Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid
Summary: 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 dif...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-11-01
|
| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004222015905 |
| _version_ | 1811250493233561600 |
|---|---|
| author | Vandana Jaiswal Abdul Rawoof Vijay Gahlaut Ilyas Ahmad Sushil S. Chhapekar Meenakshi Dubey Nirala Ramchiary |
| author_facet | Vandana Jaiswal Abdul Rawoof Vijay Gahlaut Ilyas Ahmad Sushil S. Chhapekar Meenakshi Dubey Nirala Ramchiary |
| author_sort | Vandana Jaiswal |
| collection | DOAJ |
| description | Summary: 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. |
| first_indexed | 2024-04-12T16:05:28Z |
| format | Article |
| id | doaj.art-8ef532baa4c24d14be1df06cbd558c27 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-04-12T16:05:28Z |
| publishDate | 2022-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-8ef532baa4c24d14be1df06cbd558c272022-12-22T03:26:04ZengElsevieriScience2589-00422022-11-012511105318Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybridVandana Jaiswal0Abdul Rawoof1Vijay Gahlaut2Ilyas Ahmad3Sushil S. Chhapekar4Meenakshi Dubey5Nirala Ramchiary6Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India; Corresponding authorTranslational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, IndiaBiotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, IndiaTranslational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, IndiaTranslational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Department of Horticulture, Chungnam National University, Daejeon 34134, South KoreaTranslational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi 110042, IndiaTranslational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Corresponding authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S2589004222015905Biological sciencesNatural sciencesPlant biologyPlant Genetics |
| spellingShingle | Vandana Jaiswal Abdul Rawoof Vijay Gahlaut Ilyas Ahmad Sushil S. Chhapekar Meenakshi Dubey Nirala Ramchiary Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid iScience Biological sciences Natural sciences Plant biology Plant Genetics |
| title | Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid |
| title_full | Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid |
| title_fullStr | Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid |
| title_full_unstemmed | Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid |
| title_short | Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid |
| title_sort | integrated analysis of dna methylation transcriptome and global metabolites in interspecific heterotic capsicum f1 hybrid |
| topic | Biological sciences Natural sciences Plant biology Plant Genetics |
| url | http://www.sciencedirect.com/science/article/pii/S2589004222015905 |
| work_keys_str_mv | AT vandanajaiswal integratedanalysisofdnamethylationtranscriptomeandglobalmetabolitesininterspecificheteroticcapsicumf1hybrid AT abdulrawoof integratedanalysisofdnamethylationtranscriptomeandglobalmetabolitesininterspecificheteroticcapsicumf1hybrid AT vijaygahlaut integratedanalysisofdnamethylationtranscriptomeandglobalmetabolitesininterspecificheteroticcapsicumf1hybrid AT ilyasahmad integratedanalysisofdnamethylationtranscriptomeandglobalmetabolitesininterspecificheteroticcapsicumf1hybrid AT sushilschhapekar integratedanalysisofdnamethylationtranscriptomeandglobalmetabolitesininterspecificheteroticcapsicumf1hybrid AT meenakshidubey integratedanalysisofdnamethylationtranscriptomeandglobalmetabolitesininterspecificheteroticcapsicumf1hybrid AT niralaramchiary integratedanalysisofdnamethylationtranscriptomeandglobalmetabolitesininterspecificheteroticcapsicumf1hybrid |