Proteomic and Metabolomic Profiling of Transgenic Pod Borer-Resistant Cowpea: Assessing Unintended Molecular Changes and Their Implications for Ecosystem Resilience

BackgroundThe commercialization of Nigerias single-line pod borer-resistant (PBR) cowpea (IT97KT), the first transgenic cowpea variety in the world expressing Cry1Ab gene, has raised questions about potential unintended molecular changes and their ecological implications. This study employed integrated proteomic and metabolomic profiling to compare the transgenic line with its non-transgenic isoline (IT97KN) and assess molecular indicators associated with ecosystem resilience. MethodsProteomic analyses were conducted using LC-MS/MS following filter-assisted sample preparation, while metabolomic profiling employed GC-MS and UHPLC-MS/MS platforms. Differential protein and metabolite abundance were assessed using label-free quantification, volcano plot analysis, principal component analysis (PCA), hierarchical clustering, and Gene Ontology (GO) enrichment analyses. ResultsProteomic profiling revealed substantial overlap between IT97KT and IT97KN, with only a limited subset of proteins exhibiting significant differential abundance. Upregulated proteins in IT97KT were primarily associated with seed storage, redox regulation, oxidative stress mitigation, and defense-related functions, including Late Embryogenesis Abundant Protein 1 (LEA1), vicilins, thioredoxin, and iron superoxide dismutase. Among 37 proteins linked to ecological adaptation, only LEA1, CPRD22, and Bg7S showed significant differences. Similarly, only carbonic anhydrase II displayed differential abundance among proteins associated with potential ecological risk. PCA and clustering analyses demonstrated high proteomic similarity between genotypes. Metabolomic analyses identified sixteen major metabolites, predominantly fatty acids, with no statistically significant differences in abundance or composition between transgenic and non-transgenic lines ConclusionsThe transgenic PBR cowpea exhibited minimal unintended proteomic and metabolomic alterations relative to its non-transgenic isoline. These findings indicate that Cry1Ab insertion did not substantially disrupt molecular pathways associated with ecological adaptation, environmental risk, or metabolic homeostasis, providing molecular evidence supporting the environmental and biosafety equivalence of PBR cowpea.