title: Isolation and characterization of genomic microsatellite markers for small cardamom (Elettaria cardamomum Maton) for utility in genetic diversity analysis.
abstract: Microsatellite markers in small cardamom (Elettaria cardamomum Maton) were developed using the selective hybridization enrichment method. A total of 140 microsatellite repeats were identified from 270 clones. Primers were designed for 58 microsatellites and 44 primer pairs amplified products of expected size in cardamom. These markers were used for studying the diversity of 20 important small cardamom genotypes, and six markers were found to be polymorphic. The number of alleles ranged from 2 to 7 with an average of 3.6 per locus. Polymorphic information content values ranged from 0.14 to 0.38 based on dominant scoring. The two markers ECM 47a and ECMG 28 generated specific banding patterns for the genotypes MCC7 (Pink tiller) and APG434 (MA18) respectively. Dendrogram illustrated the genetic similarity between different genotypes of Kerala and Karnataka regions. It differentiated the closely related genotypes and released varieties into separate groups. Principal coordinate analysis revealed PV1 and ICRI 1 as the most divergent genotypes. The study demonstrated that these markers are informative and can be further utilized for generating reliable molecular data for assisting the crop improvement of small cardamom. Cross generic transferability (71.4 %) of the developed primers proved that they are useful for phylogenetic studies in the family Zingiberaceae. This is the first report of de novo isolation, characterisation and utilization of microsatellite markers for the genetic diversity analysis of small cardamom.
authors.affiliation: Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Marikunnu P.O, Kozhikode, Kerala 673 012 India.
authors.forename: Anu
authors.initials: A
authors.lastname: Cyriac
authors.affiliation: Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Marikunnu P.O, Kozhikode, Kerala 673 012 India.
authors.forename: Ritto
authors.initials: R
authors.lastname: Paul
authors.affiliation: Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Marikunnu P.O, Kozhikode, Kerala 673 012 India.
authors.forename: K
authors.initials: K
authors.lastname: Anupama
authors.affiliation: Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Marikunnu P.O, Kozhikode, Kerala 673 012 India ; ICAR-IIHR Central Horticultural Experimental Station, Chettalli, Karnataka India.
authors.forename: R
authors.initials: R
authors.lastname: Senthil Kumar
authors.affiliation: Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Marikunnu P.O, Kozhikode, Kerala 673 012 India.
authors.forename: T E
authors.initials: TE
authors.lastname: Sheeja
authors.affiliation: Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Marikunnu P.O, Kozhikode, Kerala 673 012 India.
authors.forename: K
authors.initials: K
authors.lastname: Nirmal Babu
authors.affiliation: Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Marikunnu P.O, Kozhikode, Kerala 673 012 India.
authors.forename: V A
authors.initials: VA
authors.lastname: Parthasarathy
keywords: Cross generic transferability; Elettaria cardamomum; Microsatellite markers; Small cardamom