Genetic diversity in ecotypes of the scarce wild medicinal crop Zingiber moran revealed by ISSR and AFLP marker analysis and chromosome number assessment

Abstract

Zingiber moran, a rare ginger found only in a few parts of northeast India, faces the threat of extinction due to its exploitation as an important medicinal plant. In this study, the chromosome number of wild ecotypes of Z. moran was determined and the genetic analysis was carried out using two kinds of molecular markers: inter simple sequence repeats (ISSR) and amplified fragment length polymorphism (AFLP). A chromosome number of 2n = 22 was confirmed for all 10 ecotypes investigated. AFLP analysis revealed a greater amount of genetic polymorphism (95.06%), with a strong resolving power in detecting intraspecific variation, compared to ISSR analysis (34.61%). Genetic diversity parameters, such as number of observed alleles (n_a), mean number of effective alleles (n_e), mean Nei's gene diversity index (h), and Shannon index (I) for ISSR and AFLP were in the range 1.34–1.95, 1.25–1.60, 1.44–0.33, and 0.20–0.49, respectively. Marker indices and polymorphic information content varied from 0.5–19.3 and 0.03–0.27 for ISSR, and 28.2–39 and 0.3–0.39 for AFLP, respectively. Dendrograms derived by unweighted pair group method of arithmetic averages cluster analysis based on molecular data classified the ecotypes into two major clusters. The Mantel test cophenetic correlation coefficient (r) for ISSR (0.85) and AFLP (0.91) showed a good degree of confidence in the association with 10 ecotypes. Clustering was further supported by principle component analysis which demarcated individuals of hilly topography from the ones of plain land.

Keywords::

• AFLP
• chromosome count
• genetic diversity
• ISSR
• Zingiber moran

Acknowledgements

A.D. and V.K. are grateful to the Ministry of Human Resources Development (MHRD), the Council of Scientific and Industrial Research (CSIR) and the Government of India for student fellowships. We thank Dr G.C. Sarma, of the Gauhati University for the kind supply of study material. A.P., S.M., and L.R. thank the Department of Biotechnology (DBT) of the Government of India for funding the project through the DBT Twinning Programme for NE (BT/33/NE/TBP/2010).