Microsatellite-based evidences of genetic bottlenecks in the cryptic species ‘‘Andrographis paniculata Nees’’: a potential anticancer agent Alireza Valdiani • Arash Javanmard • Daryush Talei • Soon Guan Tan • Sonia Nikzad • Mihdzar Abdul Kadir • Siti Nor Akmar Abdullah Received: 11 August 2012 / Accepted: 10 October 2012 Ó Springer Science+Business Media Dordrecht 2012 Abstract Andrographis paniculata (AP) is a medicinal plant species introduced into Malaysia. To address the genetic structure and evolutionary connectedness of the Malaysian AP with the Indian AP, a DNA sequence anal- ysis was conducted based on 24 microsatellite markers. Out of the 24 primer sets, seven novel microsatellite primers were designed and amplified intra-specifically according to the available Indian AP sequences at the National Centre for Biotechnology Information (NCBI), where 17 of them were amplified using the cross-species strategy by employing the primers belonging to Acanthus ilicifolius Linn (Acanthaceae) and Lumnitzera racemosa Wild (Combretaceae). The primers were then applied on the Malaysian AP accessions. Sixteen of the new microsatellite loci were amplified successfully. Analysis of these micro- satellite sequences, revealed some significant differences between the Indian and Malaysian AP accessions in terms of the size and type of the repeat motifs. These findings depicted the cryptic feature of this species. Despite iden- tifying several heterozygous alleles no polymorphism was observed in the detected loci of the selected accessions. This situation was in concordance with the presence of ‘‘fixed heterozygosity’’ phenomenon in the mentioned loci. Accordingly, this was fully consistent with the occurrence of the genetic bottleneck and founder effect within Malaysian AP population. Apart from the amplification of new microsatellites in this species, our observations could be in agreement with the risk of genetic depletion and consequently extinction of this precious herb in Malaysia. This issue should be taken into consideration in the future studies. Keywords Genetic bottleneck  Founder effect  Microsatellite  Mutation  Cryptic species Introduction Andrographis paniculata (2n = 50) known as the king of bitters in English, is a medicinal plant belonging to the family Acanthaceae. Even though the herb is famous due to its pharmaceutical effects, the agricultural and industrial applications have been taken into consideration recently [1]. Historical background of the relations between India and Malaysia supports the idea that AP was imported for medicinal purposes by the Indians who were brought from the southern region of India during the British colonization. These introduced genotypes were then distributed A. Valdiani (&) Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia e-mail: alireza.valdiani@gmail.com A. Javanmard Agriculture Biotechnology Research Institute of Iran (ABRII), Karaj, Iran D. Talei Medicinal Plant Research Center, Shahed University, Tehran, Iran S. G. Tan  S. Nikzad Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia M. A. Kadir (&)  S. N. A. Abdullah Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia e-mail: mihdzar@gmail.com 123 Mol Biol Rep DOI 10.1007/s11033-012-2231-6