Background: Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities.

Plants frequently respond to herbivorous insect attack by synthesizing defense proteins that deter insect feeding and prevent additional herbivory. Maize (Zea mays L.) lines, resistant to feeding by a number of lepidopteran species, rapidly mobilize a unique 33-kDa cysteine protease in response to caterpillar feeding. The accumulation of the 33-kDa cysteine protease in the maize midwhorl was correlated with a significant reduction in caterpillar growth that resulted from impaired nutrient utilization. Black Mexican Sweetcorn callus transformed with mir1, the gene encoding the 33-kDa cysteine protease, expressed the protease and growth of caterpillars reared on the transgenic callus was reduced 60 -80%. Scanning electron microscopy was used to examine the effect of plant material expressing the 33-kDa cysteine protease on the structure of the caterpillar peritrophic matrix. Because the peritrophic matrix surrounds the food bolus, assists in digestive processes, and protects the caterpillar midgut from physical and chemical damage, disruption of peritrophic matrix may reduce caterpillar growth. The results indicated that the peritrophic matrix was severely damaged when caterpillars fed on resistant maize plants or transgenic Black Mexican Sweetcorn. The accumulation of the 33-kDa cysteine protease in response to caterpillar feeding, and its ability to damage the insect peritrophic matrix, represents an unusual host-plant resistance mechanism that may have applications in agricultural biotechnology.

Plants respond to insect feeding with a number of defense mechanisms. Using maize genotypes derived from Antiquan germ plasm that are resistant to Lepidoptera, we have demonstrated that a unique 33-kD cysteine proteinase accumulates in the whorl in response to larval feeding. The abundance of the proteinase increased dramatically at the site of larval feeding after 1 hr of infestation and continued to accumulate for as long as 7 days. The 33-kD cysteine proteinase was most abundant in the yellow-green portion of the whorl-the normal site of larval feeding and the tissue that has the greatest inhibitory effect on larval growth in bioassays. The proteinase was expressed in response to wounding and was found in senescent leaves. It may be a marker of programmed cell death. The gene coding for the proteinase, mir1 , has been transformed into Black Mexican Sweet callus. When larvae were reared on callus expressing the proteinase, their growth was inhibited ‫ف‬ 60 to 80%. The expression of a cysteine proteinase, instead of a cysteine proteinase inhibitor, may be a novel insect defense mechanism in plants. INTRODUCTIONOver the past 25 years, maize inbreds resistant to feeding by larvae of numerous lepidopteran species have been developed from Antiguan germ plasm (Williams and Davis, 1982;Williams et al., 1990a). Inbreds derived from this germ plasm (Mp704 and Mp708) are resistant to feeding by fall armyworm ( Spodoptera frugiperda ), southwestern corn borer ( Diatraea grandiosella), European corn borer ( Ostinia nubilalis ), sugarcane borer ( D. saccharalis), tobacco budworm ( Heliothis virescens ), corn earworm ( Helicoverpa zea ), and other Lepidoptera. Fall armyworm larvae feed extensively on whorl leaf tissue, often resulting in crop losses. Genetic and quantitative trait loci analyses indicate that resistance to these Lepidoptera is a quantitative trait regulated by several genes (Williams et al., 1989;Khairallah et al., 1998). Traits such as high hemicellulose content, low protein content, and leaf toughness appear to be correlated with reduced larval growth (Williams et al., 1998). No studies have indicated conclusively that secondary products contribute to the resistance, but two-dimensional gel electrophoresis has indicated that the presence of 36-and 21-kD proteins in the whorl may be predictive of resistance (Callahan et al., 1992).Bioassays in which fall armyworm larvae are reared on lyophilized whorl tissues indicate that larvae reared on resistant material weigh ‫ف‬ 50% less than those reared on susceptible material (Williams et al., 1990b). Larvae reared on lyophilized whorl tissue from resistant genotypes are smaller, grow more slowly, and pupate later than those reared on similar material from susceptible genotypes (Chang et al., 2000). The major effect of this germplasm is to slow larval growth and development and to increase the amount of time larvae are vulnerable to predators and parasites.The same phenotype, a 50% reduction in larval growth, is apparent when larvae are reared on nonfriable callus ...

Resistance to mycotoxin contamination was compared in field samples harvested from 45 commercial corn (maize) hybrids and 5 single-cross aflatoxin-resistant germplasm lines in years with high and moderate heat stress. In high heat stress, mycotoxin levels were (4.34 +/- 0.32) x 10(3) microg/kg [(0.95-10.5 x 10(3) microg/kg] aflatoxins and 11.2 +/- 1.2 mg/kg (0-35 mg/kg) fumonisins in commercial hybrids and 370 +/- 88 microg/kg (140-609 microg/kg) aflatoxins and 4.0 +/- 1.3 mg/kg (1.7-7.8 mg/kg) fumonisins in aflatoxin-resistant germplasm lines. Deoxynivalenol was detected (one-fourth of the samples, 0-1.5 mg/kg), but not zearalenone. In moderate heat stress, mycotoxin levels were 6.2 +/- 1.6 microg/kg (0-30.4 microg/kg) aflatoxins and 2.5 +/- 0.2 mg/kg (0.5-4.8 mg/kg) fumonisins in commercial hybrids and 1.6 +/- 0.7 microg/kg (0-7 microg/kg) aflatoxins and 1.2 +/- 0.2 mg/kg (0.5-3.0 mg/kg) fumonisins in aflatoxin-resistant germplasm lines. The results are consistent with heat stress playing an important role in the susceptibility of corn to both aflatoxin and fumonisin contamination, with significant reductions of both aflatoxins and fumonisins in aflatoxin-resistant germplasm lines.

This study was conducted to determine if constitutive levels of jasmonic acid (JA) and other octadecanoid compounds were elevated prior to herbivory in a maize genotype with documented resistance to fall armyworm (Spodoptera frugiperda) and other lepidopteran pests. The resistant inbred Mp708 had approximately 3-fold higher levels of jasmonic acid (JA) prior to herbivore feeding than the susceptible inbred Tx601. Constitutive levels of cis-12-oxo-phytodienoic acid (OPDA) also were higher in Mp708 than Tx601. In addition, the constitutive expression of JA-inducible genes, including those in the JA biosynthetic pathway, was higher in Mp708 than Tx601. In response to herbivory, Mp708 generated comparatively higher levels of hydrogen peroxide, and had a greater abundance of NADPH oxidase transcripts before and after caterpillar feeding. Before herbivore feeding, low levels of transcripts encoding the maize insect resistance cysteine protease (Mir1-CP) and the Mir1-CP protein were detected consistently. Thus, Mp708 appears to have a portion of its defense pathway primed, which results in constitutive defenses and the ability to mount a stronger defense when caterpillars attack. Although the molecular mechanisms that regulate the constitutive accumulation of JA in Mp708 are unknown, it might account for its enhanced resistance to lepidopteran pests. This genotype could be valuable in studying the signaling pathways that maize uses to response to insect herbivores.

Analysis of functional genomics (transcriptomics and proteomics) datasets is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation. To facilitate systems biology in these species we have established the curated, web-accessible, public resource ‘AgBase’ (). We have improved the structural annotation of agriculturally important genomes by experimentally confirming the in vivo expression of electronically predicted proteins and by proteogenomic mapping. Proteogenomic data are available from the AgBase proteogenomics link. We contribute Gene Ontology (GO) annotations and we provide a two tier system of GO annotations for users. The ‘GO Consortium’ gene association file contains the most rigorous GO annotations based solely on experimental data. The ‘Community’ gene association file contains GO annotations based on expert community knowledge (annotations based directly from author statements and submitted annotations from the community) and annotations for predicted proteins. We have developed two tools for proteomics analysis and these are freely available on request. A suite of tools for analyzing functional genomics datasets using the GO is available online at the AgBase site. We encourage and publicly acknowledge GO annotations from researchers and provide an online mechanism for agricultural researchers to submit requests for GO annotations.

ORCID IDs: 0000-0001-7137-8797 (J.L.); 0000-0002-3904-6984 (S.B.); 0000-0003-3192-978X (S.V.); 0000-0002-3550-5522 (V.J.); 0000-0001-9147-3871 (W.P.W.).Signaling networks among multiple phytohormones fine-tune plant defense responses to insect herbivore attack. Previously, it was reported that the synergistic combination of ethylene (ET) and jasmonic acid (JA) was required for accumulation of the maize insect resistance1 (mir1) gene product, a cysteine (Cys) proteinase that is a key defensive protein against chewing insect pests in maize (Zea mays). However, this study suggests that mir1-mediated resistance to corn leaf aphid (CLA; Rhopalosiphum maidis), a phloem sap-sucking insect pest, is independent of JA but regulated by the ET-signaling pathway. Feeding by CLA triggers the rapid accumulation of mir1 transcripts in the resistant maize genotype, Mp708. Furthermore, Mp708 provided elevated levels of antibiosis (limits aphid population)-and antixenosis (deters aphid settling)-mediated resistance to CLA compared with B73 and Tx601 maize susceptible inbred lines. Synthetic diet aphid feeding trial bioassays with recombinant Mir1-Cys Protease demonstrates that Mir1-Cys Protease provides direct toxicity to CLA. Furthermore, foliar feeding by CLA rapidly sends defensive signal(s) to the roots that trigger belowground accumulation of the mir1, signifying a potential role of long-distance signaling in maize defense against the phloem-feeding insects. Collectively, our data indicate that ET-regulated mir1 transcript accumulation, uncoupled from JA, contributed to heightened resistance to CLA in maize. In addition, our results underscore the significance of ET acting as a central node in regulating mir1 expression to different feeding guilds of insect herbivores.

Background Aspergillus flavus infection and aflatoxin contamination of maize pose negative impacts in agriculture and health. Commercial maize hybrids are generally susceptible to this fungus. Significant levels of host plant resistance have been observed in certain maize inbred lines. This study was conducted to identify maize genes associated with host plant resistance or susceptibility to A. flavus infection and aflatoxin accumulation.ResultsGenome wide gene expression levels with or without A. flavus inoculation were compared in two resistant maize inbred lines (Mp313E and Mp04∶86) in contrast to two susceptible maize inbred lines (Va35 and B73) by microarray analysis. Principal component analysis (PCA) was used to find genes contributing to the larger variances associated with the resistant or susceptible maize inbred lines. The significance levels of gene expression were determined by using SAS and LIMMA programs. Fifty candidate genes were selected and further investigated by quantitative RT-PCR (qRT-PCR) in a time-course study on Mp313E and Va35. Sixteen of the candidate genes were found to be highly expressed in Mp313E and fifteen in Va35. Out of the 31 highly expressed genes, eight were mapped to seven previously identified quantitative trait locus (QTL) regions. A gene encoding glycine-rich RNA binding protein 2 was found to be associated with the host hypersensitivity and susceptibility in Va35. A nuclear pore complex protein YUP85-like gene was found to be involved in the host resistance in Mp313E.ConclusionMaize genes associated with host plant resistance or susceptibility were identified by a combination of microarray analysis, qRT-PCR analysis, and QTL mapping methods. Our findings suggest that multiple mechanisms are involved in maize host plant defense systems in response to Aspergillus flavus infection and aflatoxin accumulation. These findings will be important in identification of DNA markers for breeding maize lines resistant to aflatoxin accumulation.