Intraspecific variations in cardamom (Elettaria cardamomum Maton): assessment of genomic diversity by flow cytometry, cytological studies and ISSR analysis

Comprehensive Evaluation and Selection of Cardamom (Elettaria cardamomum (L.) Maton) Germplasm Using Morphological Traits

Cardamom (Elettaria cardamomum (L.) Maton) plays a crucial role in Guatemala's agriculture, supporting local families and covering 169,429.29 ha (making it the world's leading producer). Since its introduction to Guatemala in 1910, limited research has focused on unraveling the diversity and defining morphological traits critical for selecting excellent accessions. In this study, we examined 17 morphological traits across 288 accessions to identify key features associated with the germplasm. The comprehensive analysis employed principal component analysis, a morphological composite value (F-value), linear regression, and hierarchical clustering. The Shannon-Wiener diversity index ranged from 0.10 to 2.02, indicating the variation in diversity among traits. Principal component analysis and hierarchical clustering revealed six distinct germplasm groups. The comprehensive analysis facilitated the selection of 14 excellent accessions, and the regression equation incorporating criteria such as plant height, capsule color, panicle number per plant, panicle length, rhizome color, cluster number per panicle, cluster node length, and capsule number per cluster to identify cardamom germplasm. To develop a conservation strategy for the two putative foreign varieties ('Malabar' and 'Mysore'/'Vazhukka') introduced in Guatemala based on plant height, another 12 accessions were selected with a second comprehensive evaluation. This information offers insights into cardamom diversity for informed selection enhancing national utilization, productivity, and conservation.

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

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.

Genome size, chromosome number variation and its correlation with stomatal characters for assessment of ploidy levels in a core subset of mulberry (Morus spp.) germplasm

The large size of the germplasm collection along with scanty information on their cytological and genome constitution have hindered well-planned breeding schemes in mulberry. To address the issue, a study was undertaken to investigate the variability in DNA content and genome size, chromosome number, ploidy and its relation with important stomatal characteristics among 162 mulberry germplasm. These germplasm comprise a core subset of 150 collections along with a representative collection of different mulberry species including the wild. Among the germplasm belonging to 16 species, we identified 122 diploids (2n = 28), 4 aneuploids (2n = 30), 13 triploids (2n = 42), 15 tetraploids (2n = 56), 7 hexaploids (2n = 84) and 1 dodecosaploid (2n = 308) based on the chromosome count. Most of the cultivated mulberries are found to be diploids. The mean nuclear 2C DNA content estimated by Flow cytometry, varied from 0.723±0.006 pg (M. australis, 2n = 2x) to 7.732 pg (M. nigra, 2n = 22x). The 2C DNA content positively correlated with the ploidy status and stomatal length (r = 0.814, p<0.001). Based on the 1Cx value, the study also suggests that the majority of the polyploid species have experienced genome downsizing in relation to their diploid progenitors. This study provides the most essential information on chromosome number, ploidy and DNA content to facilitate the utilization of a core subset of germplasm in the mulberry breeding program.

Small cardamom genome: development and utilization of microsatellite markers from a draft genome sequence of Elettaria cardamomum Maton

Small cardamom (Elettaria cardamomum Maton), the queen of spices, is the third most expensive spice in the world after saffron and vanilla, valued highly for its aroma and taste. This perennial herbaceous plant is a native of coastal parts of Southern India and displays a significant amount of morphological diversity. Its genetic potential has not been exploited due to lack of genomic resources limiting our understanding of the genome and important metabolic pathways which give it the economic advantage in the spice industry. Here, we report upon the de novo assembled, draft whole genome sequence of cardamom variety, Njallani Green Gold. We used a hybrid assembly strategy using the reads from the Oxford Nanopore, Illumina and 10x Genomics GemCode sequencing chemistries. The assembled genome length was 1.06 Gb (gigabases) which is close to the estimated genome size of cardamom. More than 75% of the genome was captured in 8000 scaffolds with a N50 of 0.15 Mb. The genome appears to have a high repeat content and 68055 gene models were predicted. The genome is close to Musa species and displays an expansion and contraction in different gene families. The draft assembly was used for in silico mining of simple sequence repeats (SSRs). A total of 2,50,571 SSRs were identified of which 2,18,270 were perfect SSRs and 32,301 were compound SSRs. Among the perfect SSRs, trinucleotides were most abundant (1,25,329) and hexanucleotide repeats appear least (2,380). From the 2,50,571 SSRs mined, 2,27,808 primer pairs were designed based on flanking sequence information. Wet lab validation was performed for 246 SSR loci and based on their amplification profiles, 60 SSR markers were used for diversity analysis of a set of 60 diverse cardamom accessions. The average number of alleles detected per locus were 14.57 with a minimum of 4 and maximum of 30 alleles. Population structure analysis revealed the presence of high degree of admixtures which could primarily be due to cross-pollination prevalent in this species. The SSR markers identified would help in the development of gene or trait-linked markers which can be subsequently used for marker-assisted breeding for crop improvement in cardamom. The information on utilization of the SSR loci for generation of markers has been developed into a public database, 'cardamomSSRdb' that is freely available for use by the cardamom community.

Intraspecific variation in genome size in Artemisia argyi determined using flow cytometry and a genome survey

Different collections and accessions of Artemisia argyi (Chinese mugwort) harbour considerable diversity in morphology and bioactive compounds, but no mechanisms have been reported that explain these variations. We studied genome size in A. argyi accessions from different regions of China by flow cytometry. Genome size was significantly distinct among origins of these 42 Chinese mugwort accessions, ranging from 8.428 to 11.717 pg. There were no significant intraspecific differences among the 42 accessions from the five regions of China. The clustering analysis showed that these 42 A. argyi accessions could be divided into three groups, which had no significant relationship with geographical location. In a genome survey, the total genome size of A. argyi (A15) was estimated to be 7.852 Gb (or 8.029 pg) by K-mer analysis. This indicated that the results from the two independent methods are consistent, and that the genome survey can be used as an adjunct to flow cytometry to compensate for its deficiencies. In addition, genome survey can provide the information about heterozygosity, repeat sequences, GC content and ploidy of A. argyi genome. The nuclear DNA contents determined here provide a new reference for intraspecific variation in genome size in A. argyi, and may also be a potential resource for the study of genetic diversity and for breeding new cultivar.

Systematics Evaluations of Morphological Traits, Chemical Composition, and Antimicrobial Properties of Selected Varieties of Elettaria cardamomum (L.) Maton

Elettaria cardamomum is cultivated in the Southern part of India showed great extinct of differences in their morphotypes and chemical compositions. In the present study, we have selected three varieties of Elettaria cardamomum “Valley Green, Palakuzhi, and ICRI”, to analyze the morphological perturbations, chemical compositions, and antimicrobial activities. The differences in the morphological character of cardamom varieties (Valley Green, Palakuzhi, and ICRI) were carried out on the basis of panicles, capsules shape, plant height, tiller, and seeds per capsule. The GC-MS analysis of the essential oils resulted in the identification of 27, 29, 30 compounds representing over 97.4%, 95.2%, and 98.8% of the Valley Green (VG), Palakuzhi (PAL), and ICRI fruit oils respectively. Monoterpene, α-terpinyl acetate varied from 35.4 to 47.5%, a major constituent while 1,8-cineole (22.8% to 27.4%) observed the second major compounds revealed in oils of these cultivars. Further, the antimicrobial activities of each essential oils were performed against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Klebsiella pneumoniae, Candida albicans, and Aspergillus niger. The maximum inhibition percentage against the microbes was observed in Valley Green essential oil as compared to oils of other varieties.

Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach

Small cardamom (Elettaria cardamomum), grown in limited coastal tropical countries is one of the costliest and widely exported agri-produce having global turnover of >10 billion USD. Mosaic/marble disease is one of the major impediments that requires understanding of disease at molecular level. Neither whole genome sequence nor any genomic resources are available, thus RNA seq approach can be a rapid and economical alternative. De novo transcriptome assembly was done with Illumina Hiseq data. A total of 5317 DEGs, 2267 TFs, 114 pathways and 175,952 genic region putative markers were obtained. Gene regulatory network analysis deciphered molecular events involved in marble disease. This is the first transcriptomic report revealing disease mechanism mediated by perturbation in auxin homeostasis and ethylene signalling leading to senescence. The web-genomic resource (SCMVTDb) catalogues putative molecular markers, candidate genes and transcript information. SCMVTDb can be used in germplasm improvement against mosaic disease in endeavour of small cardamom productivity. Availability of genomic resource, SCMVTDb: http://webtom.cabgrid.res.in/scmvtdb/.

Deep sequencing identified potential miRNAs involved in defence response, stress and plant growth characteristics of wild genotypes of cardamom

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.