Screening of some rice genotypes for salinity tolerance using agro-morphological and SSR markers

Salinity is a main obstacle of rice ( Oryza sativa L.) cultivation. Selecting rice genotypes for salinity tolerance based on phenotypic characteristics alone is inefficient and less reliable, finally will delay progress in rice breeding program. The recent advantages of molecular markers such as simple sequence repeat (SSR) could be used to detect associated salt tolerance markers in rice. This study was conducted to detect genetic variation within some rice genotypes using SSR markers and to identify salt tolerance in the studied genotypes. Forty-five rice genotypes were evaluated for their agro-morphological characteristics under non-stress and saline conditions for two growing seasons in 2018 and 2019. Using 21 SSR primers located on chromosome 8, only 18 SSR primer generated polymorphic patterns with a total of 76 alleles, whereas the other 3 primers were monomorphic. The number of alleles per locus ranged from 2 to 6 alleles with an average of 4.22 alleles per locus. The polymorphic information content (PIC) values varied from 0.30 (RM342) to 0.71 (RM6976) with an average PIC of 0.49. Out of the 18 polymorphic markers only 5 primers (RM 6976, RM7631, RM 5556, RM152 and RM342) perfectly distinguished rice genotypes. The best preforming genotypes under salinity stress were N22, IR 63731-1-1-4-3-2, GZ 7112-1-2-1-4, FL 478, TCCP 266-1-3B-10-2-1, IR 65600-127-6-2, IR 68011-15-1-1 and IR 66160-5-2-3-2. Thus, SSR markers are effective to detect high polymorphisms and variations among the rice genotypes, which could facilitate improving salt tolerance of commercial Egyptian rice varieties exhibiting high yield potential. In addition, the selected genotypes might be integrated into breeding programs for salinity tolerance. A marker’s high PIC value suggests a high probability of detecting the number of alleles between cultivars. A PIC value above 0.50 reveals a high degree of polymorphism. On this basis, the very good primers for this diversity analysis were RM408, RM5556, RM544, RM547, RM3395, RM6976, RM7631 and RM5545. The findings of this research indicate that the markers used are revealing and good for studies on genetic diversity. It is effective and cost-efficient to use microsatellites. They are abundant, co-dominant, highly reproducible and interspersed in the genome as compared with other markers. In particular, in rice genetic studies, microsatellite markers have been widely applied because they are capable of detecting high levels of allelic variation. The SSR markers play an important role in identifying salt tolerance genes that can be useful in developing new cultivars for plant breeders. In order to accelerate genetic advancement in rice, molecular markers could be used to tag QTL and determine their contributions to the phenotype by selecting desirable alleles at certain loci in the marker assisted selection (MAS) method. This is faster, more reliable and more cost-effective under saline field conditions than traditional screening (Aliyu et al., 2011). The results in this study indicate a great genetic resource for improving the salinity of rice in Egypt. In breeding programs to enhance rice materials for farmers, SSRs found here can be integrated. rice for then used assisted in