Cowpea is an excellent crop for growers with small-to-medium farms and marginal lands prevalent throughout the southeast, but a thorough understanding of its response and tolerance to aluminum toxicity is lacking. This study characterized the transcriptome of two cowpea varieties, the tolerant Mississippi Pinkeye 2 Purple Hull (MSP2PH) and sensitive White Acre (WA), using RNA sequencing 6, 24, and 48 hours after treatment with 50µM AlCl3. RNA integrity number (RIN) scores of all samples were above 9.0 indicating high-quality, and the total number of reads from each sample ranged from about 20,000,000 – 60,000,000. Sample groups clustered by variety, treatment, and time point after principal component analysis. A threshold of 1 log-fold change (logFC) and a false-positive discovery rate of p ≤ 0.01 was used to identify differentially expressed genes (DEGs) for all comparisons. The number of DEGs between plants of the same variety under control and aluminum-toxic conditions at 6, 24, and 48 hours after treatment were 308, 385, and 173 for MSP2PH and 935, 1029, and 1208 for WA. 12 and 58 of these DEGs were detected across all three time points for MSP2PH and WA, respectively. Among DEGs between MSP2PH and WA that were unique under aluminum treatment there were 401, 613, and 623 at 6, 24, and 48 hours, respectively, with 58 across all time points. The number of common DEGs detected that were unique between MSP2PH samples under aluminum and control and those between MSP2PH and WA under aluminum only were 24, 67, and 19 after 6, 24, and 48 hours, respectively. Furthermore, three DEGs across all time points were detected using these criteria, and all were up-regulated in MSP2PH. One of these genes is annotated as a leucine-rich repeat (LRR) receptor-like kinase, which are well-known to regulators of aluminum-toxicity response and tolerance. Arabidopsis homologues for corresponding genes from different up- and down-regulated DEG sets were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis. The number of enriched genes categorized into specific GO terms varied by time point, treatment, and variety. The number of transcription factors up- and down-regulated from specific transcription factor families were also evaluated for select comparisons and showed similar variability. These findings provide insights into expression pathways involved in aluminum toxicity tolerance and response while providing candidate genes that may be used to develop aluminum-tolerant cultivars.
