Gene Co-expression Network Analysis of the Comparative Transcriptome Identifies Hub Genes Associated With Resistance to Aspergillus flavus L. in Cultivated Peanut (Arachis hypogaea L.)

Abstract

Cultivated peanut (Arachis hypogaea L.), a cosmopolitan oil crop, is susceptible to a variety of pathogens, especially Aspergillus flavus L., which not only vastly reduce the quality of peanut products but also seriously threaten food safety for the contamination of aflatoxin. However, the key genes related to resistance to Aspergillus flavus L. in peanuts remain unclear. This study identifies hub genes positively associated with resistance to A. flavus in two genotypes by comparative transcriptome and weighted gene co-expression network analysis (WGCNA) method. Compared with susceptible genotype (Zhonghua 12, S), the rapid response to A. flavus and quick preparation for the translation of resistance-related genes in the resistant genotype (J-11, R) may be the drivers of its high resistance. WGCNA analysis revealed that 18 genes encoding pathogenesis-related proteins (PR10), 1-aminocyclopropane-1-carboxylate oxidase (ACO1), MAPK kinase, serine/threonine kinase (STK), pattern recognition receptors (PRRs), cytochrome P450, SNARE protein SYP121, pectinesterase, phosphatidylinositol transfer protein, and pentatricopeptide repeat (PPR) protein play major and active roles in peanut resistance to A. flavus. Collectively, this study provides new insight into resistance to A. flavus by employing WGCNA, and the identification of hub resistance-responsive genes may contribute to the development of resistant cultivars by molecular-assisted breeding.

Genome-Wide Characterization of the Phenylalanine Ammonia-Lyase Gene Family and Their Potential Roles in Response to Aspergillus flavus L. Infection in Cultivated Peanut (Arachis hypogaea L.)

“…RNA-seq data from A. flavu s-infected cultivated peanut samples were retrieved from the NCBI’s Sequence Read Archive (SRA) database (Accession No. PRJNA825125) [ 33 ]. We quantified the transcript levels of the AhPAL genes across different samples using the Fragments Per Kilobase Million (FPKM).…”

“…In our preceding study [ 33 ], we collected samples from kernels of “J-11” (a resistance cultivar) and “Zhonghua 12” (a susceptible cultivar) at various time intervals (0, 1, 3, 5, and 7 days) following inoculation with A. flavus spores. Total RNA was isolated from the collected kernels using the RNAprep Pure Plant Plus Kit (Tiangen Biotech, Co., Beijing, China) according to the manufacturer’s protocol.…”

Advances in omics research on peanut response to biotic stresses

“…Transcriptomic network analysis from the publically available RNA-seq datasets of resistant and susceptible peanut cultivars infected with A. flavus revealed a series of candidate genes involved in resistance response against A. flavus , including genes encoding R proteins, pattern recognition receptor genes, protein P21, laccase, thaumatin-like protein 1b and pectinesterases ( Jayaprakash et al., 2021 ). Core genes positively associated with peanut resistance to A. flavus were determined by weighted gene coexpression network analysis (WGCNA) and comparative transcriptome approach ( Cui et al., 2022 ). About 18 genes encoding pattern recognition receptors (PRRs), MAPK kinase, serine/threonine kinase (STK), 1 aminocyclopropane-1-carboxylate oxidase (ACO1), pathogenesis related proteins (PR10), phosphatidylinositol transfer protein, SNARE protein SYP121, cytochrome P450, pentatricopeptide repeat (PPR) protein and pectinesterase, might contribute to peanut resistance to A. flavus ( Cui et al., 2022 ).…”

Seed coat mediated resistance against Aspergillus flavus infection in peanut

“…Pathogenesis Related proteins (PR) proteins, peroxidases, and chitinases, were reported as predominantly expressed in the resistant cultivars of peanut and their expression differences help in A. flavus resistance. Similarly, comparative transcriptomics and weighed gene co-expression network analysis (WGCNA) of peanut genotypes resistant (J-11, R) and susceptible (Zhongua-12, S) cultivars revealed 18 genes producing PR10, ACO1 (1amino cyclopropane 1-carboxylate oxidase), MAPK kinase, STK (serine/ threonine kinase), PRR's (pattern recognition receptors), cytochrome P450, SNARE protein, Pectinesterase, Phosphatidylinositol transfer protein and PPR (pentatricopeptide repeat) protein in A. flavus defenses (Cui et al, 2022). Two MAP kinases namely, arahy.…”