Genetic Diversity and Association Analysis of Rice Genotypes for Grain Physical Quality Using iPBS, IRAP, and ISSR Markers

The economic value of different rice varieties depends on their characteristics. Knowing the genetic control of the traits will help the breeder. Genetic diversity of 85 rice genotypes evaluated using six iPBS, one IRAP, and nine ISSR markers. The studied traits included the grain area, grain length, grain width, and diameter and grain perimeter, eccentricity of brown and white. The polymorphic alleles detected by each marker (varied from 3 to 8 alleles), and an average of 5.33 alleles per locus was observed. The iPBS1854 and iPBS2242 markers with 11 bands have the highest number of bands and the iPBS2240 and iSSR55 markers with 5 bands of the least band bands. The content of the polymorphic information varied from 0.018 (iPBS2241) to 0.241 (iPBS2240) and averaged 0.195. The iPBS2240 marker with high levels of polymorphic information identified as the best marker for genetic diversity evaluation. Regression analysis was performed between phenotypic traits and molecular data for association analysis. 54 alleles were identified for evaluated traits. Of these, in a normal condition of one allele linked to the area, length, width, the eccentricity of the brown rice grain. Also, two, three, four alleles associated with the area, length and width of the white grain. In Drought stress, one single allele correlated to the area, length and width of the brown rice grain. Eight and one alleles detected for exertion from canter and perimeter of the brown rice. Also, two, four, four and eight alleles associated with the area, length, width, from canter and perimeter of the heard rice grain, respectively. Among identified alleles, ISSR1-2, iPBS2241-2, ISSR16-4, ISSR55-1, ISSR57-1, iPBS2242-2 and iPBS2240-1 associated with several traits in both normal and stress conditions The presence of common alleles is probably due to the linkage of genetic locations which control these traits or pleiotropy. We suggest that linked markers with common traits be used for breeding programs.