Genetic diversity analysis of rice cultivars (Oryza sativa L.) differing in salinity tolerance based on RAPD and SSR markers

Abstract

Thirty rice cultivars were evaluated for salinity tolerance during the seedling stage and were divided into five tolerance groups including tolerant (T), moderately tolerant (MT), moderately susceptible (MS), susceptible (S) and highly susceptible (HS) which comprised 5, 10, 9, 4 and 2 cultivars respectively. Genetic diversity of all rice cultivars was evaluated using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) markers. The cultivars were evaluated for polymorphisms after amplification with 20 random decamer primers and 20 SSR primer pairs. A total of 161 RAPD markers and 190 SSR alleles were produced which revealed 68.94% and 89.47% polymorphism respectively. Mean genetic similarity coefficient was 0.82 for RAPD and 0.70 for SSR. Cluster analysis based on RAPD markers was effective in grouping cultivars based on their salt tolerance ability. Group IA1, IB and IV contained three T, three S and two HS rice cultivars respectively. The MT and MS cultivars which showed similar physiological responses to salinity were resolved into two groups: Group IA2 and Group II comprising ten and eight MT/MS cultivars respectively. Cluster analysis based on SSR markers separated rice cultivars into groups based on genetic relatedness which did not correspond to salinity tolerance level. The results from this study provided some useful implications for salt tolerance breeding programs. The evaluation of genetic similarity and cluster analysis together with salt tolerance ability provides some useful guides for assisting plant breeders in selecting suitable genetically diverse parents for the crossing program.

Comprehensive phenotypic analysis of rice (Oryza sativa) response to salinity stress

“…Their conclusions where based on the fact that in rice Na + uptake is mechanistically different from K + uptake (Garcia et al ). This observation is particularly important because several studies assume that a low K + /Na + ratio is the most important goal in terms of ion concentrations in rice salinity tolerance and emphasize this value (Theerakulpisut et al , Kanawapee et al ). Also, the content of Na + and K + , independently assessed, is less affected by measurement errors, since a ratio always combines the errors associated with the measurement of the variable in the denominator and with the measurement of the variable in the numerator.…”

“…The third mechanism, tissue tolerance, is achieved by Na + compartmentalization in vacuoles, or in different tissues/organs of the plant, and by the accumulation of compatible solutes such as proline, sucrose or glycine betaine. Most salinity tolerance studies focus on the second tolerance mechanism (Hauser and Horie , Munns et al , Platten et al ) or in a general response to salinity that does not discriminate between the three tolerance mechanisms (Bhowmik et al , Theerakulpisut et al ). For this reason, it is still unclear if a specific mechanism is preferred by some species or if a plant can shift tolerance strategies depending on salt concentrations (Roy et al ).…”

Gene Expression and Molecular Differences in Two Wheat Genotypes under Salt and Drought Stresses

“…Thus, OPM-05 marker might not consider completely appropriate to tolerant genotype. Note worthy is that many authors published numerous studies for utilizing RAPD markers to detect the salt and drought tolerant genotypes (Kanawapee et al, 2011, Islam et al, 2013and Damor et al, 2016. However, this study evidenced that the two genotypes were differentiated using RAPD markers.…”

“…However, five SSR markers revealed ten alleles with average of 2 per locus. The low number of alleles of five SSR reflected the low possibility to detect tolerance genes in the genotypes used (Kanawapee et al, 2011). However, the low number of bands might due to the quality of figurative agarose used to split the amplified products or the exclusion of the monomorphic and spurious bands from analysis, reducing the number of alleles (Shah et al, 2013).…”

Molecular screening of traditional rice varieties using tsv1-linked simple sequence repeat markers

“…There have been several studies that have used molecular markers with emphasis on determining genetic diversity (Ni et al ., 2002; Ravi et al ., 2003; Chakravarthi and Naravaneni, 2006; Thomson, et al ., 2007; Rahman et al ., 2010; Sajib et al ., 2012; Ashraf et al ., 2016). On one hand, there are studies that have looked into genetic diversity in terms of responses of different rice cultivars to abiotic stress such as salinity (Kanawapee et al ., 2011), iron toxicity (Onaga et al ., 2013), drought (Anupam et al ., 2017) and aerobic condition tolerance (Singh and Sengar, 2015). On the other hand, very few studies have utilized molecular markers to showcase diversity such as bacterial leaf blight (Sabar et al ., 2016) and blast-linked markers (Anupam et al ., 2017).…”