Exploring the genetic potential of Pakistani soybean cultivars through RNA-seq based transcriptome analysis

Mol Biol Rep. 2022 Apr;49(4):2889-2897. doi: 10.1007/s11033-021-07104-3. Epub 2022 Jan 28.


Background: Soybean is largely grown and considered among the top oilseed crops. Three Pakistani cultivars, NARC-II (N), Swat-84 (S), and Rawal-I (R) were employed for RNA-Seq based transcriptome analysis to explore their genetic potential and performance in our local environment.

Methods and results: We grew the plants in glass house at same conditions and sampled leaves for RNA-Seq analysis in triplicate for each variety. We retrieved 2225 differentially expressed genes (DEGs) between S vs R, 2591 DEGs between S vs N, and 1221 DEGs between R vs N cultvars. These genes consist of transcription factors representing Basic Helix-loop Helix, myeloblastosis, ethylene response factors, and WRKY amino acid motif (WRKY) type major families that were up-regulated. KEGG pathway analysis revealed that MAPK, plant hormone signal transduction, and Phenylpropanoid biosynthesis pathways were the most dominant pathways involved in plant defense and growth. Comparative analysis showed that Swat-84 (S) cultivar had better gene expression among these varieties having higher number of DEGs, where mostly genes related to important phenotypic traits were up regulated.

Conclusions: This is a pilot study to investigate and functionally characterise the DEG involved in the stress response in the cultivars studied.

Keywords: Differential gene expression (DGE); Pakistani soybean; RNA-Seq; Transcription factors.

MeSH terms

  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Plant* / genetics
  • Humans
  • Pakistan
  • Pilot Projects
  • RNA-Seq
  • Soybeans* / genetics
  • Soybeans* / metabolism
  • Transcriptome / genetics