Genetic diversity'refers to the variation of genes within a population or species, that is the combination of different genes found within a population of a single species, and the pattern of variation found within different populations of the same species. This covers distinct populations of the same species or genetic variation within a population. Ultimately, genetic diversity resides in changes in the sequence of the four base pairs of the DNA that constitutes the genetic code. Analyzing genetic variation with molecular technologies gives information at the DNA level. It can be neutral diversity, identified along the DNA sequence in regions whose function is unknown, such as when we use anonymous types of markers (e.g. AFLPs, RAPDs) or, the diversity can be based on known genes, that is, within the coding regions of the DNA sequence. This diversity affects the expression of those genes and, consequently, the RNAthe nucleic acid in charge of translating the information of the genetic code into proteins. Proteins, in their turn, are the elements that make up the structure of organisms, which means they are responsible for what we see, the phenotype. Hence, genotype and phenotype are closely associated. Phenotypic measures of diversity can also be used and, if correctly taken, they may reflect the molecular constitution of a given individual. Researcher must take into account that molecular tools can offer greater depth to diversity studies and that they provide a common groundfor measuring and analyzing diversity. However, molecular data are often complementary to other characterization data (e.g. morphology, pathology) and the combined analysis of these data may offer a more comprehensive ground for interpretation. Molecular markers have already played a major role in the genetic characterization and improvement of many crop species. They have also contributed to and greatly expanded our abilities to assess biodiversity, reconstruct accurate phylogenetic relationships, and understand the structure, evolution and interaction of plant and microbial populations. The first generation of molecular markers, RFLP, were based on DNA-DNA hybridization and were slow and expensive. The invention of the polymerase chain reaction (PCR) to amplify short segments of DNA gave rise to a second generation of faster and less expensive PCR-based markers. As technology grows new detection systems are developed in search for even more efficient marker systems and cost effective markers for the breeders of the 21st century for germplasm characterization and other uses. The TNAU is involved in the complete range of activities for the conservation and documentation of genetic resources in major cereals (rice, maize and ragi) and pulses (green gram, black gram and soy bean). This includes both domestic and foreign exploration, seed increase, characterization, evaluation, preservation, rejuvenation and documentation. Genomic tools will be employed maintenance and understanding to study the molecular diversity of these crops.

High level of sequence similarity and genetic conservation within plants of same family allow us to use the informations and cDNA microarray obtained from a model plant such as Arabidopsis for better understanding of non-model plants within the same family, for example, rapeseed. Several lines of rapeseed plants with different sensitivity to cold stress were selected and the gene expression profiles under cold stress were examined using 1.6K specialized cDNA microarray. For the comparative analysis between Arabidopsis, economic plants and rapeseed, we adopted a recently developed computational method called "Gene Set Enrichment Analysis (GSEA)" which determines whether defined set of genes show statically significant and concordant differences between two biological states. Along this, five different gene sets including a network gene set based on a regulatory gene network model for early cold stress response and a co-expression gene set based on ∼ 1,500 expression data were built in this lab. With these gene sets and GSEA method, the expression data was analyzed to pinpoint the group of genes potentially responsible for the difference of stress sensitivity between two different plants. Since the plant encounters stress combinations concurrently or separated temporally and must present an integrated response to them, we built 'Cross-talk map' using ∼ 63 expression data of Arabidopsis under 9 different environmental stresses. Utilizing this cross-talk map, the significance of the identified group of genes was evaluated for their practical application to enhance stress tolerance. Currently, we identified several promising genes at a cross-talk point and are pursuing transgenic engineering to enhance the stress tolerance against more than two stress conditions.

A single recessive gene, rxp, controls bacterial leaf pustule (BLP) resistance in a soybean. The Rxp locus appears to be linked to the malate dehydrogenase (Mdh) locus and Satt372 on linkage group (LG) D2. Around the Rxp locus, four bacterial artificial chromosome (BAC) clones are anchored by Satt486, Satt498, BARC-022037-04263, and BARC-040963-07870. Using these BAC clone sequences, possible orthologous region of Rxp locus was identified: Medicago truncatula contig 962 at chromosome 3 and contig 283 and contig 1108 at chromosome 8. Sequence analysis of contig 962 had revealed microsynteny with three soybean BAC clones on LG A1, which are duplicated with other two soybean BAC clones anchored by Satt486 and Satt498. After BLAST search was performed with M. truncatula contig 962 against soybean ESTs, several soybean ESTs were identified. With developed single nucleotide polymorphism (SNP) markers and the RIL population from the cross of Pureunkong and Jinpumkong 2, SNP genotyping was able to locate twos oybean ESTs: CO979743 at 1 cM away from Satt195 on LG C1 and BE021935 at 5 cM away from Satt363 on LG C2. Thus, our results indicate that structure of soybean genome around Rxp locus is very complicated.