RNA-Seq–based transcriptomics reveals differential gene expression between two Pisum sativum subspecies and uncovers their molecular marker profiles

Abstract Field pea (Pisum sativum) holds substantial economic importance as a food and feed crop. Although Pisum sativum ssp. abyssinicum contains more protein than Pisum sativum ssp. sativum, it remains understudied and persists as an orphan crop cultivated primarily in Ethiopia and Yemen. Using RNA-Seq, gene expression patterns between these subspecies were compared, and 108,612 unigenes were identified. Off them, 69, 512 (64%) unigenes showed significant matches in major databases, yet only 2,184 matched P. sativum sequences, highlighting limited availability of pea genomic resources. Gene expression analysis revealed 6,704 significantly differentially expressed genes (DEGs) (3,723 down-regulated and 2,980 up-regulated in ssp. sativum). Most DEGs (68%) were annotated as key functional categories, including cellular processes, catalytic activity, and DNA binding. Enrichment analysis identified stress responses, defense mechanisms, and metabolic processes as prominent biological functions. Major metabolic pathways included purine metabolism, glycolysis/gluconeogenesis, and starch/sucrose metabolism. DEGs homologous to major transcription factors (bHLH, MYB, NAC, WRKY, etc.) involved in stress responses were also identified, indicating substantial transcriptional regulation differences between the two subspecies. The study also revealed the distribution of simple sequence repeats (SSRs) in the transcriptome sequences of both subspecies (10,063 in ssp. sativum and 11,014 in ssp. abyssinicum), with trinucleotide repeats predominating, along with 4,402 polymorphic SNP markers (most showing high polymorphism information content) shared between them. These genomic resources will facilitate both the identification of genes underlying desirable traits and genomics-aided breeding, particularly benefiting the underutilized ssp. abyssinicum.