Integrated Metabolomic and Transcriptomic Analysis to Characterize Cutin Biosynthesis between Low- and High-Cutin Genotypes of Capsicum chinense Jacq

Purushothaman Natarajan,Padma Nimmakayala,Umesh K Reddy,Tolulope Abodunrin Akinmoju,Benjamin J Thompson,Marleny Garcia-Lozano,John Stommel,Carlos Lopez-Ortiz

doi:10.3390/ijms21041397

Abstract

Habanero peppers constantly face biotic and abiotic stresses such as pathogen/pest infections, extreme temperature, drought and UV radiation. In addition, the fruit cutin lipid composition plays an important role in post-harvest water loss rates, which in turn causes shriveling and reduced fruit quality and storage. In this study, we integrated metabolome and transcriptome profiling pertaining to cutin in two habanero genotypes: PI 224448 and PI 257145. The fruits were selected by the waxy or glossy phenotype on their surfaces. Metabolomics analysis showed a significant variation in cutin composition, with about 6-fold higher cutin in PI 257145 than PI 224448. It also revealed that 10,16-dihydroxy hexadecanoic acid is the most abundant monomer in PI 257145. Transcriptomic analysis of high-cutin PI 257145 and low-cutin PI 224448 resulted in the identification of 2703 statistically significant differentially expressed genes, including 1693 genes upregulated and 1010 downregulated in high-cutin PI 257145. Genes and transcription factors such as GDSL lipase, glycerol-3 phosphate acyltransferase 6, long-chain acyltransferase 2, cytochrome P450 86A/77A, SHN1, ANL2 and HDG1 highly contributed to the high cutin content in PI 257145. We predicted a putative cutin biosynthetic pathway for habanero peppers based on deep transcriptome analysis. This is the first study of the transcriptome and metabolome pertaining to cutin in habanero peppers. These analyses improve our knowledge of the molecular mechanisms regulating the accumulation of cutin in habanero pepper fruits. These resources can be built on for developing cultivars with high cutin content that show resistance to biotic and abiotic stresses with superior postharvest appearance.

Highlights

Hot peppers (Capsicum chinense Jacq.), popularly known as habaneros, are domesticated from tropical regions of Central America and have great economic significance in terms of culinary, pharmaceutical and ornamental perspectives
We performed deep paired-end RNA-Seq of the two samples by using the Illumina Nextseq 500 platform to identify differentially expressed genes (DEGs) and pathways associated with cutin and other traits by comparing PI 257145 and PI 224448. This is the first study to generate transcriptome and metabolome data pertaining to cutin in habanero peppers
We report transcriptome and metabolome data pertaining to cutin in habanero peppers along with the predicted putative cutin biosynthetic pathway for habanero peppers

Summary

Introduction

Hot peppers (Capsicum chinense Jacq.), popularly known as habaneros, are domesticated from tropical regions of Central America and have great economic significance in terms of culinary, pharmaceutical and ornamental perspectives. Their fruits are a good source of vitamins, antioxidants and other phytonutrients, including major important alkaloids such as phenolics, carotenoids, flavonoids and capsaicinoids [1,2]. A hydrophobic polymer synthesized by the epidermal cells, is a major physiological trait acquired by plants during evolution for survival in dehydrated conditions It coordinates the interaction between a plant and its environment by limiting UV radiation and mechanical damage and is a defense against pathogen entry. In terms of chemical composition, the cuticle is a polyester matrix of cutin embedded with waxes [8]

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Results

Conclusion