Pathways associated with FAW damage levels
The pathway analysis was run in four separate tests on FAW damage. Pathways associated with reduced FAW damage scores at the p < 0.05 level were identified in the 7-day and 14-day ratings datasets, and pathways associated with increased FAW damage scores were run on the ratings datasets collected at 7 and 14 days. Following these pathway analyses, 31 pathways were associated with increased FAW damage: 26 with the 7-day ratings, 18 with the 14-day ratings, and 5 in common. Another 42 pathways were associated with decreased FAW damage: 29 with the 7-day ratings, 22 with the 14-day ratings, and 9 in common (Supplemental Table 4). There were no common pathways between the analyses for increased damage vs. decreased damage, but three related pathways were found between the increased and decreased analyses. Triacylglycerol biosynthesis was associated with reduced FAW damage, while triacylglycerol degradation was associated with increased damage; phospholipid biosynthesis was associated with increased damage, and phospholipid conversion to another compound was associated with reduced damage. On the other hand, UDP-β-L-arabinose biosynthesis was associated with both increased and decreased damage (via different pathways).
Some pathways share genes, and one or both pathways may become significantly associated with reductions in FAW damage scores. Which causes the reduction (or if both do) may not be readily apparent. For example, the top pathway for damage scores collected on both 7 and 14 days is the sporopollenin precursors biosynthesis pathway (32 genes total), at p < 0.001 and 0.006, respectively, but the suberin biosynthesis pathway (55 genes total) is also significantly associated with a reduction in FAW damage rated at 14 days, at p < 0.05, and the two pathways have 26 genes in common. The cutin biosynthesis pathway (42 genes) is significantly associated with reduced damage at 7 days, and cutin and sporopollenin precursors biosynthesis pathways also have 26 genes in common. However, suberin biosynthesis is not associated with reduced damage at 7 days and cutin is not associated with reduced damage at 14 days. All three pathways could plausibly be associated, but sporopollenin precursors (which are carotenoids and carotenoid esters) may have better statistical evidence for association. Most pathways with shared genes create related compounds, such as homoserine and L-homoserine biosynthesis. Most pathways contained several genes that jointly contributed to association with the trait. Few pathways had only one gene contributing to the trait and these, such as acyl-CoA hydrolysis, generally had only a few genes in the pathway so statistical evidence that they are actually associated is lower.
Looking at the 31 pathways associated at a more stringent significance threshold p < 0.02 (Table 2), mechanisms that may be highlighted by the current study as involved with FAW feeding resistance include the biosynthesis of carotenes including zeaxanthin and other pathways that also utilize geranylgeranyl pyrophosphate, including ent-kaurene and chlorophyll (Fig. 1). These are highly associated with FAW damage levels, both increasing and decreasing. Other mechanisms of resistance may include hormone signaling, as the IAA and sterol biosynthesis (of which brassinosteroids are a subset) as well as the ent-kaurene biosynthesis pathway (which can be converted to gibberellins, Fig. 1) were all identified as associated with damage levels. Reactions associated with FAW damage (Table 2) include the S-adenosyl-L-methionine cycle, which was associated with increased damage; acyl-CoA hydrolysis (decreasing damage); and thioredoxins and glutathione redox reaction (related reactions, associated with decreased damage). The production of lipids and waxes, including cuticular wax, phosphatidylethanolamine, and phospholipids (compounds in biological membranes) and the essential oil linalool and β-caryophyllene), all associate with increased levels of damage. The biosynthesis of several other compounds is associated with decreased FAW feeding damage, including ascorbate, flavin or riboflavin, myo-inositol and phytate, and the amino acid cysteine. Some compounds associated with an increase in damage ratings include ammonia, 1,4-dihydroxy-2-naphthoate, the phenolic compound coumarin, and the amino acids homoserine, methionine, and homocysteine.
Figure 1 : Many of the pathways associated with Fall Armyworm leaf damage rating scores were in the carotenoid biosynthesis pathway or pathways branching off from or downstream of it. Pathways significantly associated with damage scores are circled in red (solid line circles p < 0.02; dashed line p < 0.05).