RNA Sequencing of Contaminated Seeds Reveals the State of the Seed Permissive for Pre-Harvest Aflatoxin Contamination and Points to a Potential Susceptibility Factor

Abstract

Pre-harvest aflatoxin contamination (PAC) is a major problem facing peanut production worldwide. Produced by the ubiquitous soil fungus, Aspergillus flavus, aflatoxin is the most naturally occurring known carcinogen. The interaction between fungus and host resulting in PAC is complex, and breeding for PAC resistance has been slow. It has been shown that aflatoxin production can be induced by applying drought stress as peanut seeds mature. We have implemented an automated rainout shelter that controls temperature and moisture in the root and peg zone to induce aflatoxin production. Using polymerase chain reaction (PCR) and high performance liquid chromatography (HPLC), seeds meeting the following conditions were selected: infected with Aspergillus flavus and contaminated with aflatoxin; and not contaminated with aflatoxin. RNA sequencing analysis revealed groups of genes that describe the transcriptional state of contaminated vs. uncontaminated seed. These data suggest that fatty acid biosynthesis and abscisic acid (ABA) signaling are altered in contaminated seeds and point to a potential susceptibility factor, ABR1, as a repressor of ABA signaling that may play a role in permitting PAC.

Genotypic Regulation of Aflatoxin Accumulation but Not Aspergillus Fungal Growth upon Post-Harvest Infection of Peanut (Arachis hypogaea L.) Seeds

“…Heat and drought stress in the field exacerbates aflatoxin contamination [ 18 ]. Peanut host genes altered by A. flavus contamination were discovered by a genome wide RNA-seq analysis [ 19 ]. Disruption of peanut abscisic acid signaling pathway by A. flavus invasion was suggested to facilitate aflatoxin accumulation.…”

Machine learning as an effective method for identifying true SNPs in polyploid plants

“…The re-sequencing data set was created using 21 tetraploid A. hypogaea genotypes described in Clevenger et al (2017) [8] and deposited publically at ncbi.nlm.nih.gov (Bio Project PRJNA340877 and Bio Samples SAMN05721179 to SAMN05721198). The RNA-seq data set has information from nine tetraploid peanut genotypes described in Clevenger et al (2015, 2016a, 2016b) [18-20]. Validated true and false-positive SNP sets were based on testing the Arachis Affymetrix array with 384 peanut genotypes [8].…”

Functional Biology and Molecular Mechanisms of Host-Pathogen Interactions for Aflatoxin Contamination in Groundnut (Arachis hypogaea L.) and Maize (Zea mays L.)

“…For instance, in case of groundnut, an integrated IVSC and RNA-seq approach that analyzed the four different stages of infected seed samples from J11 (resistant) and JL24 (susceptible) identified 4,445 differentially expressed unigenes (DEGs) that were involved in multiple pathways such as defense-related, PR or metabolic pathway targeting genes provided a more solid understanding of cross-talk between host-pathogen interactions (Nayak et al, 2017). Likewise, an RNA-seq-based approach was deployed in groundnut to identify genes that confer resistance during PAC (Clevenger et al, 2016). The study was able to associate the role of abscisic acid (ABA) signaling pathway during drought stress-induced aflatoxin contamination and/or PAC, and also revealed the role of genes from the fatty acid metabolism, cell wall restructuring and morphology, sugar metabolism and nitrogen metabolism pathways during A. flavus contamination in soil.…”