Development of an ISSR based SCAR marker to identify small cardamom Malabar (prostrate panicle) variety (Elettaria cardamomum (L.) Maton.)

Abstract

Small cardamom (Elettaria cardamomum (L.) Maton), a perennial cash crop exhibits an array of natural variations. Malabar, Mysore and Vazhukka are the three major cultivated forms/natural varieties of cardamom, with prostrate, erect and semi-erect panicles respectively. In terms of several qualitative and quantitative features, the Malabar variety is relatively superior to the three varieties. However, the major morphologically discriminative characteristic, panicle orientation, is only visible until the plant has reached physiological maturity. A variety-specific marker was developed and defined in this study for the rapid and accurate differentiation of Malabar varieties at the juvenile stage. In total, 35 ISSR primers were initially screened in 50 small cardamom accessions and two outgroup types, with 18 of them yielding distinct, reproducible profiles. In individuals of the Malabar variety, the ISSR primer (UBC 866–1500 bp) generated an intact, distinct, variety-specific amplicon, which was therefore cloned, sequenced and characterized. Small cardamom accessions from the Malabar variety (prostrate panicle) from different geographic regions, as well as varieties with erect panicles and hybrids, were used to validate the developed SCAR (sequence characterized amplified region) marker(named SBBT4F/SBBT3R). Consistent amplification of a distinct 1350 bp fragment in Malabar variants validated the marker's specificity. According to the findings, the SCAR marker is promising in identifying cardamom varieties with prostrate panicles (Malabar) and thus is expected to make significant contributions in the authentication of varietal selection from F1 hybrids during breeding programmes by reducing the time and labor involved in hybridization experiments in this perennial crop.