Whole Genome Sequence and SSR Markers of Small Cardamom (Elettaria cardamomum)

Small cardamom (Elettaria cardamomum), commonly referred to as the “Queen of Spices”, is a highly valued spice crop, which is known to have its origin in South India and Sri Lanka. It is one of the oldest spices of the world and is the third most expensive spice after saffron and vanilla. Despite its economic importance, in terms of global market price that this crop commands, very scarce genomic information is available for this crop. This severely limits the feasibility and success of various crop improvement endeavours. To overcome this limitation, the genome of the small cardamom variety, Njallani Green Gold was sequenced. This is the first report for the de novo assembled draft genome sequence of small cardamom. The assembled genome length was 1.06 Gb (gigabases), captured in 8000 scaffolds with a N50 of 0.15 Mb. A total of 68,055 gene models were predicted. The whole genome sequence (WGS) was utilized for the development of 2,27,808 SSR (simple sequence repeat) markers, based on flanking sequence information. A few of these were validated by performing molecular profiling of sixty diverse cardamom accessions. The SSR marker EC 49 was identified to possess the highest polymorphism information content (PIC) of 0.80. Many other highly polymorphic SSR markers, namely EC 1, EC 33, EC 47, EC 89, EC 90, EC 106, EC 183, EC 193, EC 196 and EC 212 were identified with a PIC value > 0.60. The SSR markers identified will serve as important genomic resources in cardamom. Many of these can be used for marker-assisted breeding for crop improvement and for germplasm characterization. The information on utilization of the SSR loci for generation of markers has been developed into a public database, the ‘cardamomSSRdb’. This database is freely available for use by the cardamom community.