRNAs and mRNAs was constructed by using GENIE3, a random forest machine learning algorithm. Transient overexpression of StLNC0004 in Nicotiana benthamiana significantly suppresses P. infestans growth compared with a control, and the expression of extensin (NbEXT), the ortholog of the StLNC0004 target gene, was significantly upregulated in the overexpression line. Together, these results suggest that lncRNAs play potential functional roles in the potato response to P. infestans infection.

Highlights

The potato (Solanum tuberosum L.) is the fourth most important staple crop in global production after rice, maize, and wheat, and it is the most important non-grain crop for human consumption (Birch et al, 2012)
The lengths of 76.79% Long non-coding RNA (lncRNA) ranged from 200 to 1000 bp; 57.43% mRNAs were longer ranging than 1000 bp (Figure 1D), suggesting that the sequence components of the mRNA exhibit differently when compared with the lncRNAs
The lncRNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection in potato and P. infestans infection in tomato were identified, but no information on lncRNAs associated with the potato response to P. infestans infection is available

Summary

Introduction

The potato (Solanum tuberosum L.) is the fourth most important staple crop in global production after rice, maize, and wheat, and it is the most important non-grain crop for human consumption (Birch et al, 2012). Multiple diseases can severely devastate the production and quality of potatoes, including late blight (Mizubuti and Fry, 2006), bacterial wilt (Wullings et al, 1998), and necrotic ringspot (Ohshima et al, 2000). The Irish famine of 1845–1852 caused by late blight led to around one million deaths and one million more people emigrated out of Ireland (Cantwell, 2017). Potato late blight disease has attracted the attention of researchers, and more than 3,000 reports associated with the disease have been published (Fry et al, 2015). Control methods for the disease are divided into mainly two kinds: pesticide application and resistance breeding. Breeding resistant varieties is the most effective control method. Investigating the mechanism of potato resistance to P. infestans plays an important role in the process of breeding resistant varieties

Methods

Results

Conclusion