Next-Generation Genomics and Omics in Crop Enhancement and Sustainable Agriculture

For centuries, agriculture has served as the foundation of human civilization, providing food, raw materials, and livelihoods to millions worldwide. Traditional breeding methods, based on repeated selection, often take years to develop improved plant varieties. However, their limitations in enhancing yield and resilience have led to the emergence of next-generation sequencing (NGS) technologies as powerful tools in modern agriculture. Incorporating both second- and third-generation platforms, NGS has revolutionized agricultural genomics by enabling high-throughput and cost-effective analysis of entire genomes, exomes, mRNA, small RNAs, and other non-coding RNAs. NGS allows the simultaneous sequencing of millions of DNA fragments, offering in-depth insights into genome architecture, genetic variations, gene expression patterns, and epigenetic modifications. Combining genomic, transcriptomic, and metabolomic data, a multi-omics approach provides a comprehensive understanding of plant growth, stress responses, and adaptation mechanisms. This comprehensive strategy is vital for enhancing crop yield, improving stress tolerance, and accelerating breeding programs, thus contributing to long-term agricultural sustainability and global food security. This chapter reviews key sequencing technologies, recent advances, and emerging trends in agricultural genomics. It also discusses the technical and analytical challenges of NGS and highlights its transformative role in crop improvement and the future of plant breeding.

Nadiya, F., Sabu, K.K., Rajalakshmi, R. (2026). Next-Generation Genomics and Omics in Crop Enhancement and Sustainable Agriculture. In: Al-Khayri, J.M., Yatoo, A.M., Jain, S.M., Penna, S. (eds) Handbook of Agricultural Technologies. Springer, Singapore. https://doi.org/10.1007/978-981-99-0862-2_72-1 

Nadiya, F., N. Anjali, Jinu Thomas, A. Gangaprasad, K. K. Sabu. 2018. Deep sequencing identified potential miRNAs involved in defense response, stress and plant growth characteristics of wild genotypes of cardamom. Plant Biology. Published online: 11 August 2018 https://doi.org/10.1111/plb.12888

Abstract

• Cardamom has long been used as a food flavouring agent and in ayurvedic medicines for mouth ulcers, digestive problems and even depression. Extensive occurrence of pests and diseases adversely affect its cultivation and result in substantial reductions in total production and productivity. Numerous studies revealed the significant role of miRNAs in plant biotic stress responses.
• In the current study, miRNA profiling of cultivar and wild cardamom genotypes was performed using an Ion Proton sequencer.
• We identified 161 potential miRNAs representing 42 families, including monocot/tissue‐specific and 14 novel miRNAs in both genotypes. Significant differences in miRNA family abundance between the libraries were observed in read frequencies. A total of 19 miRNAs (from known miRNAs) displayed a twofold difference in expression between wild and cultivar genotypes. We found 1168 unique potential targets for 40 known miRNA families in wild and 1025 potential targets for 42 known miRNA families in cultivar genotypes. The differential expression analysis revealed that most miRNAs identified were highly expressed in cultivars and, furthermore, lower expression of miR169 and higher expression of miR529 in wild cardamom proved evidence that wild genotypes have stronger drought stress tolerance and floral development than cultivars.
• Potential targets predicted for the newly identified miRNAs from the miRNA libraries of wild and cultivar cardamom genotypes involved in metabolic and developmental processes and in response to various stimuli. qRT‐PCR confirmed miRNAs were differentially expressed between wild and cultivar genotypes. Furthermore, four target genes were validated experimentally to confirm miRNA–mRNA target pairing using RNA ligase‐mediated 5′ Rapid Amplification of cDNA Ends (5′RLM‐RACE) PCR.

Keywords: Cardamom, microRNA, next generation sequencing, RNA sequencing

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.

High quality RNA extraction from small cardamom tissues rich in polysaccharides and polyphenols

Abstract

Due to the presence of a diverse array of metabolites, no standard method of RNA isolation is available for plants. We noted that polysaccharide and polyphenol contents of cardamom tissues critically hinder the RNA extraction procedure. Hence, we attempted several methods for obtaining intact mRNA and small RNA from various cardamom tissues. It was found that protocols involving a combination of commercial kits and conventional CTAB (cetyl trimethylammonium bromide) methods yielded RNA with good purity, higher yield, and good integrity. The total RNA isolated through this approach was found to be amenable for transcriptome and small RNA analysis through next-generation sequencing platforms.

Keywords

• RNA isolation; Next-generation sequencing (NGS); mRNA; miRNA; RIN value
• • http://dx.doi.org/10.1016/j.ab.2015.05.017 
  • Full paper: http://authors.elsevier.com/a/1RJrWlbACuNf
• 
  
• Analytical Biochemistry

• Fasiludeen Nadiya^a, 
• Narayanannair Anjali^a, 
• Appukuttannair Gangaprasad^b,
• Kalluvettankuzhy Krishnannair Sabu^a, , 

• ^a Biotechnology and Bioinformatics Division, Jawaharlal Nehru Tropical Botanic Garden & Research Institute (JNTBGRI), Thiruvananthapuram 695562, Kerala, India
• ^b Department of Botany, University of Kerala, Thiruvananthapuram 695037, Kerala, India

Received 22 May 2015, Accepted 28 May 2015, Available online 3 June 2015

Corresponding author

Kalluvettankuzhy Krishnannair Sabu - sabu@jntbgri.res.inBiotechnology and Bioinformatics Division, Jawaharlal Nehru Tropical Botanic Garden & Research Institute (JNTBGRI), Thiruvananthapuram 695562, Kerala, India.