| Grain quality improvement is a very important area of rice breeding. In this study, the backcross recombinant inbred line population derived from Nipponbare (japonica)/ Kasalath (indica)//Nipponbare and its genetic linkage map were used to map the QTLs controlling cooking and nutrient quality traits in two distinct environments, Hangzhou and Hainan. QTLs for Cu, Cd, Pb and Zn contents were also studied under heavy metal stress. Molecular markers tightly linked to the QTLs were identified based on the study and could be used for grain quality improvement by marker-assisted selection (MAS). The results are summarized as follows:1. QTL detection for rice cooking quality traitsFour main effect QTLs (qAC6, qGC6, qASV6-1 and qASV6-2) were identified in the BIL population by using of QTLMAPPER 1.6 software. Among them, qAC6, qGC6 and qASV6-l were also detected to have significant G×E interaction. In addition, 4 pairs of QTLs with additive×additive epistasis (qAC5 vs qAC6, qGC6 vs qGC9, qASV1 vs qASV6-1 and qASV6-2 vs qASV9 ) were detected, but they had no G×E interaction. Three out of four main effect QTLs detected above, qAC6, qGC6 and qASV6-2, were also detected in both two experimental locations by using of WinQTLCart 1.13a software. In Hangzhou and Hainan, totally 21 putative QTLs for cooking quality traits were identified on chromosome 1, 2, 4, 6, 7 and 8. 11 out of 21 QTLs were found near the loci of Wx and ALK genes on chromosome 6.2. QTL detected for rice nutrient quality traitsProtein content (PC) and amino acids content are very important nutrient quality trait. The identification of QTL for PC and amino acids content and analysis of possible epistasis among the QTLs and QTL×environment interaction were conducted using QTLMAPPER 1.6. For PC, one main effect QTL (qPC6-3) and 4 pairs of epistatic QTLs (qPC1 vs qPC8, qPC6-1 vs qPC6-4, qPC6-2 vs qPC6-6 and qPC6-5 vs qPC12) were identified. Among 16 types of amino acids tested, only 6 main effect QTLs (qLYS6-1, qLYS6-2, qTHR6-1, qTHR6-2, qASP6 and qGLY6 ) and 3 pairs of epistatic QTLs (qTHR3 vs qTHR6-2, qTHR10-1 vs qTHR10-2 and qGLY6 vs qGLY11 ) for 4 types of amino acids ( Lys, Thr, ASP and Gly) content were detected. Results showed that the same region near the Wx and ALK loci on chromosome 6 was also an important region for main effect QTLs of PC and the amino acids content. A total of 35 and 69 putative QTLs were detected in Hangzhou and Hainan, respectively, but very few QTLs except for lysine content were detected commonly in the two experimental locations. It can be deduced that enhancing cooking and nutrient quality simultaneously was a complicated and tough job, and further research needs to be done.Two putative QTLs (qLYS6-1 and qLYS6-2) for lysine content with genetic main effects were detected on chromosome 6, which contributed to 27.08% and 47.56% of the total phenotypic variations, respectively. The qLYS6-1 was also detected to have significant G×E interaction. The additive effects of qLYS6-1 came from Kasalath while qLYS6-2 came from Nipponbare. In addition, no QTLs with additive×additive epistasis were detected in this experiment. Both qLYS6-1 and qLYS6-2 were detected in Hangzhou and Hainan, respectively. The results could be useful for pyramiding qLYS6-1 and qLYS6-2 by MAS in breeding programs to enhance lysine content in rice grain.3. Feasibility of QTL detection by the near infrared spectroscopy (NIRS)In this study, cooking and nutrient quality traits were determined by the established near infrared spectroscopy (NIRS) predication model. Comparison QTLs controlling cooking quality traits detected in this study with other studies revealed that those QTLs controlling AC, GC and ASV with large effect were detected in the same or different populations. The results proved that mapping QTLs of grain quality traits via the use of the NIRS measurement is feasible.4. Screening genotypes with low heavy metals accumulation in grains and QTL detection for heavy metals accumulation traitsThree hundred sixty seven rice genotypes were planted in a paddy field contaminated by toxic heavy metals. Concentrations of Copper (Cu), Cadmium (Cd), plumbum (Pb) and zinc (Zn) in rice grain were analyzed. The results showed that there was a great difference in heavy metal concentrations in rice grains among the genotypes. Some rice genotypes with low Cu, Cd, Pb and Zn concentrations were identified. Among them, 27 rice genotypes were found with a jointly Cu, Cd, Pb and Zn concentrations below 0.1, 10.0, 0.2 and 50.0 mg/kg, tolerance limit of the national hygienic standards for foodstuffs, respectively.Copper (Cu), Cadmium (Cd), plumbum (Pb) and zinc (Zn) content of the parents and BIL lines were determined in rough rice powder. The quantitative trait loci (QTLs) for each trait were analyzed based on the constructed molecular linkage map of this population. Totally, 13 QTLs for accumulation of 4 heavy metals were detected on chromosome 3, 4, 5, 7, 9, 11 and 12. Their variance explained by each of them ranged from 7.26%-15.92%. Three putative QTLs for Cu content (qCu3, qCu9 and qCu12) were mapped on chromosome 3, 9 and 12, respectively. Three QTLs for Cd content (qCd3, qCd7 and qCd11) were located on chromosome 3, 7 and 11, respectively. Four QTLs for Pb content (qPb4, qPb5, qPb12-1 and qPb12-2) were identified on chromosome 4, 5 and 12, respectively. Three QTLs for Zn content (qZn4, qZn6 and qZn7) were detected on chromosome 4, 6 and 7, respectively.
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