Genetic studies in rattan palms (Calamus sp.) using SSR markers

Natural variation is essential for conservation and utilization of plant genetic resources. Human interference on forests may cause depletion of natural genetic variation in the gene pool and even to genetic erosion of certain species. Rattans are one such species currently under crisis due to over-exploitation. They represent high value non-wood forest produce primarily used for making furniture, handicraft items and an important raw material in the cottage industry which contributes significantly in rural economy. There are about 1 lakh people in Kerala living out of this valuable resource. However, number of small scale industrial (SSI) units depending on these forest produce are decreasing drastically.  Besides, over exploitation of the rattans has exerted severe pressure on existing populations and sometimes resulted in loss of genetic diversity.

There are about 600 rattan species in 13 genera globally and 51 species in 4 genera in India, of which 75% are endemic and 40.5% threatened. The Western Ghats region of India is rich in species diversity of rattans with one genus, viz. Calamus having 27 species of which 21 are identified.

Presently associated (as Principal Investigator) to a research project on ‘Genetic studies on selected rattan palms (Calamus sp.) using microsatellite markers’.

Objectives of the project are to collect natural populations of the selected rattan palms, viz. C. brandisii, C. gamblei, C. nagabettai, C. thwaitesii, C. travancoricus and C. hookerianus and analyze genetic diversity, population structure and differentiation using SSR markers.

The project is being funded by Kerala Biotechnology Commission/KSCSTE.

Genetic Structure of Oryza rufipogon Griff. Natural Populations

Genetic Structure of Oryza rufipogon Griff. Natural Populations in Malaysia: Implications for Conservation and Genetic Introgression of Cultivated Rice

Abstract
Thirty polymorphic Oryza sativa microsatellite loci (SSRs) were used to study population genetic structure of O. rufipogon Griff. natural populations in Malaysia. A total of 445 alleles were detected with an average of 14.8 alleles per locus in 176 individuals of O. rufipogon sampled from the states of Penang, Kedah, Kelantan and Terengganu where the natural populations are still found. The Kelantan population in the northeast of Peninsular Malaysia had the highest level of genetic diversity as measured by the mean number of alleles per locus, Aa=7.67, average number of effective alleles, Ae=5.50, percentage of polymorphic loci, P=100%, observed heterozygosity, Ho=0.631 and expected heterozygosity, He=0.798. In contrast, the Terengganu population in the east showed the lowest level of genetic diversity measured by the same criteria (Aa=4.23, Ae=2.10, P= 100%, Ho=0.549 and He=0.449). Model–based clustering analysis using the STRUCTURE 2.2 program placed all the individuals into 12 clusters that corresponded to the geographic sampling locations. Neighbour-joining tree was constructed based on Nei’s genetic distance to further assess the genetic structure of the O. rufipogon individuals, showed good agreement (93.8%) with the model-based cluster analysis. However, the neighbour-joining tree identified subpopulations that STRUCTURE could not identify. The classification of individuals from the same populations under the same cluster supported the population differentiation. These two analyses seemed to indicate expansion of populations from the northeast of Peninsular Malaysia (Tumpat, Pasir Mas and Kota Bahru, Kelantan) not only to the immediate south of the region i.e. Terengganu but also into the northwest (i.e. Penang and Kedah) with the former being more recent. Oryza rufipogon accession IRGC105491 and O. sativa ssp. indica cultivar MR219, which were included in this study for comparisons with the local wild rice accessions, indicated that introgression of cultivated rice could change genetic composition and affect the population genetic structure of wild rice. This possibility should be carefully considered in plans to conserve this wild rice.

Published in:
Tropical Plant Biol. (2010) 3:227–239