Allele variation for markers related to physical and chemical quality of rice under flood and drought stress conditions

Introduction Rice is a major source of food for more than half of the world's population. Rice is one of the smallest genomes in grain size, and it has been used as an ideal crop for evolutionary research of cereals and important crop species. Rice is a diploid plant and its genome length is short. Rainfed lowland rice is the second most important rice ecosystem, representing about 25% of the total rice production area. Fields do not receive irrigation, relying entirely on rainfall or drainage from higher lands in a watershed. Quality is of paramount importance as rice is consumed in full grain form. In Iran, rice quality is generally more important than yield, and Iranian tastes prefer aromatic rice with long grain length and low grain breadth. The purpose of this study was to identify effective markers on morphological traits, with a total of 20 indicative markers identified in both crop conditions. According to the results obtained from this assessment, they can be used in breeding programs. Materials and methods This study was carried out in a research field of Gonbad-e-Kavous University in the year 2015-2016, in the form of Latis design in 3 replications, from 90 rice genotypes under normal conditions and drought stress using 11 drought tolerant markers. In this experiment, six physical traits of grain (brown and white rice) and three qualitative traits of rice grain were evaluated. These included: grain length, grain width, grain size, grain circumference, Equilibrium grain balance and Eccentricity of rice grain and percentage of protein, Amylose content and gelatinization temperature. DNA extractions were then extracted according to the CTAB method. Results The beneficial results of microsatellite markers indicated that there were 54 polymorphic alleles, with the highest number of RM333 and RM589 with 7 alleles. In the analysis of the main components of SSR markers related to drought tolerance, the first 10 components were able to justify 55.58% of the variation. Clustering results divided genotypes into six groups. Investigating the adhesive patterns formed on acrylamide gel from 11 markers on 90 rice genotypes. The genotypes were grouped together in order to match the allelic pattern. Amylose content, protein content, gelatinization temperature for qualitative traits and quantitative traits of grain length and width (brown and white rice) of each group as a measure of groups. A comparison was made for drought tolerance, with a total of 20 groups identified. The results of the analysis of the relationship between the measured traits showed that among the 104 effective alleles on the traits, the effect of the RM6349-D allele with 9.99 had the greatest effect on the traits of the grain environment. Seedlings are affected by 8 alleles, the equivalent diameter of seeds with 7 alleles, length and area characteristics of seedlings with 6 alleles Conclusion Band pattern showed that genotypes can be grouped into a group in terms of matching the allelic pattern. The analysis of the main components of SSR-related drought tolerance markers with 10 components could justify more than 50% of the variation. Cluster analysis by line grouping identified the value of each group for the traits assessed.