Abstract
Rice (Oryza sativa, L.) is one of the strategic crops in Egypt, and the improvement of its productivity is an essential requirement to ensure food security. Salinity is one of the major environmental stresses that limit the productivity of rice crop. 14 SSR markers linked to salinity were used to study the genetic diversity within salinity tolerance QTLs in 18 rice genotypes. All the utilized primers were polymorphic, the number of alleles ranged from 2 to 6 with an average of 3.42 per locus. The major frequency alleles ranged from 0.33 to 0.78 for RM562 and RM412, respectively.The PIC values varied from 0.79 to 0.37 with an average of 0.50. Seven SSR markers i.e. RM562, RM493, RM1287, RM223, RM242, RM10720, and RM5 were informative markers with PIC values more than 50%. Jaccard's similarity coefficients ranged from 0.07 to 0.93 with an average of 0.45.The studied genotypes were grouped into two major clusters at 0.18 similarity. The PCA analysis had the ability to classify the studied genotypes into clearly four separate clusters based on the origin and salinity tolerance.13 haplotypes other than the reference haplotype were identified. The number of genotypes per haplotype ranged from one to five. The current investigation highlighted the high amount of genetic diversity among the studied genotypes. Egyptian Yasmine, the fragrant genotype, was the most promising genotype where it has 50% of Pokkali alleles at Saltol QTL region and this makes it suitable to be used as salt tolerance donor for MAS in salinity tolerance molecular breeding program.
Highlights
Rice is the most important crop being the dominant food in most of the countries around the world
Molecular analysis and genetic diversity for salinity tolerance were studied in different rice genotypes using different types of markers (Reddy et al, 2017)
The effective number of alleles ranged from 1.61 and 5.26 with an average of 2.45 allele per locus. These results indicated the existence of high allelic diversity in salt tolerance QTLs among the tested genotypes
Summary
Rice is the most important crop being the dominant food in most of the countries around the world. In Egypt, rice is considered among the most adapted summer crops to the salt-affected coastal areas. Rice can withstand water-logging and standing water helps in diluting and leaching salts from surface soil (Ismail et al, 2008). According to the final report of the geological society of America, sea level is rising annually 3 mm on average and the current saline intrusion reaches the central delta sectors (Stanley and Clemente, 2017). Salinity considered one of the major abiotic stresses affecting rice sustainability and yield. Rice scientists in Egypt at Rice Research and Training Center (RRTC) have long worked on developing new cultivars and promising lines to overcome adverse environments for rice cultivation, among these cultivars Sakha104, Giza178 and Giza179 (Zayed et al, 2017)
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