Abstract
Chili pepper (Capsicum annuum L.) is economically one of the most important spice. But, it's productivity is highly affected by the pathogen, Phytophthora capsici L. Our current understanding of the molecular mechanisms associated with the defence response in C. annuum-P. capsici pathosystem is limited. The current study used RNA-seq technology to dissect the genes associated with defence response against P. capsici infection in two contrasting landraces, i.e. GojamMecha_9086 (Resistant) and Dabat_80045 (Susceptible) exposed to P. capsici infection. The transcriptomes from four leaf samples (RC, RI, SC and SI) of chili pepper resulted in a total of 118,879 assembled transcripts along with 52,384 pooled unigenes. The enrichment analysis of the transcripts indicated 23 different KEGG pathways under five main categories. Out of 774 and 484 differentially expressed genes (DEGs) of two landraces (under study), respectively, 57 and 29 DEGs were observed as associated with defence responses against P. capsici infection in RC vs. RI and SC vs. SI leaf samples, respectively. qRT-PCR analysis of six randomly selected genes validated the results of Illumina NextSeq500 sequencing. A total of 58 transcription factor families (bHLH most abundant) and 2095 protein families (Protein kinase most abundant) were observed across all the samples with maximum hits in RI and SI samples. Expression analysis revealed differential regulation of genes associated with defence and signalling response with shared coordination of molecular function, cellular component and biological processing. The results presented here would enhance our present understanding of the defence response in chili pepper against P. capsici infection, which the molecular breeders could utilize to develop resistant chili genotypes.
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The transcriptome sequencing data for the four-leaf samples with BioProject ID PRJNA665332, BioSample accession number RC: SAMN16251280; RI: SAMN16251798; SC: SAMN16251797; SI: SAMN16251799 were archived on SRA at the link https://www.ncbi.nlm.nih.gov/biosample/16251797.
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Acknowledgements
We acknowledge Eurofins Genomics India Pvt. Ltd., Bengaluru, India, for Illumina sequencing and Bioinformatics analysis. TR is highly thankful to the Ministry of Education, Ethiopia (former Ministry of Science and Higher Education) for sponsoring the Fellowship Program and Department Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India, for providing all necessary laboratory facilities.
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The Ministry of Education, Ethiopia (former Ministry of Science and Higher Education) has supported through sponsoring a fellowship program for T.R during the research work. Besides, Department Bio & Nanotechnology, Guru Jambheshwar University of Science and Technology, has provided all necessary laboratory facilities for experimentation, analysis and validation.
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Conceptualization [Tilahun Rabuma, Vinod Chhoakr]; Methodology: [Vinod Chhokar, Tilahun Rabuma, Om Prakash Gupta]; Formal analysis and investigation: [Vinod Chhokar, Tilahun Rabuma]; Writing—original draft preparation: [Tilahun Rabuma, Manju Yadav]; Writing—review and editing: [Vinod Chhokar, Om Prakash Gupta]; Resources: [Vinod Chhokar]; Supervision: [Vinod Chhokar].
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Rabuma, T., Gupta, O.P., Yadav, M. et al. Integrative RNA-Seq analysis of Capsicum annuum L.-Phytophthora capsici L. pathosystem reveals molecular cross-talk and activation of host defence response. Physiol Mol Biol Plants 28, 171–188 (2022). https://doi.org/10.1007/s12298-021-01122-y
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DOI: https://doi.org/10.1007/s12298-021-01122-y