Discovery of MicroRNAs in Cardamom (Elettaria cardamomum Maton) under Drought Stress

Dataset Papers in Science
Volume 2017 (2017), Article ID 9507485, 4 pages
https://doi.org/10.1155/2017/9507485

Dataset Paper

Discovery of MicroRNAs in Cardamom (Elettaria cardamomum Maton) under Drought Stress

N. Anjali, F. Nadiya, Jinu Thomas, and K. K. Sabu

Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram 695562, India

Correspondence should be addressed to K. K. Sabu

Received 31 December 2016; Revised 21 March 2017; Accepted 19 April 2017; Published 31 July 2017

Academic Editor: Michael Hackenberg

Copyright © 2017 N. Anjali et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

MicroRNAs (miRNAs) are endogenous, 19–24-nucleotide-long, noncoding RNAs found in animals, plants, and some viruses. Drought is one of the major limiting factors that negatively affect productivity of plants. To date, nothing is known about the regulatory roles of miRNAs in response to drought stress in cardamom. Cardamom collected from the natural forest area in Therakkudi in the Idamalayar forest range was selected for the study. Total RNA was isolated from leaves and stems of control and drought treated cardamom plant, which was used for library construction. Ion torrent sequencing of the two small RNA libraries prepared from plants raised under well irrigated and drought stressed treatments, respectively, created 3,938,342 and 4,083,181 primary reads. A total of 150 conserved and 20 novel microRNAs were identified from both the control and the treated libraries. Discovery of 17 differentially expressed miRNAs under drought stress suggests that these might have been involved in various biological processes to improve plant tolerance to water stress. This study is the first report of drought responsive miRNAs and their targets in cardamom. The outcome of this research could provide insights into the miRNA based regulatory mechanisms in response to drought stress in monocot plants.

Biodiversity Mining Through Transcriptome Analysis

Secondary metabolites or chemical constituents of plants are functional products synthesized through more complex multienzymatic secondary metabolite pathways. The release of few secondary metabolites is related to the exertion of morphological differentiation and maturation during plant development. Secondary metabolite compounds designate huge chemical diversity, i.e., each plant possesses its own complex diverse set of metabolites. This diversity imparts analytical challenges, characterization of a number of metabolites in parallel, and quantification of particular compound of interest. These compounds itself are related to significant plant traits (color and fragrance of flowers, taste and color of food, and resistance toward pests and pathogens) and also for the synthesis of fine chemicals such as medicines (anticancer, anti-inflammatory, antioxidants, etc.), flavors, fragrances, dyes, insecticides, pheromones, and antimicrobial agents. The emergence of cost-effective high throughput sequencing or next-generation sequencing (NGS) technology quickly expanded transcriptome information of several plant species, which could be analyzed for quick identification of previously unknown genes and enzymes and elucidation of biosynthetic pathways. The present chapter details diverse secondary metabolites, gene expression patterns, molecular basis of chemical diversity of the compounds, and application of NGS based transcriptome profiling for biosynthetic pathway elucidation.

Citation: Sabu, K. K. and F. Nadiya. 2017. Biodiversity Mining Through Transcriptome Analysis. In: Bioresources and Bioprocess in Biotechnology, Volume 1: Status and Strategies for Exploration, Part II. Eds. Sabu A, N.S. Pradeep, S. Shiburaj. pp 207-246. doi: 10.1007/978-981-10-3573-9_10. Springer, Singapore.

Development and validation of EST-SSR and identification of EST-SNP markers for snake gourd (Trichosanthes cucumerina var. cucumerina L.)

Snake gourd is a natural antibiotic and the plant is commonly used in folk medicines throughout India. The present study was carried out using transcriptomic sequence of Trichosanthes kirilowii Maxim. for the development and validation of EST-SSR markers and EST sequences of T. dioica Roxb. for identification of EST-SNPs in T. cucumerina var. cucumerina L. A total of 382 primers were developed and out of which 58 were found to be suitable for genetic analysis. For experimental validation, 20 primers were randomly selected and amplified in T. cucumerina var. cucumerina and two related genera, viz. Coccinia grandis and Momordica charantia. It was found that 90% of the primers generated PCR products in T. cucumerina var. cucumerina and considerable cross generic amplification in M. charantia and C. grandis. Further, identification of EST-SNPs in T. cucumerina var. cucumerina was also carried out. The SNPs detected were converted to CAPS markers using the tool SNP2CAPS. The newly developed SSR and SNP markers offer novel additions to the genomic resources of this important medicinal herb for population studies, phylogenetics analyses and estimation of genetic diversity.

Citation: Silpa S, Shinsy M Y, Sabu K K. 2016. Development and validation of EST-SSR and identification of EST-SNP markers for snake gourd (Trichosanthes cucumerina var. cucumerina L.). Abrahamia 2: 51-56

Development and Cross-genera Transferability of Ginger EST-SSR Markers for Cardamom

Background: Cardamom (Elettaria cardamomum Maton) is an important commodity spice that comes under the ginger family (Zingiberaceae). Several genetic markers are widely being used to analyze plant genomes. However, genetic mapping of cardamom has never been attempted owing to the lack of sufficient number of high quality genetic markers and other pertinent genome information.

Objective: The goals of the present study were to design SSR markers from the EST sequences of ginger (Zingiber officinale) and to validate the same in cardamom for demonstrating cross generic transferability. Method: 38,116 expressed sequence tags of ginger downloaded from the NCBI dbEST database were used to develop and validate co-dominant, multi-allelic SSR markers.

Results: A total of 1214 SSRs including mono, di, tri, tetra and hexa repeats were identified in the study. The validation through SSR-PCR followed by agarose gel electrophoresis was carried out for the developed markers. Genetic analysis of the SSR markers showed polymorphism and it clearly differentiated wild genotypes from cultivars and wild escapes from the plantations. Large cardamom, Amomum subulatum Roxb. was used as an outgroup and the newly developed EST-SSR markers were amplified well in this species.

Conclusion: The newly developed EST-SSRs could be useful as reproducible markers for cardamom genetic studies.

See https://benthamscience.com/journals/current-bioinformatics/article/147712/

Genoproteomics-assisted improvement of Andrographis paniculata: toward a promising molecular and conventional breeding platform for autogamous plants affecting the pharmaceutical industry

Andrographis paniculata (Burm. f.) Wall. ex Nees. (AP) is a hermaphroditic, self-compatible, and habitual inbreeding plant. Its main bioactive component is andrographolide, which is capable of inducing autophagic cell death in some human cancer cells and helps fight HIV/AIDS. Increasing the andrographolide content by investigating the genetic mechanisms controlling its biosynthesis in order to improve and develop high-yielding cultivars are the main breeding targets for AP. However, there might exist some limitations or barriers for crossability within AP accessions. Recently, this problem was addressed in AP by using a combination of crossbreeding and biotechnology-aided genetic methods. This review emphasizes that development of a breeding platform in a hard-to-breed plant, such as AP, requires the involvement of a broad range of methods from classical genetics to molecular breeding. To this end, a phenological stage (for example, flowering and stigma development) can be simplified to a quantitative morphological trait (for example, bud or stigma length) to be used as an index to express the highest level of receptivity in order to manage outcrossing. The outcomes of the basic crossability research can be then employed in diallel mating and crossbreeding. This review explains how genomic data could produce useful information regarding genetic distance and its influence on the crossability of AP accessions. Our review indicates that co-dominant DNA markers, such as microsatellites, are also capable of resolving the evolutionary pathway and cryptic features of plant populations and such information can be used to select the best breeding strategy. This review also highlights the importance of proteomic analysis as a breeding tool. In this regard, protein diversification, as well as the impact of normal and stress-responsive proteins on morphometric and physiological behaviors, could be used in breeding programs. These findings have immense potential for improving plant production and, therefore, can be regarded as prospective breeding platforms for medicinal plants that have an autogamous mode of reproduction. Finally, this review suggests that novel site-directed genome editing approaches such as TALENs (Transcription Activator-Like Effector Nucleases) and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein-9 nuclease) systems together with other new plant breeding technologies (NPBT) should simultaneously be taken into consideration for improvement of pharmaceutical plants.

Keywords: Andrographolide, xenogamy, crossbreeding, transcriptome analysis, metabolic pathways, molecular plant breeding

Alireza Valdiani, Daryush Talei, Surrinder K. Lattoo, Rodomiro Ortiz, Søren

Kjærsgaard Rasmussen, Jacqueline Batley, Mohd Yusop Rafii, Mahmood

Maziah, Kallevettankuzhy K. Sabu, Rambod Abiri, Suchirat Sakuanrungsirikul

& Soon Guan Tan

To cite this article: Alireza Valdiani, Daryush Talei, Surrinder K. Lattoo, Rodomiro

Ortiz, Søren Kjærsgaard Rasmussen, Jacqueline Batley, Mohd Yusop Rafii, Mahmood

Maziah, Kallevettankuzhy K. Sabu, Rambod Abiri, Suchirat Sakuanrungsirikul & Soon

Guan Tan (2017): Genoproteomics-assisted improvement of Andrographis paniculata:

toward a promising molecular and conventional breeding platform for autogamous

plants affecting the pharmaceutical industry, Critical Reviews in Biotechnology, DOI:

10.1080/07388551.2016.1260525

To link to this article: http://dx.doi.org/10.1080/07388551.2016.1260525