Development of Microsatellite markers for small cardamom lettaria cardamomum Maton

Abstract

Small cardamom (Elettaria cardamomum Maton) of the family Zingiberaceae is an important newlinespice and occupies a unique position in the national as well as international spice market. However, newlineunderstanding of this crop at molecular level is very limited and little genomic research has been newlinedone. The present study was aimed to develop a repository of reproducible SSR markers to study newlinegenetic diversity and taxonomic inter relationships in small cardamom. For this three approaches were newlinefollowed viz. i) selective hybridization enrichment method ii) development of SSR markers from EST newlinedatabases iii) transferability of previously reported SSR markers to cardamom. newlineThe denovo isolation of microsatellites from small cardamom resulted in the identification of newline140 microsatellite repeats from 270 clones. Primers were designed for 58 microsatellites and 44 newlineamplified products of expected size in cardamom. Among them six SSR markers were polymorphic newlineand detected a total of 22 alleles among the 20 cardamom genotypes with an average of 3.6 alleles per newlinelocus. The allelic variants ranged from 2-7alleles. The PIC value for the markers ranged from 0.14 to newline0.38 with an average of 0.28. The mining of SSR sequences in the dbEST database (NCBI) of newlineZingiber resulted in 188 EST SSR primers from the contigs. A set of 22 primers were shortlisted for newlinetransferability to cardamom and utilized with 79 SSR primers from different related genera (Rice, newlineZingiber, Curcuma and Amomum). In total 30 SSR primers from different related genera was newlineproduced consistent amplification in cardamom out of which three markers (one ginger EST SSR newlineprimer and two large cardamom primers) were polymorphic. A total of fifteen alleles were detected newlinewith a range of 2-7 alleles per SSR marker. The average number of alleles per SSR marker was five. newlineFour SSR markers generated unique banding patterns for different cardamom genotypes. The nine newlinepolymorphic SSR markers differentiated the 20 genotypes into two major clusters at 53% similarity newlinebased on their genetic characters and the genotypes showed a correlation with their geographic origin. newlineThis is the first report of development of microsatellite markers in small cardamom. This study is an newlineinitiative towards molecular profiling of more unexploited accessions of small cardamom that can newlineprovide insights into patterns of genetic diversity. newline