Validation of molecular markers linked to grain physical and chemical characteristics in recombinant inbred lines of Iranian rice (Oryza sativa L.)

Rice grain quality is a complex characteristic that can be divided into milling quality, appearance quality, cooking quality, and nutritional quality. Most studies on rice grain quality show the importance of chromosomes number one and six in the genetic control of various traits in rice. In the present study, the validation of 35 microsatellite markers linked to grain quality characteristics which all located on two chromosomes one and six, was performed in 144 recombinant inbred lines of F10 population resulted from the cross between Sepidrood (an Iranian improved cultivar with inferior quality) and Gharib (an Iranian local cultivar with good quality). The results of regression analysis showed that 25 markers were linked to different quantitative and qualitative traits, and explained from 16 to 39% of the variance of different traits, but the markers RM253, RM246, RM190, RM104, RM314, RM3827 and RM7434 had stronger linkage. Construction of the linkage map of 35 microsatellite markers in the studied population showed that the map length was 236.5 cM and the average distance between adjacent markers was 6.95 cM. QTL analysis by the composite interval mapping method showed that 40 QTLs controlled the measured traits in the studied population and the phenotypic variance controlled by the identified QTLs ranged from 7.57 to 37.41% for milling quality and head rice percentage, respectively. Based on this analysis, 23 markers were closer to the QTLs controlling the studied traits in this research. Of these, some markers were linked to several different traits. In total, the results of regression analysis and QTL analysis showed that the markers RM253, RM246, RM340, RM243, RM4128, RM314, RM3827, RM7434, RM104 and RM190 were the informative markers linked to grain quality characteristics, which can be used in marker-assisted selection programs in the future.