Genetic diversity of saline coastal rice (Oryza Sativa L.) landraces of Bangladesh

Abstract

Traditional rice landraces from coastal Bangladesh are adapted not only to soil salinity but also to excess magnesium, calcium and sulphate as well as zinc deficiency. They can also tolerate water inundation to a certain extent, because they may be subjected to tidal saline intrusion as well as water stagnation during the monsoon season. These landraces are diverse with respect to their morphology, saline stress response as well as yield components. Characterization of these landraces can suggest how they survive in adverse soils and indicate suitable target genes for transfer to modern rice varieties. Genetic variation of 31 landraces (LRs) collected from the saline coastal belt of Bangladesh, salt tolerant Pokkali, Nona Bokra and sensitive IR29 and BRRIdhan 29 were analyzed with 60 evenly distributed rice microsatellite DNA markers. A total of 196 reproducible polymorphic alleles were identified from the band loci. 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. Morphological observations of plant type, such as tiller, leaf and flag leaf angle, height, as well as yield in non-saline soil indicated low variability among the different LRs. 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. UPGMA clustering using the Pearson product-moment correlation coefficient suitable for the quantitative physiological data on seedling saline stress, grouped all 6 LRs with Pokkali. When the landrace DNAs were analyzed with DNA markers linked to the major QTL of Pokkali within a 5cM region of chromosome 1, no similarity was detected between any of the traditional cultivars and Pokkali. Primers homologous to the coding region and part of the upstream as well as downstream region of the SOD, LEA and SalT genes when used for amplification show polymorphic DNA bands. These analyses 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 as well as Nona Bokra. The similarity and distinction between the cultivars chosen for the study can be used as a valuable tool for further study of specific landraces and also suggest a proper choice of parents for mapping or breeding purposes. © 2006 Springer. All Rights Reserved.