Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid

Vandana Jaiswal; Abdul Rawoof; Vijay Gahlaut; Ilyas Ahmad; Sushil S Chhapekar; Meenakshi Dubey; Nirala Ramchiary

doi:10.1016/j.isci.2022.105318

Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F₁ hybrid

iScience. 2022 Oct 9;25(11):105318. doi: 10.1016/j.isci.2022.105318. eCollection 2022 Nov 18.

Authors

Vandana Jaiswal^{1

2}, Abdul Rawoof¹, Vijay Gahlaut², Ilyas Ahmad¹, Sushil S Chhapekar^{1

3}, Meenakshi Dubey^{1

4}, Nirala Ramchiary¹

Affiliations

¹ Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
² Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India.
³ Department of Horticulture, Chungnam National University, Daejeon 34134, South Korea.
⁴ Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi 110042, India.

Abstract

Hybrid breeding is one of the efficacious methods of crop improvement. Here, we report our work towards understanding the molecular basis of F1 hybrid heterosis from Capsicum chinense and C. frutescens cross. Bisulfite sequencing identified a total of 70597 CG, 108797 CHG, and 38418 CHH differentially methylated regions (DMRs) across F₁ hybrid and parents, and of these, 4891 DMRs showed higher methylation in F₁ compared to the mid-parental methylation values (MPMV). Transcriptome analysis showed higher expression of 46-55% differentially expressed genes (DE-Gs) in the F₁ hybrid. The qRT-PCR analysis of 24 DE-Gs with negative promoter methylation revealed 91.66% expression similarity with the transcriptome data. A few metabolites and 65-72% enriched genes in metabolite biosynthetic pathways showed overall increased expression in the F₁ hybrid compared to parents. These findings, taken together, provided insights into the integrated role of DNA methylation, and genes and metabolites expression in the manifestation of heterosis in Capsicum.

Keywords: Biological sciences; Natural sciences; Plant Genetics; Plant biology.