MICROSATELLITE AND RAPD MARKERS: STUDYING POLYMORPHISM, DISTRIBUTION, MAPPING AND APPLICATIONS IN RICE GENETICS AND BREEDING

"MICROSATELLITE AND RAPD MARKERS: STUDYING POLYMORPHISM, DISTRIBUTION, MAPPING AND APPLICATIONS IN RICE GENETICS AND BREEDING" ABSTRACT By Roohi Mushtaq Molecular linkage maps have been constructed for most of the plant species during the last decade. These saturated linkage maps are essential tools for genetic studies like positional gene cloning, tagging and mapping of qualitative and quantitative traits, marker-assisted selection and comparative mapping. The construction of linkage maps relies on the choice of parental lines. Present study was undertaken to achieve following major objectives: 1. Development of new linkage map with additional RAPD and microsatellite markers using a double haploid population. 2. Standardization of low cost microsatellite marker technology to practice Marker-assisted selection (MAS) and 3. Identification and mapping of QTLs for drought related component traits in rice. Two DH populations i.e., CT 9993-5-10-1-M X IR 62266-42-6-2 (indica x indica cross) and IR 64 X Aazucena ( indica X japonica cross) were used in the present study. These populations were grown in field during wet season 2000 and summer season 2001. Two types of molecular markers viz. , RAPD and microsatellites were used for exploiting the parental polymorphism. In the present study, a new genetic linkage map has been constructed based on a double haploid (DH) population derived from a cross between two genotypes viz., CT 9993-5-10-1-M and IR 62266-42-6-2. The double haploid population was composed of 154 double haploid lines. The parental survey was performed using a set of 269 random 10-mer RAPD primers, of which 82 primers (31.48%) showed polymorphism between the two parental lines. 19 of 82 primers showed reproducible and clearly scorable polymorphic bands, which later were assayed on the double haploid population containing 154 DH lines. Two hundred and sixty nine RAPD primers amplified a total of 1802 bands. The total number of bands amplified per primer ranged from 3 to 9 whereas, the number of polymorphic bands amplified per primer varied between 1 to 3. On an average, 6.7 bands were amplified per primer. Average numbers of polymorphic bands per primer were 2.21. 42 polymorphic bands generated by RAPDs, which were easy to score had been selected and scored on 154 DH lines derived from the above mentioned mapping population. The corresponding loci represented by these scored bands were mapped on rice genome using MAPMAKER ver.3. 0. Out of 42 RAPD markers scored on 154 lines of DH population, eight markers were mapped. Seven markers were mapped on chromosome #7 and oneon chromosome #4. Three microsattelite (STMS) markers were also scored on the above population and put as anchor markers on chromosome #9 , 11, and chromosome #12 Another DH population of IR 64 X Azucena was planted in field under defined set of conditions and studied for identification of Quantitative trait loci (QTL) associated with leaf rolling under water stress condition. Two QTLs were identified, which were placed on chromosome #4 and chromosome #11 between the markers RG788RZ565 and RG1109-RZ536. A new linkage map with additional 8 RAPDs and 3 microsatellite markers was developed with enhanced resolution of the existing genetic map of rice on this population. These markers revealed a good percentage of polymorphism and can be used for genotype identification, gene and QTL analysis. Department of Biotechnology College of Agriculture IGAU, Raipur Dr. S. Major Advisor