Genome-wide identification, characterization, and expression analysis of the MADS-box gene family in grass pea (Lathyrus sativus) under salt stress conditions

Abstract

Abstract Background The MADS-box gene family possesses significant potential to improve crop production under harsh conditions by regulating growth, development, and the expression of floral organs. The grass pea (Lathyrus sativus), a crop grown predominantly in arid and semi-arid regions, could benefit greatly from the functions of MADS-box genes, which are not yet well characterized in this promising plant. Results In this study, a comprehensive analysis of all MADS-box genes in grass pea was performed at both the genomic and transcriptomic levels. A total of 46 genes were identified and classified based on their MADS-box domains. A comparative phylogenetic analysis with apple, Arabidopsis, and rice categorized the grass pea genes into 31 type I genes (M $$\alpha$$ α , M $$\beta$$ β , M $$\gamma$$ γ ) and 15 type II genes (MIKCc, MIKC*). Annotation analysis revealed variations in the intron-exon structures of the genes, with most type I genes being intronless. Ten distinct conserved motifs were identified across the genes. Structural analysis revealed the presence of MEF2-like and SRF-TF domains in the grass pea proteins. Protein-protein interaction analysis revealed extensive interactions among type II MADS-box genes, while enrichment analysis showed their involvement in various aspects of plant life, particularly floral organ development. Examination of the cis-elements in the promoter regions of the genes revealed up to 76 potential cis-elements, which were categorized into four groups based on their putative role in transcriptional regulation. RNA-seq was used to profile gene expression under different conditions to gain insights into their potential functional significance. Quantitative PCR (qPCR) analysis validated the expression levels of eight selected genes (LSMADS_D1, LSMADS_R5, LSMADS_R7, LSMADS_R9, LSMADS_D11, LSMADS_D13, LSMADS_R13, and LSMADS_D29) under salt stress conditions and confirmed their involvement in stress responses. Conclusion This study represents the first genome-wide exploration of the MADS-box gene family in grass pea. Our results provide valuable insights that could improve our understanding of the plant’s genomics, contribute to strengthening its resilience to challenging conditions, and help position it as an important crop in arid regions.

Keywords

• Grass pea
• LSMADS
• MADS-box
• Expression profiles
• RNA-seq
• Salt stress