Genetic variation in microsatellite DNA, physiology and morphology of coastal saline rice (Oryza sativa L.) landraces of Bangladesh

Genetic variation of Oryza sativa L. landraces (LRs) collected from the saline coastal belt of Bangladesh, modern varieties (MVs), as well as Pokkali, Nona Bokra and salt tolerant modern varieties (SMVs) derived from the last two were analyzed with 60 evenly distributed rice microsatellite DNA markers. A total of 196 reproducible polymorphic alleles were identified from the band loci. Heterozygosity among the 31 LRs was found to be 0.57, 0.46 in the 5 MVs and 0.40 in the 8 SMVs. Computation of genetic similarity with this data, using Jaccard's coefficient followed by UPGMA clustering, divided the landraces into 6 distinct groups. Three groups were composed of LRs only from the highly saline southwest. Two groups consisted of LRs from the mild to moderately saline mid-east and northeast coasts. The sixth group was heterogeneous, with LRs from the northeast, LRs from the southwest and Nona Bokra. Pokkali and Gunshi, a LR of the southwest, branched out individually. When all the 46 O. sativa L. cultivars were clustered together, most of the MVs and SMVs were found to be linked within the heterogeneous group. The measure of seedling Na and K concentration, Na/K ratios, affected leaf area as well as survival under salinity stress in hydroponics identified 6 LRs from the highly saline southwest as the most tolerant. These group with Pokkali when UPGMA clustering using the Pearson product-moment correlation coefficient suitable for the quantitative physiological data on seedling saline stress was computed. Morphological observations of plant type and height, days to maturity and yield components in non-saline soil indicated low variability among the different LRs. When yield performance as well as tolerance scores were considered, 7 LRs from the southwest and 1 LR from the mid-northeast show potential as donors for breeding salt tolerant rice. The microsatellite fingerprinting analysis thus revealed that some of the salt tolerant landraces of the coastal region have unique polymorphic loci, quite distinct from the popular salt tolerance donor Pokkali. The similarity matrices between the O. sativa L. cultivars chosen for the study can be used as a valuable tool for the proper choice of parents for mapping or breeding purposes.