More than half of the world's population lives near the coast and with the increase in population, its pressure on coastal resources is rising. This pressure is causing a rapid decline in the quality of coastal systems. Owing to lack of space, coastal communities have been settling near shore areas, which are actually unsafe for permanent habitation thereby leading to increasing loss of life and property by storm floods and raising the demand for better sea defences. A principal cause of coastal ecosystem degradation is the unsustainable exploitation of natural resources stemming from the rapid population growth. A second set of problems pertains to the pollutants released in the marine environment. Mangrove and coral reef are the most threatened ecosystems. With a view to preventing further destruction of mangrove forests, for sustained improvement and utilization of mangrove forest genetic resources, and to conserving and enhancing the biological diversity in mangrove ecosystems, it is felt that an integrated approach for the preparation of a 'global strategy' is required. The conservation and preservation of mangrove genetic resources is the first step towards this end.

At the M. S. Swaminathan Research Foundation, the initial focuses was on molecular mapping and phylogenetic relationships among the different mangrove species with a view to gain an insight to intra and inter population and species diversity. However, later, molecular marker systems were used to genetic fingerprint many of the important crop species - their land races and their wild relatives.

MANGROVES

Mangroves are one of the complex and unique plant communities that are salt-tolerant and inhabit estuarine aI).dintertidal regions of the tropical and subtropical regions of the world. Ever-increasing threat to this ecosystem warrants conservation and sustainable I utilization. Since understanding the genetic structure of the mangrove plant species is a pre-requisite for conservation, analysis of genetic polymorphism was carried out in four important mangrove 1pecies viz. Avicennia marina, Acanthus ilicifolius and Excoecaria agallocha, Rhizophora spp using RAPO and RFLP, PCR-RFLP, AFLP markers.

The study showed greater degree of polymorphism in E. agallocha than in A. ilicifolius and A. marina. Ten species belonging to four genera of the mangrove tribe Rhizophoreae found in the Indian subcontinent were analysed for species identification and genetic relationship using nine mitochondrial gene probes. RFLP pattern observed with 27 probe enzyme combinations the genera Rhizophora, Bruguiera, Ceriops and Kandelia differentiated these species into three classes of mitotypes. The taxonomic and phylogenetic relationships between different species and genera of the tribe Rhizophoreae were studied through markers. Clustering of these mitotypes indicated that Rhizophora was more closely related to Ceriops-Kandelia than to the Bruguiera. Though the component species of each genus clustered together, a high degree of heterogeneity was observed among four species of the genus Rhizophora and three species of genus Bruguiera.

Species belonging to Rhizoplloraceae : Molecular phylogeny and genetic diversity in all the nine species (Rhizophora mucronata, R. apiculata, R. stylosa, Bruguira cylindrical, B.parviflora, B.gymnorriza, Ceriops tagal and C. decandra) and a natural Rhizophora hybrid, of the mangrove Rhizophoraceae, occurring in the Indian sub-continent were analysed using random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP) and RFLP of polymerase chain reaction amplified chloroplast genes (PCR-RFLP) as markers. Rhizophora mucronata was found to be the chloroplast donor for the natural interspecific hybrid. The putative parents of the naturally occuring interspecific hybrid in Pichavaram were reconfirmed to be R. apiculata and R. mucronata. A dendrogram based on the data sets from all the three marker systems revealed that the four genera segregated into three species groups.

RFLPs for the mitochondrial genome were readily observed, and the RFLP profile of R. apiculata was exactly the same as that of the hybrid, establishing its maternal status for the hybrid. This is the first report on characterizing the parentage of a Rhizophora hybrid using molecular markers.

Our focus was also to study diversity and DNA fingerprinting of some of the important crop species and their landraces. Towards this, we have done extensive collection and documented the genetic fingerprint in Pennicetum, Rice, Cajanus, Vigna mungo, Millets. Recently, we also used molecular markers with the aim of distinguishing male genotypes from female genotypes early in the vegetative growth phase in Pandanus fascicularis.

Pennisetum

Thirteen accessions of pearl millet (Pennisetum typhoides (L) Leeke) collected from different states of India and eight wild species of the genera Pennisetum across the world were analyzed for genetic diversity using AFLP markers. A combined analysis of eight primer combinations showed 35% polymorphism among P. typhoides accessions while analysis with five primer combinations showed 99% polymorphism among the wild species.

Among accessions of each geographical region, considerable variation was revealed by SW index with samples from Tamil Nadu being most polymorphic among the analyzed samples. The genetic diversity in the accessions could be utilized for future breeding work.

Cajanus Species

Pigeonpea (Cajanus cajan (L.) Millspaugh) is one of the major grain legumes of the tropics and subtropics. The phylogenetic relationship in 30 different Cajanus samples and its wild relatives has been studied based on data obtained from the Southern analysis. The existence of interspecific mtDNA variation was clearly evidence in the genus Cajanlls, Rynchosia, Paracalyx, Dllnbaria, Fleminga of subtribe Cajaninae. RFLP analysis using mitochondrial DNA probes were undertaken, in 29 species belonging to four genera, to assess the extent and degree of degree of genetic similarity within and between the genera. It includes 15 species of Cajanus, 11 species of Rynchosia, 1 species in each of the genus Paracalyx, Dllnbaria, Fleminga. Results indicate that the mitochondrial genome of Cajanus species is distinct from that of Rynchosia species, the mitochondrial genome of Fleminga macrophylla is distinct from that of Cajanlls species and Rynchosia species, the mitochondrial genome of Paracalyx scariosa and Dllnbaria jerruginea is distinct from that of Cajanus species and F.macrophylla, however it showing some similarity with Rynchosia. Herlan and Wet (1971) classified the pigeonpea as three distinct gene pools. Thus our data, demonstrates the use of mtDNA RFLP to study the phylogenetic relationships in the cultivated C. cajan and its wild relatives. This work could be used for planning a strategy for breeding of this economically important crop species.

Blackgram (Vigna mungo)

Twenty-six landraces of black gram collected from Orissa, India were analysed for genetic diversity using amplified fragment length polymorphism (AFLP) markers. A dendrogram was constructed based on the UPGMA clustering method, which revealed 3 major clusters. A principal component analysis of the same dataset revealed similar results to that of the dendrogram, with the first principal component accounting for 58% of the total variation. The analysed samples formed 5 significant groups. Three samples were distinct in their clustering and remained separate from the other samples. The influence of soil pattern and topography in the genetic make up of the land races was visible and seemed to contribute to the genetic distinctness of the landraces.

Rice

Genetic diversity among 49 Indian accessions of rice (Oryza sativa subsp. indica), including 29 landraces from Jeypore, 12 modern cultivars, and 8 traditional cultivars from Tamil Nadu, was investigated using AFLP markers. In total, nine primer combinations revealed 664 AFLPs, 408 of which were found to be polymorphic. The percentage of polymorphic AFLPs was approximately the same within the cultivars and landraces. Similar results were obtained when genetic diversity values were estimated using the Shannon-Weiner index of diversity. Genetic diversity was slightly higher in the modern cultivars than in the traditional cultivars from Tamil Nadu. Among the land races from Jeypore, the lowland landraces showed the highest diversity. The present study showed that the process of breeding modern cultivars did not appear to cause significant genetic erosion in rice. Cluster analysis and the first component of principle component analysis (PCA) both showed a clear demarcation between the cultivars and land races as separate groups, although the genetic distance between them was narrow. The modern cultivars were positioned between the landraces from Jeypore and the traditional cultivars from Tamil Nadu. The second component of PCA further separated medium and upland landraces from lowland landraces, with the lowland landraces found closest to the traditional and modern cultivars.

Millets

Millets encompass ten genera and about fourteen species and are generally referred to as the orphan crops, as with the exception of E. coracana none of the other millets has been studied in any detail. A great deal of morphological differences exists among the land races of these millets owing to various ecogeological regions they are grown in making classification of these species confusing. It was in this context, that the present study was undertaken to study the level of genetic divergence and to infer their ' phylogenetic relationships using molecular markers. The present study details the results of the study carried out in 24 nutritive millet germplasm accessions belonging to seven species and five genera using the three extensively used molecular markers systems, viz., random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP) and amplified fragment length polymorphism (AFLP) for a comprehensive insight into the species diversity and relationships. Speciesspecific polymorphic loci were observed for all the marker systems.

Seven millet species that are grouped as minor millets, represented by 24 races and 106 accessions were used in the present study to analyze the level of diversity using amplified fragment length polymorphism (AFLP). It was observed that all the AFLP primer-combinations used were able to distinguish individual species very clearly. At the land race level, there was a high degree of variation observed in Eleusine coracana (58.3%). However, all other six species showed very low level of intra-specific polymorphism with Echinochloa colona showing the least variation of 0.72% polymorphic AFLPs. The results are discussed in relation to the low level of genetic diversity encountered among the races analyzed despite their distinct morphological features and the species relationship between the millet species.

Pandanus

Pandanus jascicularis is a dioecious plant native to South Asia with significant numbers in coastal areas. With the aim of distinguishing male genotypes from female genotypes early in the vegetative growth phase, the current study was initiated using molecular markers. Based on the principle of bulked segregant analysis, the sampled plants were separated into 2 bulks depending on their sex. Of the 89 random amplified polymorphic DNA and inter-simple sequence repeat markers used, one decamer (OPO-08) consistently amplified a 1263 bp band in the males that was absent in the females. Its DNA sequence did not exhibit significant similarity to previously characterized sequences, but the presence of mononucleotide and dinucleotide repeats suggested that it was a repeat-rich region. A sequence-characterized amplified region marker (MSSRF-01)designed for this fragment continued to amplify the specific allele in all the male plants. Southern hybridization performed using the sex-specific fragment as a probe yielded results consistent with those previously obtained by polymerase chain reaction. These results strongly suggest that MSSRF-01 is a male-specific molecular marker. With no information available on the presence of sex chromosomes in Pandanus, this marker can be used to differentiate the sexes.