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Article|01 Mar 2022|OPEN
Universal gene co-expression network reveals receptor-like protein genes involved in broad-spectrum resistance in pepper (Capsicum annuum L.)
Won-Hee Kang1 , , Junesung Lee2 , Namjin Koo3 , Ji-Su Kwon2 , Boseul Park2 , Yong-Min Kim3,4 , Seon-In Yeom,1,2 ,
1Institute of Agriculture & Life Science, Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828, Republic of Korea
2Department of Horticulture, Division of Applied Life Science (BK21 four), Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828, Republic of Korea
3Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
4Genome Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
*Corresponding author. E-mail: wh81kang@gmail.com,sunin78@gnu.ac.kr

Horticulture Research 9,
Article number: uhab003 (2022)
doi: https://doi.org/10.1093/hr/uhab003
Views: 351

Received: 15 Feb 2021
Revised: 08 Mar 2022
Accepted: 08 Sep 2021
Published online: 01 Mar 2022

Abstract

Receptor-like proteins (RLPs) on plant cells have been implicated in immune responses and developmental processes. Although hundreds of RLP genes have been identified in plants, only a few RLPs have been functionally characterized in a limited number of plant species. Here, we identified RLPs in the pepper (Capsicum annuum) genome and performed comparative transcriptomics coupled with the analysis of conserved gene co-expression networks (GCNs) to reveal the role of core RLP regulators in pepper–pathogen interactions. A total of 102 RNA-seq datasets of pepper plants infected with four pathogens were used to construct CaRLP-targeted GCNs (CaRLP-GCNs). Resistance-responsive CaRLP-GCNs were merged to construct a universal GCN. Fourteen hub CaRLPs, tightly connected with defense-related gene clusters, were identified in eight modules. Based on the CaRLP-GCNs, we evaluated whether hub CaRLPs in the universal GCN are involved in the biotic stress response. Of the nine hub CaRLPs tested by virus-induced gene silencing, three genes (CaRLP264CaRLP277, and CaRLP351) showed defense suppression with less hypersensitive response-like cell death in race-specific and non-host resistance response to viruses and bacteria, respectively, and consistently enhanced susceptibility to Ralstonia solanacearum and/or Phytophthora capsici. These data suggest that key CaRLPs are involved in the defense response to multiple biotic stresses and can be used to engineer a plant with broad-spectrum resistance. Together, our data show that generating a universal GCN using comprehensive transcriptome datasets can provide important clues to uncover genes involved in various biological processes.