RNA-Seq and Gene Ontology Analysis Reveal Differences Associated With Low R/FR-Induced Shade Responses in Cultivated...

Area of Science:

• Plant Biology
• Genomics
• Agricultural Science

Background:

• Lentil is a vital pulse crop with nutritional and ecological benefits.
• Previous research indicated differential responses to light, particularly shade, between cultivated and wild lentil germplasm.
• Understanding shade response mechanisms at the gene expression level is crucial for lentil improvement.

Purpose of the Study:

• To investigate and compare the transcriptomic responses of cultivated (Lupa, *L. culinaris*) and wild (BGE 016880, *L. orientalis*) lentils to shade conditions.
• To identify differentially expressed genes and enriched biological pathways associated with shade responses in both genotypes.
• To provide foundational transcriptomic data for understanding lentil adaptation to light environments.

Main Methods:

• Transcriptomic profiling of *L. culinaris* (Lupa) and *L. orientalis* (BGE 016880) at multiple growth stages.
• *De novo* transcriptome assembly for both lentil genotypes.
• Differential gene expression analysis and Gene Ontology (GO) enrichment analysis.

Main Results:

• Both genotypes showed transcriptomic similarities, but differential gene expression varied.
• Wild lentil BGE 016880 exhibited more differentially expressed genes than cultivated lentil Lupa.
• Upregulation of genes related to gibberellin, brassinosteroid, and auxin pathways was observed in both, explaining similar stem elongation under shade. Wild lentil uniquely downregulated jasmonic acid and flavonoid pathways, with enriched defense responses.

Conclusions:

• Transcriptomic data reveal distinct shade response mechanisms between cultivated and wild lentils.
• Differential regulation of transcription factors (WRKY, MYB) may underlie variations in defense responses under shade.
• Insights into shade responses can guide genetic strategies for improving lentil adaptation to changing light environments and enhancing crop resilience.