Identification of genes involved in fruit development/ripening in Capsicum and development of functional markers

Meenakshi Dubey; Vandana Jaiswal; Abdul Rawoof; Ajay Kumar; Mukesh Nitin; Sushil Satish Chhapekar; Nitin Kumar; Ilyas Ahmad; Khushbu Islam; Vijaya Brahma; Nirala Ramchiary

doi:10.1016/j.ygeno.2019.01.002

Identification of genes involved in fruit development/ripening in Capsicum and development of functional markers

Genomics. 2019 Dec;111(6):1913-1922. doi: 10.1016/j.ygeno.2019.01.002. Epub 2019 Jan 4.

Authors

Affiliations

¹ Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Department of Biotechnology, Delhi Technological University, Delhi 110042, India.
² Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
³ Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Department of Plant Science, School of Biological Sciences, Central University of Kerala, Kararagod 671316, India.
⁴ Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Department of Bioengineering and Technology, Institute of Science and Technology, Gauhati University, Gopinath Bordoloi Nagar, Guwahati 781014, India.
⁵ Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
⁶ Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Department of Biotechnology, Delhi Technological University, Delhi 110042, India. Electronic address: nrudsc@gmail.com.

PMID: 30615924
DOI: 10.1016/j.ygeno.2019.01.002

Abstract

The molecular mechanism of the underlying genes involved in the process of fruit ripening in Capsicum (family Solanaceae) is not clearly known. In the present study, we identified orthologs of 32 fruit development/ripening genes of tomato in Capsicum, and validated their expression in fruit development stages in C. annuum, C. frutescens, and C. chinense. In silico expression analysis using transcriptome data identified a total of 12 out of 32 genes showing differential expression during different stages of fruit development in Capsicum. Real time expression identified gene LOC107847473 (ortholog of MADS-RIN) had substantially higher expression (>500 folds) in breaker and mature fruits, which suggested the non-climacteric ripening behaviour of Capsicum. However, differential expression of Ehtylene receptor 2-like (LOC107873245) gene during fruit maturity supported the climacteric behaviour of only C. frutescens (hot pepper). Furthermore, development of 49 gene based simple sequence repeat (SSR) markers would help in selection of identified genes in Capsicum breeding.

Keywords: Capsicum; Fruit development/ripening; Orthologous genes; Real time; Simple sequence repeats.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Capsicum / physiology*
Computer Simulation
Fruit / genetics
Fruit / physiology*
Gene Expression Regulation, Plant
Genes, Plant*
Genetic Markers*
Genetic Variation
Genome, Plant
Microsatellite Repeats
Plant Proteins / genetics
Reproducibility of Results
Solanum lycopersicum / genetics

Substances

Genetic Markers
Plant Proteins