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.

Graphical abstract

The illustration signifies how genomic resources in spices can contribute to generating next-generation spices with enhanced attributes, which are in alarming demand globally.

Highlights

• •Spices are high-worth but low-volume commodities of commerce produced in a confined area of the world.
• •They play an impetus role to improve human nutrition and health by their inherent medicinal and antioxidant properties.
• •Their consumption and utility have been dramatically enhanced during the pandemic and post-pandemic period.
• •Genomic resources of spices are an auxiliary wealth to augmenting their production and sensory attributes.
• •Ascertaining their utilities provides a next-generation spices for sustainable health and nutrition security.

1. Introduction

Spices are natural plant-based aromatic substances significantly used for food seasoning preferred over nutrition (https://www.fda.gov/). They possess powerful antioxidant, anti-inflammatory, and therapeutic properties and can be used in remedies, herbal preparations, or dietary supplements to promote and address specific health concerns (Mandal et al., 2023). Traditionally, they are used as flavors, condiments, preservatives, pesticides, medicines, anesthetic in dental medicine, essential oil therapy, beverages, colorings, and cosmetics, including perfumes (Sachan et al., 2018; Mandal et al., 2023). These properties possessed by different classes of spices are due to the synthesis of different chemicals during the growth and development of their respective plants (Yashin et al., 2017). These plants produce derivatives of a heterogeneous group of molecules with low molecular weight, derived from amino acids, fatty acids, and carbohydrate components of various functional groups, including aldehydes, alcohols, ketones, ethers, esters, sulfur, and nitrogen (Jessica Elizabeth et al., 2017). The plant synthesize them essentially to protect itself from predators, herbivores, other harmful organisms, etc. (Jessica Elizabeth et al., 2017; Mandal et al., 2023). The increasing global demand for spices brings several challenges, mainly related to food sustainability, traceability, and safety standards. India is one of the leading producer of spices (https://www.fao.org) accounts for 25–30% of the global spice trade. Spice production in India is 10.68 Million tonnes from an area of 4.5 Million ha (https://www.dasd.gov.in/), where southern states account for the production of 63 major spices, 21 of which have high commercial value (Malhotra et al., 2021). These include Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large and small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, turmeric, and Vanilla. Due to its high agro-climatic diversity, it is the source of exotic spice cultivars, introducing >1000 accessions of spices and condiments from different ecological areas (Pedapati et al., 2014). Some of the spices with specific characteristics are ginger (extra fat, low fiber, high dry recovery, small rhizomes, rounded fingers, compact rhizomes, globose smooth, closed nodes, firm, long, and slender rhizomes), Apium spp. (tolerant to high temperatures), and coriander (long duration) (Pedapati et al., 2014; Sachan et al., 2018). Emphasis is placed on the introduction of specific genotypes with distinctive traits, particularly resistance to various biotic and abiotic stresses, early upright ripening, long spikes with high alkaloid content, vigorous seeds, and being suitable for high-density planting (Pedapati et al., 2014; Saji et al., 2019). A detailed comprehension of the discussed spices with their origin, main cultivated states, area, and production statistics is provided in Supplementary Table 1.

Spice production and quality are primarily determined by genotype, ambient conditions, and cultivation management (Anandaraj et al., 2014; Paul and Debnath, 2018). With the advances in sequencing and other emerging molecular technologies, it has become possible to decipher the entire genomic resources of several spice crops. Spice genomic resources are becoming ever more crucial for understanding the genetic makeup and biology of flavour, aroma production, and other special attributes of candidate spices (Trindade, 2010). These tools provide critical data and insights that aid in the improvement and long-term management of spice cultivation. Genomic resources and molecular breeding are two essential components of modern plant breeding strategies (Thudi et al., 2021). The relationship between them is symbiotic, as genomic resources provide valuable data and tools that enable more effective and efficient molecular breeding approaches (Xu et al., 2017; Paul and Debnath, 2018; Thudi et al., 2021). These resources could be helpful for trait discovery, marker development and assisted selection, genomic selection, speed and precision breeding, gene editing, and diversity exploration (Sonah et al., 2011). These can be further utilized by breeders to track and efficiently introduce desirable genes into new breeding spice lines. Nevertheless, genetic gain in spices can be increased by maximizing potential, which has evolved and been supplemented with current breeding techniques and platforms, mostly driven by molecular and genomic tools, in conjunction with improved agronomic practice (Xu et al., 2017). Therefore, the integration of genomic resources and molecular breeding in spice crops has the potential to dramatically improve productivity, quality, and tolerance to biotic and abiotic challenges. Breeders may use these modern approaches to generate new spice varieties that match consumer expectations, handle the problems of changing climates, and ensure the long-term production of these valuable agricultural commodities.

2. Spices as a food: medicinal properties and sensory attributes

Spices are a seed, fruit, root, bark, or other plant material that is primarily used as a food and is rich in antioxidants, anti-inflammatory compounds, and other bioactive health-beneficial compounds (Mandal et al., 2023). They have been used for taste, color, and aroma since antiquity and are extensively used to preserve food and beverages due to their phytochemical properties (Embuscado, 2015). Apart from this, they have different uses, namely, essential oil manufacture, colorants, antioxidants, antiseptics, and antibiotic materials. Many spices are rich in essential oils with antimicrobial effects (Macwan et al., 2016). Spices such as Allium sativum, Zingiber officinale, Cinnamomum, Zeylanicum, and Capsicum annuum have been found to have antifungal properties in their aqueous and ethanolic extracts. This helps combat responsible post-harvest losses from their industrial application. These are mainly isolated from intact or diseased fruit (Birhanu et al., 2014). There are multifold health and medicinal benefits of spices, besides many other unrecognized values (Fig. 1) Supplementary Table 2. A few notable examples include Cinnamon, lowers blood sugar levels and has a strong antidiabetic effect (Ribeiro-Santos et al., 2017). Peppermint relieves pain associated with irritable bowel syndrome (Haber and El-Ibiary, 2016). Turmeric contains curcumin, a substance with powerful anti-inflammatory effects (Das et al., 2019), Cayenne pepper contains capsaicin, which helps to reduce weight and has anti-cancer properties (Hernandez-Perez et al., 2020). Ginger treats nausea and has anti-inflammatory properties (Ballester et al., 2022), fenugreek improves blood sugar control (Wani and Kumar, 2018), garlic fights disease and improves heart health (Sahidur et al., 2023) and saffron has the ability to fight depression, improve vision and improve memory, making it quite useful for treating fever, melancholy, and enlarged liver and spleen (Siddiqui et al., 2022). Apart from this, spices are involved in high antioxidant activities, which have been found in chemical compounds specifically present in spices, such as safranal, crocin, and crocetin in saffron (Gohari et al., 2013; Siddiqui et al., 2022), curcuminoids and curcumin in turmeric, allicin and allyl isothiocyanate in garlic (Schaffer et al., 2015; Ozma et al., 2022), eugenol in cinnamon (Ribeiro-Santos et al., 2017), gingerol, zingiberone and zingiberene in ginger (Ballester et al., 2022), piperine, piperidine, limonene, myrcene, linalool, α-phellandrene and pinene in black pepper (Lee et al., 2020). Moreover, the potential phytochemical and pharmacological properties of curry plant, celery, cardamom large, asafoetida, vanilla, dill and nutmeg have been reviewed (Singh et al., 2014; Rajendran et al., 2014; Sowbhagya, 2014; Gautam et al., 2016; Amalraj and Gopi, 2017; Ferrara, 2020; Kaur et al., 2021; Ashokkumar et al., 2022). Additionally, spices are well-known for their sensory qualities which are important in culinary applications and have been utilized for ages to improve the flavor, aroma, heat, pungency, texture, color, mouth feel, bitterness, cooling effect, aftertaste and appearance of many dishes (Ozcan, 2022). Diverse spice combinations are used in different cuisines around the world to produce distinct and wonderful culinary experiences (Regu et al., 2016; Ozcan, 2022). The medicinal properties and major flavor components of spices and their industrial utility are additionally summarized in Supplementary Table 2.

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.

3. Genomic resources: treasure for spices improvements

In recent decades, there have been drastic positive changes in the consumer basket for spice consumption globally due to health awareness, consumer preferences, urbanization, rising incomes, and changing demographic and social factors (Spence, 2021). The low growth rates in area, production, and productivity of the various spices (except chilli) are a major concern (Rana et al., 2021). There is an urgent need to increase the production and productivity of spices through accelerated breeding and biotic and abiotic stress management, in which omics research has to play a major role. In addition, the post-COVID surge in demand for spices due to their immune-boosting and immunomodulating properties has solidified research priorities in spices (Elsayed and Khan, 2020; Vishwakarma et al., 2022). With the advent of high-speed sequencing technologies at much lower cost, there is a strong need to tap the enormous genomic and proteomic data that are being generated for a better understanding of the biological systems of spices at the molecular level (Sonah et al., 2011). Numerous genomic resources, such as complete genome sequences and assemblies, a wide range of ESTs, large insert genomic libraries, molecular markers, and high-density genetic maps, are available. The genomic resources such as nucleotides, ESTs, GSS, SRA, and GEO datasets, protein counts, and assembly counts of the major spices available in NCBI are listed in Supplementary Table 3, These are broadly categorized as Expressed sequence tags, transcriptomics, genome assemblies, molecular markers, noncoding RNAs, organelles, and web-based resources Fig. 2. These genomic resources are not only being used for annotation, mapping, and cloning of genes but are also useful for functional trait discovery, genetic diversity assessment, identification of QTL, gene editing through CRISPR-Cas9, and marker-assisted and genomic selection in spice crops (Paul and Debnath, 2018). However, there are relatively few and scattered genomic resources available as compared to cereals. Collating and cataloguing these limited genomic resources for commercially significant available spices will assist researchers to identifying and addressing future challenges as well as research gaps for enhancing the production and productivity of all twenty-four spices. This will also help to accelerate the research activities in all diverse areas for better understanding and management of species' resources for their exploration for the betterment of humanity.

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.

4. Expression sequence tag (EST): expressive and regulatory resources

EST sequencing provides information about the highly expressed fractions of genes (Barboza et al., 2018). These are also known as gene signatures, which can be used to clone and analyses full-length genes. ESTs have been generated for a number of plant species and deposited in online databases (D'Agostino et al., 2007; Chand et al., 2015). This sequence data has been generated for many horticultural crops, and full-length cDNA clones have been derived for several fully characterized genes. The highest number of spice EST data available in the NCBI EST database (dbEST; www.ncbi.nlm.nih.gov/dbEST/) is for ginger, i.e., 38,201, followed by garlic, and turmeric, i.e., 22,771, and 12,678, respectively. Because of spices' anti-inflammatory properties, they have been used as medicinal plants to treat a variety of diseases. These plants possess medicinal properties that are attributed to two groups of compounds, namely diarylheptanoids and gingerol-related compounds (Gang and Ma, 2008). A comparative analysis of the EST of ginger is reported along with Resistance gene candidates (RGCs) (Aswati Nair and Thomas, 2007). Rhizome rot (Pythium aphanidermatum) of Zingiber species has been studied by differential display cDNA libraries (Kavitha and Thomas, 2008). Reports are also available for EST and metabolite profiling of selected ginger somaclones (Sreeja, 2017). For black pepper, 87 ESTs, were reveled through Suppression subtractive hybridization (SSH) sequences from roots infected with F. solani f. sp. Piperis, uncovering relationships among host pathogen nexuses (de Souza et al., 2011). Trait- and tissue-specific (such as clove, scion, root, stem, leaf, flower, rhizome, mixed bulb, seed, tuber, fruit, salt, etc.). Among these, saffron, an economically important spice, harbors 6767 publicly available ESTs, of which approximately 6224 are from scar tissue and 151 from tuber tissue (D'Agostino et al., 2007). Spice improvement programmes can optimize breeding strategies to, accelerate the development of new and improved spice varieties, by understanding gene expression patterns, identifying genes for specific traits, alternative splicing and transcript diversity, marker development and genomic mapping, and functional genomics by leveraging discussed EST resources (D'Agostino et al., 2007; de Souza et al., 2011; Chand et al., 2015).

5. Transcriptomic studies: comprehensive and quantitative resources

The transcriptome contains all RNAs that are transcribed in an organism or cell in a given state or environment, including mRNAs and non-coding RNAs (Vibhuti et al., 2017). Transcriptome sequencing gradually became the basis for studies of genetic structure and function (Gaur et al., 2016; Vibhuti et al., 2017). It involved several biological processes, such as gene expression profiles among diverse samples, identifying biomarkers among them, discovering genes, determining gene contents, and isolating conserved homologous genes through molecular systematics after experimentation (Trindade, 2010; Jain et al., 2016; Kumar et al., 2023). The detailed transcriptome studies on candidate spices are provided in Supplementary Table 4. The outline of the methodology adopted for such transcriptome analysis is presented in Fig. 3. In a genome-wide analysis, microarray experiments on black pepper were conducted to (i) decipher the role of piperine in regulating genes associated with lipid metabolism (Park et al., 2012), (ii) find the factors involved in the transport of nutrients across the membrane, and (iii) study defense against abiotic stress, namely, salt stress and dehydration, and biotic stress and factors of cell organization, biogenesis, and transcription (Vibhuti et al., 2017). RNA-seq was first used in Black pepper to generate the root transcriptome data set (Gordo et al., 2012), followed by studies on leaf (Joy et al., 2013), fruit (Hu et al., 2015), and phenylpropanoid metabolism in response to the foot rot disease pathogen (Hao et al., 2016). A comparative transcriptome of three different black pepper cultivars for exploring the genetic regulation of flower and fruit development (Khew et al., 2020), a leaf transcriptome in response to Fusarium solani infestation (Lau et al., 2020) for drought tolerance (Negi et al., 2021) are also reported. A novel natural cyclobutane-containing alkaloid, piperine from Piper species has also been reviewed (Vasavirama and Upender, 2014).

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.

Transcriptomic studies on leaves, stems, flowers, flower buds, capsule rot disease (Nadiya et al., 2017; Mathew et al., 2019), mosaic virus disease (Khan et al., 2020) of small cardamom, and Chirke disease (Mathew et al., 2020) of large cardamom are reported. In turmeric species (C. longa), inter-cultivar differential gene expression in rhizomes of Nattu, Erode, Mysore, and Suvarna, along with SNP discovery, has been described (Annadurai et al., 2013; Sahoo et al., 2016). Interspecies differential gene expression of ginger and mango ginger in bacterial wilt infection has also been reported (Prasath et al., 2014). Similarly, ginger transcriptomic studies revealed the biosynthesis of essential oil, gingerols, and diarylheptanoids (Gaur et al., 2016; Jiang et al., 2017, 2018a). To reveal key candidate genes involved in ginger bacterial wilt caused by Ralstonia solanacearum, transcriptomic studies have been reported using contrasting soil moisture environments (Jiang et al., 2018a; Lv et al., 2020). Studies are also reported in this species for tissue- and stage-specific genes, and abiotic stress (ABA and salt stress)-related genes (Jiang et al., 2018b; Lv et al., 2020). In the case of garlic (Allium sativum), several transcriptomic studies are reported revealing (i) sulfur metabolism (Sun et al., 2012), and (ii) fertility traits along with inflorescences and flowers (Kamenetsky et al., 2015) (iii) Carnation shape traits (Chen et al., 2018) (iv) green coloration with temperature effects (Li et al., 2018), (v) salt stress response (G.L. Wang et al., 2019), (vi) aerial bulbs under dormancy and low-temperature induction (Dong et al., 2019) (vii) tuber yield traits (Zhu et al., 2019a) (vii) organosulfur metabolism (Mehra et al., 2020), (ix) lignification (Kong et al., 2021), (x) phenylpropanoid pathway (Wu et al., 2021) and (xi) photoperiodic signaling (Atif et al., 2021). Furthermore, Mint (Mentha) transcriptome analysis reveals trichomes development, and secondary metabolite accumulation (Mishra et al., 2021), monoterpene synthesis and light-induced impact on biosynthesis (Qi et al., 2018; Yu et al., 2021; An et al., 2023), salicylic acid induced enhanced antioxidant potential (Figueroa-Pérez et al., 2019), and biosynthesis of peltate-glandular trichomes (Jin et al., 2014). Moreover, in depth-transcriptome of vanilla suggests orchid pod growth, and Fusarium infection suggest translational control during the early stage of infection (Rao et al., 2014; Adame-García et al., 2019). In the case of cayenne peppers (Capsicum annuum), transcriptomic studies are reported highlighting genes involved in pepper gold mosaic virus (PepGMV) infection (Gongora-Castillo et al., 2012a), biosynthesis of capsaicinoids (Liu et al., 2013), marker discovery (SNPs and SSRs), >24 K candidate gene models (Ashrafi et al., 2012), cold injury processes (Ge et al., 2019), and different storage temperatures (Tang et al., 2019).

Studies have reported that the world's most expensive spice species, saffron (Crocus sativus L.), has excellent medicinal properties due to its high apocarotenoid content, like crocins, which provide the stigma's crimson color. Several studies are reported revealing apocarotenoid biosynthesis (Baba et al., 2015; Jain et al., 2016; Ahrazem et al., 2019; Tan et al., 2019; Yue et al., 2020; Gao et al., 2021) and flower development regulating genes (Choudhary et al., 2019; Hu et al., 2020). Spice coriander (Coriandrum sativum), which has been cultivated since the second millennium BC, is well known for its fruits and leaves used as seeds, and cilantro is an important ingredients in several cuisines (Eriksson et al., 2012). Involvement of transcriptomic signatures of pathways involved in stem gall disease (Choudhary et al., 2019) and terpene biosynthesis (Tulsani et al., 2020) has also been investigated and described in Supplementary Table 4. In ajwain (Trachyspermum ammi), transcriptomic studies have been reported, and key candidate genes have been unveiled along with the molecular mechanism of terpene synthase along with thymol biosynthesis (Soltani Howyzeh et al., 2018), and genes involved in inflorescences development (Amiripour et al., 2019). In curry leaf (Murraya koenigii), genes encoded for terpene synthases were functionally characterized to ascertain their role in the synthesis of leaf volatiles by wide transcriptome studies (Meena et al., 2017). Further studies unlock gene families for polyketide synthases, prenyltransferases, methyltransferases, and cytochrome P450s involved in the production of carbazole alkaloids and leaf development (Meena et al., 2017; Shivakumar et al., 2019). A tissue-specific transcriptome identifies genes involved in terpenoid and phenylpropanoid metabolism in ferula species (Amini et al., 2019). In celery, transcriptome analysis reveals key transcription factors and flower development processes (Li et al., 2020a), heat stress responses (Li et al., 2022a), terpenoids and phthalide metabolism (Yan et al., 2021), mined SSR (Li et al., 2014), and a response for selenium (Zhang et al., 2019). Furthermore, transcriptome analysis of Apium phloem tissue (Vilaine et al., 2003), involvement of WRKY and NAC in abiotic stress (Wu et al., 2021; Duan et al., 2020), MYB-mediated apigenin regulation (Yan et al., 2019), and lignin synthesis during leaf development (Jia et al., 2015) have also been described. Such transcriptomic studies can be used to better understand gene expression patterns and regulatory mechanisms, ultimately assisting in spice improvement through the identification of key genes, their expression profiles, functional annotation, integrated regulatory networks, and stress resilience. A better understanding of the genetic basis of spice traits subsequently facilitate targeted breeding approaches and genetic interventions for spice improvement.

6. Genome sequencing and assembly: constructive and comparative resources

The genome assembly and its annotation provide basic information for further research on particular species (Qin et al., 2014; Sun et al., 2020; Chakraborty et al., 2021). It helps in (i) getting a complete genome sequence, (ii) chromosome-wise organization, (iii) annotation of protein-coding gene sequence and its regulatory element, (iv) identification of genetically important functional features of different sequence segments of chromosomes, etc. The genome sequencing and assemblies of the major discussed spices whose information is available are summarized below and catalogued in Supplementary Table 5. Apart from this, their timelines are shown in Fig. 4. This includes, black pepper (Piper nigrum), or ‘Black Gold’, as it is a globally highly used spice (Sun et al., 2012). The genome size of black pepper is 761.2 Mb and is assembled into 26 pseudochromosomes (45 scaffolds with a N50 of 29.8 Mb). Piperine production in black pepper is elucidated by this reference genome (Sun et al., 2012). Turmeric (Curcuma longa) has had medicinal use since ancient times, as it has a wide range of therapeutic benefits. On the other hand, the lack of a reference genome sequence for turmeric has been a major hurdle to understanding the genomic basis of its therapeutic effects. Using 10x Genomics linked reads and Oxford Nanopore Long Reads, the draft genome sequence of C. longa was constructed. The size of the draft genome is 1.02 Gb with 70% repeat sequences and 50,401 gene coding sequences (Chakraborty et al., 2021). In addition, Ginger (Zingiber officinale) is also the most valuable spice plant in the world. Due to its culinary and folk medicinal uses, it has significant economic and cultural value (Cheng et al., 2021b). Its genome has a chromosome-scale arrangement for diploid ginger, linked to 11 pseudo-chromosome pairs with a total length of 3.1 Gb. i.e., haplotype-resolved. This arrangement of ginger provides a strong basis for future functional genomics, molecular breeding, and genome editing (Cheng et al., 2021b). Garlic (Allium sativum) is one of the most commonly grown Allium species and is used as a spice or food. It has unique organosulfur compounds that are used to treat many diseases (Sahidur et al., 2023). Its chromosome-level assembly yielded a genome of ∼16.24 Gb, along with annotation of >5.7 thousand coding genes, making it the first Allium species for which, the genome has been sequenced (Sun et al., 2020).

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.

Further, Cayenne pepper (Capsicum annuum) is commonly cultivated worldwide as a spice for its spicy taste and medicinal properties. The whole genome assembly of cultivated pepper Zunla-1 (C. annuum) and its wild progenitor Chiltepin (C. annuum var. glabriusculum) shows their estimated genome sizes to be 3.26 Gb and 3.07 Gb, respectively (Kim et al., 2014). The cayenne pepper genome sequence provides insights into its typical pungency property revealing capsaicin synthase, ethylene synthesis, and fruit ripening pathways (Kim et al., 2014) and capture large structural variants for sweet and hot genotypes (Lee et al., 2022). Furthermore, Retro duplication was critical in the vast development of NLR genes in cyanine pepper, including the evolution of functional disease-resistance genes (Kim et al., 2017) and their intra-species divergence (Kim et al., 2021). This information is crucial for the study of the evolution of the pepper genome as well as the Solanaceae family for effective breeding programs (Qin et al., 2014). Coriander (Coriandrum sativum), a plant in the Apiaceae family, also known as cilantro or Chinese parsley, is an important global crop used as a vegetable, spice, fragrance, and traditional medicine. A high-quality assembly and analysis of its genome sequence, which contained 11 chromosomes with a total length of 2118.68 Mb were reported (Song et al., 2020a). Saffron (Crocus sativus) is the most expensive but low-yielding crop of medicinal and culinary importance. Despite its economic status, omics information about this plant is very sparse. The draft genome sequence of C. sativus was the first genome sequence of a member of the family Iridaceae. Illumina sequencing followed by assembly resulted in a genome with a size of 3.01 Gb and a genome coverage of 84.24% (Ambardar et al., 2022). From a total of functionally annotated genes, MYB and MYB-related family proteins were found to be more abundant among the transcription factors discovered so far (Ambardar et al., 2022). In a nutshell, genome assembly is a critical tool in spice improvement because it provides critical genetic information that can be used to understand the origins of desirable traits, develop improved varieties, and implement targeted genetic interventions to improve the wider quality and productivity of spice crops.

A high-quality genome sequence of coriander unveiled two whole-genome duplication events as well as gene retention and expression of the terpene synthase gene family, which is involved in the terpenoid biosynthesis pathway that contributes to the unique flavour of coriander (Song et al., 2020a). A high-quality chromosome-scale genome assembly of clove provides a comparison between the genomes of two Myrtaceae species and indicates remarkable genome structural conservation and intrachromosomal rearrangements on seven of the eleven chromosomes, as well as insights into the eugenol production pathway (Ouadi et al., 2022). Celery, a widely cultivated spice, contains nutrients and biologically active ingredients. Evolutionary analysis suggests a recent whole-genome duplication event in celery may have contributed to its large genome size. The genome sequence identifies genes involved in disease resistance, flavonoid biosynthesis, and apigenin biosynthesis, which explain celery's high apigenin content (Li et al., 2020b). Moreover, a high-quality genome sequence assembly indicates successive paleo-polyploidizations, karyotype evolution, and a decrease in resistance genes in the apiales (Song et al., 2021). A first draft of fennel genome sequencing reveals simple sequence repetitions that are useful for marker-assisted selection and breeding (Palumbo et al., 2018). A draft de novo genome and plastome assembly for a wilt-resistant accession of Mentha provides valuable information for metabolic engineering and molecular breeding and characterizes promoters for their utility as glandular trichome-specific promoters in modulating essential oil composition (Vining et al., 2017). A chromosome-scale Vanilla planifolia genome reveals gene variants affecting the vanillin pathway, bean quality and productivity, post-harvest losses through pod dehiscence, flower anatomy, and disease resistance (Hasing et al., 2020) and accurate haplotype-phased genome reveals partial endoreplication (Piet et al., 2022).

7. Molecular markers: desirable selection resources

Molecular markers, namely, SSRs, SNPs, and InDels, plays important role in breeding to identify important traits and develop genetic maps through QTL tagging (Verma and Rana, 2013; Negi et al., 2021). They are widely used in gene identification for horticultural plant breeding programmes (Sonah et al., 2011), and to study genetic diversity among species and cultivars to compare the chemical composition of spices (Trindade, 2010). Often, EST data are useful to generate significant SSR and SNP markers (Y. Wang et al., 2019). In spices, linkage maps have been developed for many agronomically advantageous traits using different types of markers and mapping populations. In peppers, an intraspecific double haploid population was used for linkage mapping by AFLP and RAPD markers and the HEGS system (Rao et al., 2003; Sugita et al., 2005; Mimura et al., 2012). An EST-SSR marker was developed for species identification in peppers and was also mapped to tomato genome sequences (Shirasawa et al., 2013). Supplementary Table 6 illustrates the source of various markers along with their descriptions for major spices. Wide transcriptome studies suggest putative SSR markers and variants in the black pepper genome in response to drought (Negi et al., 2021). Markers from closely related genera, Curcuma longa, Zingiber officinale, and Amomum subulatum were used in a heterologous mode in small cardamom. Such studies would help to determine the genetic similarity and closeness of Elettaria and Amomum (Cyriac et al., 2016). The intraspecific variation in small cardamom has been analyzed by cytological studies, molecular data, and genome size (Anjali et al., 2016). Similarly, functional domain markers have been reported to reveal pathways of mosaic disease in small cardamom (Khan et al., 2020).

In Curcuma longa, EST-based SSRs are reported with a density of one SSR in every 14.73 Kb (Joshi et al., 2010). In ginger, EST studies have reported with significant SNPs and indels associated with specific traits (Chandrasekar et al., 2009). These were originated from unigenes and coding regions (Vidya et al., 2021). In garlic, several studies have reported the discovery of molecular markers from ESTs (Cunha et al., 2012), 642 SSRs from 21,694 EST sequences with an average frequency of 1 per 14.9 kb (Chand et al., 2015), and 14,879 SNPs and indels (Havey and Ahn, 2016). A comparative SSR study of Allium species (A. cepa, A. fistulosum, and A. tuberosum) and non-Allium monocot species has been reported (Barboza et al., 2018). In another study, 17374 SSRs with >1 hundred thousand variants were reported from transcriptomic data (Mehra et al., 2020). RNA-Seq association mapping with three garlic yield traits, namely, bulb weight, diameter, and the number of garlic cloves, has been reported, which are associated with 25, 2, and 30 SNPs, respectively (Zhu et al., 2019a). In another study, 4372 EST-SSR markers have been reported for diversity analysis (Li et al., 2022b). A set of unique markers has been developed in celery, and SSR has been mined between two cultivars (Fu et al., 2013; Li et al., 2014). In addition, the development of microsatellites for Myristica (Kusuma et al., 2020), EST-SSR in Mentha (Kumar et al., 2015a), and SSR for Dill (Jethra et al., 2018), and their applicability to other interrelated species, have been dissected.

In pepper, 623 ncRNA-based SSRs (119 miRNASSRs and 504 lncRNASSRs) were discovered, which are distributed over 12 chromosomes (Jaiswal et al., 2020). The 120 ncRNASSRs (60 each miRNASSR and lncRNASSR) were used to genotype 96 capsicum accessions belonging to C. annuum, C. chinense, and C. frutescens, with 75% of the SSRs being polymorphic. In another aromatic herb, cumin, which is grown for the presence of important metabolites for food, medicines, and essential oils (Heidari and Sadeghi, 2014), 8086 SSR markers have been reported for cross-transferability and diversity analyses (Bharti et al., 2018). In saffron, the gene regulatory pathway of flowering has been discovered with 79,028 functional domain markers (Qian et al., 2019). A Random amplified polymorphic DNA based ancestral species phylogenetic relationship has been studied (Caiola et al., 2004). Curry leaf, a fragrant plant known for its flavour, nutrition, and medical benefits, often face the challenge of discriminating among wild and cultivated populations unveiled by RAPD, DAMD, and ISSR markers (Verma and Rana, 2011, 2013). Systematic investigations with ISSR and ITS of wild Vanilla and their relatives (Villanueva-Viramontes et al., 2017), the involvement of diversity in vanilla germplasm (Ramos-Castellá et al., 2017), and varying premature fruit abortion histories (Perez et al., 2016). Overall, the precise incorporation of molecular markers in spice breeding programmes can lead to more efficient and targeted spice improvement by improving genetic diversity assessment, marker-assisted selection, disease resistance, an accelerated breeding cycle, and the improved resilience of spice crops to environmental challenges and diseases.

8. Noncoding RNAs: switch guiding switch resources

The eukaryotic genome consists of protein-coding RNAs (pcRNAs) and non-coding RNAs (ncRNAs). These RNAs play a vital role in gene regulation and expression (Kumar et al., 2023). It was recently discovered that ncRNAs play important regulatory roles in a variety of biological processes in plants, including spices (Kumar et al., 2023; Chandra et al., 2023). lncRNA is a form of non-coding RNA that has more than 200 nucleotides but does not code for proteins (Guttman et al., 2013). Several other plant species have been found to have numerous lncRNAs that have been reported to play an important role in cell differentiation (Kumar et al., 2023), gene splicing (Bardou et al., 2014), plant growth and development (Wang et al., 2017a), yield and stress response (Kumar et al., 2023), and provide resistance for Phytophthora (Yin et al., 2021). They also act as precursors of miRNAs and mimic miRNA target genes (Kumar et al., 2023). lncRNA expression is cell-type- or tissue-specific, developmentally regulated, and may differ in response to numerous stimuli (Derrien et al., 2012). miRNAs are a new class of small, non-coding RNAs (20–24 nucleotides in length) that regulate gene expression at the post-transcriptional level through mRNA cleavage or translational inhibition (Snigdha and Prasath, 2021; Chandra et al., 2023). In recent years, the identification and functional analysis of plant miRNAs has become one of the hottest research areas in plant science due to their role in almost all biological and metabolic processes, including plant organ development, signaling pathways, disease, and stress responses (Sun et al., 2012; Anjali et al., 2017; Chandra et al., 2023). Thousands of plant miRNAs have been deposited in publicly available miRNA databases, including miRBase (Griffiths-Jones, 2006), (http://microrna.sanger.ac.uk/) and the plant microRNA database (PMRD) (Zhang et al., 2010) (http://bioinformatics.cau.edu.cn/PMRD/). These results clearly show that plant miRNA research is still limited to a small number of plant species (Zhang et al., 2010). Several studies also reported that ncRNAs act by interacting with one or more protein-coding genes (Zhang et al., 2019; Statello et al., 2021). Identifying ncRNA targets is therefore a crucial step in understanding how ncRNAs work. Recently, many computational techniques for predicting plant miRNA and lncRNAs have been developed. In the past, limited progress has been made in identifying miRNAs and lncRNAs in spices, including black pepper, cardamom, turmeric, ginger, garlic, cayenne pepper, and saffron Supplementary Table 7. A study was conducted through small RNA sequencing to identify 110 known miRNAs, 18 novel miRNAs, and 1007 unique targets from various black pepper tissues to elucidate the functions of miRNAs in secondary metabolism, particularly piperine biosynthesis (Ding et al., 2021). In black pepper, >23,000 putative lncRNAs have been reported in response to dryness (Negi et al., 2021). In cardamom, drought-responsive differentially expressed genes (Zhang et al., 2019) and miRNAs depict the mechanism of resilience under water stress (Anjali et al., 2017).

In turmeric, miRNA families responding to Phythium and regulating secondary metabolites are reported (Chand et al., 2016a; Singh and Sharma, 2017). Transcriptome analysis reveals miRNAs differentially expressed in turmeric accessions in response to drought stress (Santhi et al., 2016) and the involvement of conserved miR319 showing a negative correlation with curcumin, a promising candidate for enhanced bioaccumulation (Sheeja et al., 2018). In the case of ginger, transcriptomic studies have been reported for the production of a bioactive component, gingerol, along with 16 miRNA families (Singh et al., 2016). Comparative transcriptomic studies of ginger and mango ginger are also reported to have 13 miRNA families with >300 target regions that are involved in cell signaling, reproduction, metabolism, and bacterial wilt stress (Snigdha and Prasath, 2021). Another study also reported 104 new miRNAs, and 28 differentially expressed miRNA families, along with their targeted genes involved in rhizome development (Xing et al., 2022). In the case of garlic, by EST approach, six miRNA families are reported to regulate stress response (Panda et al., 2014). Similarly, 8 and 6 lncRNAs are reported to be associated with clove-shaped features (Chen et al., 2018) and tuber yield (Zhu et al., 2019a), respectively. A functionally conserved miRNA 394 exerts an immune response to Fusarium infection in garlic, along with multiple others (Chand et al., 2016b, 2017). In pepper, lncRNA reports are available for fruit development (>2500 putative lncRNAs) and cold response (380 lncRNAs, 36 circRNAs, 18 miRNAs) (Ou et al., 2017), along with another report on the chilling response (Zuo et al., 2018). In pepper ripening, 43 miRNAs, 125 circRNAs, and 366 lncRNAs are reported (Zuo et al., 2019). In Capsicum, >12,000 lncRNA are reported to be available against abiotic stress like heat, cold, osmotic, and salt stress (Baruah et al., 2021). A total of 2525 lncRNAs, 47 miRNAs, and 71 circRNAs in seedling and flowering are also reported (Shu et al., 2021). The role of lncRNA and long intergenic ncRNAs (lincRNAs) in this species in graft tolerance and hybrid vigor is also reported (Yin et al., 2021) Supplementary Table 7. In saffron, flowering regulation has been reported with the role of miRNA, with its targeted genes mainly encodes for transcription factors (Taheri-Dehkordi et al., 2021) and putative lncRNAs (>70,000) (Choudhary et al., 2019). Recent discoveries on high-throughput sequencing-based identification of miRNAs from the curry leaf and their functional implications in secondary metabolite biosynthesis open a new avenue for miRNAs based regulation underlying spice accumulation (Gutierrez-Garcia et al., 2021).

9. Organelle genome: phylogenetic and evolutionary resources

In addition to the nuclear genome, the organelle genome contains genes related to the growth and development of species (Raveendar et al., 2015). Variations in the lengths of large single copy (LSC), small single copy (SSC), and inverted repeat (IR) regions were the main contributors to the size variation in the chloroplast genome in the evolution of plants (Xiao-Ming et al., 2017). The black pepper chloroplast genome, about 161,522 bp long and quadripartite, offers insights into evolutionary and molecular studies, aiding in genetic development and breeding (Gaikwad et al., 2023). Tabulation of organelles genomic resources and their utilization for various spices growth and developments have been presented as Supplementary Table 8. An interspecies comparison of chloroplast genomes provides insights on the use of structural variation in phylogenetic analysis in Allium and Piper, respectively (Huo et al., 2019; Li et al., 2022c). The mitochondrial genome of chiltepin pepper has been sequenced with 218 fully annotated genes (Magdy and Ouyang, 2020). The Chloroplast genome in Capsicum frutescens has been studied for species identification and phylogenetic analysis using DNA barcoding genes (rbcL and matK) (Shim et al., 2016). In another study, SSR repeats and InDels from the chloroplast genome have been reported (Jo et al., 2011). A complete chloroplast genome of chiltepin pepper of 156,817 bp, harboring 125 SSRs and 48 InDels, has been studied (Jo et al., 2011; Raveendar et al., 2015). The complete chloroplast genome sequencing of Ferula and Myristica sheds new perspectives on the phylogeny, taxonomy, plastomes, and evolution of this genus (Fan et al., 2021; Yang et al., 2022; Kusuma et al., 2023). Advancing Celery's full mitochondrial genome sequence and the discovery of a potential gene linked to cytoplasmic male sterility have been delineated (Cheng et al., 2021a), however, the chloroplast genome showed species interrelationships (Zhu et al., 2019b). Examining cytoplasmic male sterile accessions in the fennel mitochondrial genome assembly reveals two distinct ATP6 genes for the determination of male sterility (Palumbo et al., 2020). The chloroplast genome of Myristica, annotated, supports phylogenetic studies and species identification (de Oliveira et al., 2020). Chloroplast genomes reveal mint species diversity and phylogenetic evaluation through comparative studies (Wang et al., 2017b; Zubair Filimban et al., 2022). Furthermore, Chloroplast Rbcl gene-based phylogenetic diversity analysis revealed high genetic diversity and evolutionary landscapes among Tanzanian allspice collections (Lutege et al., 2023). Overall, these organelle resources are critical for spice health, survival, and efficient functioning, ensuring energy production, compartmentalization, and the identification of novel spice species for spice improvement in a multifaceted ways.

10. Web genomic resources

A genomic database contains resources compiling information about genome sequences, ESTs, transcriptome assembly, various non-coding RNAs, molecular markers, etc. from which sequence data can be retrieved for downstream functional analysis. Herein, we reviewed several available databases on various spices provided in Supplementary Table 9. For black pepper, microsatellite markers have been identified and characterized throughout the genome, providing a significant resource for improving genomics applications (Kumari et al., 2019). In addition, they developed a database of black pepper SSR markers called PiNigSSRdb, which contains 69,126 identified SSRs from assembled P. nigrum genomic sequences along with the in-silico predicted black pepper genomic microsatellites (Kumari et al., 2019). Another black pepper protein and peptide database, PiperPep, was constructed using black pepper mass spectrometry-derived data and contain the annotation of more than 1000 peptides (Umadevi et al., 2016). BPDRTDb, a Black Pepper Drought Transcriptome Database, has been developed (Negi et al., 2021), which contains a total of 114,598 transcripts, 4914 differentially expressed genes, 20124 putative gene region SSR markers, 14,742 primers, 259,236 variants (246,458 SNPs and 12,778 indels), 2110 transcription factors, 786 domains, and 1137 families. The transcriptome-based Mosaic Virus Database, SCMVTDb in small cardamom contains 123,338 transcripts, 5317 differentially expressed genes, 24,000 putative gene region markers, 147,442 and 154,217 SNPs and indels (Khan et al., 2020). The Curcumin Resource Database, CRDB is populated with 1186 curcumin analogs, 195 molecular targets, 9075 peer-reviewed publications, 489 patents, and 176 cultivars (Kumar et al., 2015b). Another database called SpicEST has been developed on the basis of EST's compilation of ginger and turmeric (Chandrasekar et al., 2009). CeleryDB is an online database for researchers to study celery's genome, genes, and proteins (Feng et al., 2018). For garlic, GarlicESTdb contains 21,595 ESTs (Kim et al., 2009). A database, AlliumMap, has genetic maps and marker data for 107 markers (73 EST-SSRs, 3 genomic SSRs, and 31 EST-SNP markers) of numerous Allium species, along with an AFLP-based linkage map (McCallum et al., 2012). In the Coriander Genomics Database, CGDB, 40,747 genes, of which 37,772 (92.7%) are annotated, and 7233 noncoding RNAs (339 miRNAs, 780 tRNAs, 5440 rRNAs, and 674 snRNAs) are available (Song et al., 2020b). A pepper EST database, PepperEST, contains 122,582 ESTs from 21 pepper EST libraries (Kim et al., 2008). Capsicum transcriptome DB contains tissue-specific EST data for capsicum root, stem, leaf, flower, and fruit (Gongora-Castillo et al., 2012b). The Saffron Genes database contains 6603 high-quality ESTs obtained from the stigma of the plant (D'Agostino et al., 2007).

11. Genomic prediction and machine learning-based resources

Marker-assisted breeding could not tackle quantitative traits governing loci and introduce a promising method for quantitative trait improvements called genomic selection or prediction (Hong et al., 2020). The potential of genomic selection uses genotype and phenotypic data from a training population to predict the phenotypes of a test population using genotype data (Hong et al., 2020). It can further uncover several attributes to increase the accuracy of predictions in yield data under genotype-environment interactions, and geographical effects (Tsai et al., 2020). Though the studies on genomic selection are confined to only a few spices, it would certainly be the best alternative way to improve spice breeding which faces enormous challenges and often fails due to unannotated desired gene loci, a lack of marker footprints, and signature elements of spices and their wild relatives (Hong et al., 2020; Kim et al., 2022). To increase the effectiveness of selection, genomic selection employs genome-wide random markers for capsaicinoid concentration in pepper breeding lines (Kim et al., 2022).

The routine advancement of plant genotypes and phenotypes has been transformed by technological advancements, resulting in the frequent production of huge, complicated data sets. As a result, there are now more efforts being made to combine different data sets and interpret these metrics (van Dijk et al., 2021). Hitherto, few reports have highlight the use of machine learning in spice production and improvement. Several different spices of good quality with numerous health benefits have been identified and classified using machine-learning approaches (Kukade et al., 2019). Autonomous machine-learning algorithms have been used to dissect three and multiple stigmas in saffron (Beiki and Keify, 2012). Being an expensive spices, saffron adulteration is one of the major issues rectified by visual computing and machine learning algorithms (Husaini et al., 2022). Machine learning has been widely used for feature-specific nutritional dosage detection and field classification detection for garlic (Hahn et al., 2022), grading in Cardamom (Jose and Krishnan, 2015), pest and disease management in chili (Ahmad Loti et al., 2021), simulation of isoquercitrin in Coriander (Usman et al., 2021), Mono-disperse carbon quantum dot characterization in fennel (Dager et al., 2019), detection of Fusarium in black pepper (Karadag et al., 2020), effects of peptide-protein interaction as drug targets in Cinnamon (Wang et al., 2021), and clove bud origin (Gunawan and Kresnowati, 2020). Furthermore, adulteration is a common practice in the spice market, and commercialization is largely managed by machine learning for turmeric and ginger powder (Jahanbakhshi et al., 2021). Moreover, the integration of machine learning with unrevealed spice species can provide sustainability to the spice world and even discover new spices for our food.

12. Future perspective and challenges

Spices have been the most important crop in agriculture and horticulture for decades. In the post-pandemic world, it has gained further consumer interest. It has been a rich source of flavorings and aromas in delicious foods. As it contains natural ingredients, it is preferred over synthetic ingredients that have adverse health effects. A plethora of Genomic resources on spices and their utility for the creation of next-generation spices has been illustrated in Fig. 5. The spices are still neglected as a crop of secondary importance. In our study, we found two main problems.

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/).

First, in the spice community, many economically and medicinally important spice plants have limited genomic resources, i.e., there is a lack of data availability. The main challenge here with spices is the unavailability of completed genomes and their proper molecular genetic linkage maps.

Moreover, most spices are inherently perennial, which hampers their study at the genetic and molecular levels, as well as, in the development of mapping populations and map-based studies. These challenges can be overcome by advanced tools and techniques like, optical mapping and haplotype-based sequencing. There is a need for the development of trait-related markers to improve the germplasm's ability to stand up to climate change-induced biotic and abiotic stresses. Unless the complex genome architecture of spices is decoded to develop genomic resources with high-density genetic markers, the varietal improvement program cannot be accelerated. Even after identifying specific genes from the genomic resources, functional validation is required. Various transcriptome studies related to specific biotic and abiotic strains are used for spice improvement and management. With the intervention of molecular and genomic tools to characterize trait-specific reference panels, genomic resources such as alleles, candidate genes, and regulatory genes for efficient breeding approaches can be generated.

Secondly, limited spice genomic resources, such as ESTs, GSS, nucleotides, SRA, GEO datasets, proteins, unigenes, and gene-based markers, are available but have not yet been used in breeding and management. With the decreasing cost of NGS data generation, the pace of genomic resource development can be further accelerated. These are imperative in molecular core-based genomic resource management, Multi-parent advanced generation inter-cross (MAGIC) and nested association mapping (NAM) studies, and molecular assisted breeding (MAB) for varietal improvement. Furthermore, there is a greater need for the development of global consortia for spice genomic resource research and improvement. Resource pooling across the world can reduce cost through the evaluation of resources in a diverse ecosystem. Such evaluations of resources are relevant in the development of climate-resilient spices for future requirements. To make the best use of genomic resources, more investment is required for machine-based advanced genotyping and phenotyping for health molecules like secondary metabolites and AMPs. There is a greater need to pay attention to this neglected crop of spices, especially in the post-pandemic world, which is already challenged with AMR and immunity.

CRediT authorship contribution statement

Parinita Das: Data curation, Writing – original draft, collected and curated all information. drafted the manuscript. Tilak Chandra: Data curation, Writing – original draft, collected and curated all information. drafted the manuscript. Ankita Negi: Data curation, Writing – original draft, collected and curated all information. drafted the manuscript. Sarika Jaiswal: Writing – review & editing, conceived the theme of the study. collected and curated all information. reviewed and edited the manuscript. Mir Asif Iquebal: Writing – review & editing, conceived the theme of the study. collected and curated all information. reviewed and edited the manuscript. Anil Rai: Writing – review & editing, reviewed and edited the manuscript, All authors read and approved the final manuscript and contributed to the article and approved the submitted version. Dinesh Kumar: Writing – review & editing, conceived the theme of the study. reviewed and edited the manuscript.

Declaration of competing interest

The authors affirm that they have no known financial or interpersonal conflicts that would have appeared to have an impact on the research presented in this study.

Handling Editor: Dr. Quancai Sun

Abbreviations

GWAS

Genome wide association studies

QTL

Quantitative trait loci

MAB

Marker assisted breeding

BC

Before Christ

EST

Expressed sequence tag

GSS

Genomic survey sequences

SRA

Sequences read archives

GEO

Gene expression omnibus

NCBI

National center for biotechnology information

MYB

Myeloblastosis viral oncogene homolog

SSR

Simple sequence repeat

SNP

Single-nucleotide polymorphism

Indel

insertion or deletion

AFLP

Amplified fragment length polymorphism

RAPD

Random amplification of polymorphic DNA

HEGS

High efficiency genome scanning

LSC

Large single copy

SSC

Small single copy

AMR

Antimicrobial resistance

MAGIC

Multi-parent advanced generation inter-cross

NAM

Nested association mapping

AMP

Antimicrobial peptides

HEGS

High efficiency genome scanning

DAMD

Directed amplification of minisatellite-region DNA

AMR

Antimicrobial resistance

WRKY

Heptapeptide motif WRKYGQK

SSH

Suppression subtractive hybridization

RGC

Resistance gene candidates

PepGMV

Pepper golden mosaic virus

Appendix A. Supplementary data

The following are the Supplementary data to this article.

Data availability

No data was used for the research described in the article.