Agri Gene

Volume 8, June 2018, Pages 18-27

Genome-wide differential expression profiling in wild and cultivar genotypes of cardamom reveals regulation of key pathways in plant growth and development

Author links open overlay panelNadiyaF.a  AnjaliN.a   JinuThomasa  Gangaprasad A.b  SabuK.K.a

https://doi.org/10.1016/j.aggene.2018.03.002

Highlights

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Transcriptome sequencing data of five cultivars and a wild genotype of cardamom was used to find the differential expression profiling of the cultivar and wild genotypes of cardamom.

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Differential expression profiling of the cultivar and wild genotypes of cardamom exhibited 132 unigenes as differentially expressed (log2>4) with 105 up regulated and 27 down regulated genes in cultivars comparing with its wild genotype.

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This work represents the first report on differential expression profiling and functional annotation of wild and cultivar genotypes which will enhance the genomic resources of the species.

Abstract

Cardamom (Elettaria cardamomum Maton) is an economically valuable spice crop and the essential oil of cardamom possesses splendid medicinal properties. To get insight into the domestication related traits and varied gene regulation, differential expression profiling of wild and cultivar cardamom was performed by analyzing the transcriptome data available for cardamom. Functional annotation using seven different publicly available databases identified significant genes coding for enzymes participating in monoterpenoid biosynthesis. Differential expression profile of cultivar and wild genotypes of cardamom exhibited 132 unigenes as differentially expressed (log2 > 4) with 105 up regulated and 27 down regulated genes in cultivars comparing with its wild genotype. Expression analysis showed wild cardamom has increased drought stress tolerance, defense response, and various plant growth regulations. Most of the genes coding for enzymes participating in flavanoid biosynthesis were up regulated, while resistance related genes (cinnamoyl CoA reductase) and few genes involved in the monoterpenoid biosynthetic pathway were down regulated in cultivars when compared to its wild progenitor. Transcriptome data were validated and correlated using qPCR using 10 randomly selected differentially expressed genes. Our study is the first application of next generation RNA-seq to explore the genes involved in various metabolic pathways and quantification of transcript expression levels in cultivar and wild cardamom genotypes.

Keywords

Cardamom, 

Transcriptome, 

Differential expression, 

Up regulation, 

Down regulation, 

Essential oil biosynthesis