A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges

Abstract

In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is ∼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25-30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.

Keywords: Databases; Genome assembly; Genomic resources; Molecular markers; Non-coding RNAs; Spices; Transcriptome.

Graphical abstract

Fig. 1

An illustration of cardinal industrially significant spices and their premier beneficial effects on consumer health, excluding others, by effective dosage consumption of intact spices and their derived ingredients. The representative spice images have been taken from Pexels.com and figure has been redrawn.

Fig. 2

An overview of genomic resources that could be utilized for spice productivity and development. These are expressed sequence tags, transcriptome, genome sequencing and assembly, molecular markers, non-coding RNA, organelles, and web-based resources. These resources could be precisely integrated with recent breeding and biotechnological interventions to escalate spice quality and production.

Fig. 3

Illustration of representative varied spice transcriptome assembly from heterogeneous populations and their downstream approaches to identify differentially expressed genes, relative abundance, coding and noncoding RNA expression and their regulation, gene ontology, and phylogenetic analysis for spice identification, utilization, and productivity enhancement.

Fig. 4

A landmark roadmap illustrating the important occurrences in the area of spices genome sequencing and assembly assisted studies to uncover genomics potential to enhance spices productivity and medicinal values subsequently proceeds for the spice revolution.

Fig. 5

A roadmap illustrating the seven omics resources to improve spice genotypes in seven ways. These included whole genome sequencing for trait discovery and wide association studies, molecular markers for mapping QTL and marker assisted breeding, EST and transcript for expressive signature elements, noncoding RNA to regulate a plethora of metabolite synthesis pathways, organelles for phylogeny and domestication studies, web and database access to retrieve scientific information and updates, machine learning and AI resources to develop novel genotypes with enhanced flavor, fragrance, aroma, and sensory quality, to intensifying spices productivity by creating next-generation spices. The figure has been complied with a few drawings from BioRender (https://www.biorender.com/).