Study of Physicochemical Properties of Rice Grains, Association and Haplotype Analysis Using SSR Genetic Markers

Improvement of eating and cooking quality is one of the main objectives in rice breeding programs in Iran. In this study various rice genotypes, including upland, aerobic rice, Iranian improved varieties and landraces known for grain quality, were studied for eating, cooking, physicochemical characteristics as well as molecular evaluation with SSR molecular marker and three genes based markers (GBSSI (Wx), GW8/OsSPL1 and AGPase-S), at the University of Guilan, Rasht, Iran across two years: 2015 and 2017. According to the results, the best quality and aromatic varieties showed moderate values for amylose content (AC) and gelatinization temperature (GT) 21.06 and 4.27%, respectively and also moderate trough viscosity (TV) 149.06, final viscosity (FV) 276.77 and setback viscosity (SBV) 67.05. Association analysis revealed that SSR marker, RM589 was associated significantly with AC, peak viscosity (PV), SBV and consistency viscosity (COV). SSR marker, RM190 was also found as the common SSR marker associated with peak viscosity (PV), TV, and FV and RM3498 was correlated with GT, SBV and COV in both the years. On the other hand, haplotype analysis with reference to Domsiah as a famous aromatic variety revealed the best quality Iranian rice varieties such as Hashemi, Hasansaraei and Sadri had the Domsiah alleles for RM276, RM190, and RM3498 markers. The results suggest that the identified informative markers have a strong association with rice grain quality and could be utilized in subsequent studies and marker-assisted breeding aiming to improve grain quality.