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Near infrared (NIR) spectroscopy has made rapid progress as analytical technique in recent years. Being capable of making nondestructive, rapid, high efficient and convenient analysis, NIR technique is suitable to analyze seed quality traits. In this study, the method of measuring protein content of rice kernel was built with near infrared reflectance spectroscopy (NIRS) by using brown rice. With the NIRS method, amylose content (AC), protein content (PC) of a RI population with 187 lines from the cross between Zhenshan97B and IRAT109 were investigated and analysed under water stress and non-stress conditions.QTLs conforming those quality traits were mapped using the built linkage map and a mixed model approach(QTLMapper1.6). The results were as the following:1)Using the chemometric method of partial least square (PLS) regression, a study was conducted to investigate the feasibility and method of measuring protein in brown rice by near infrared reflectance spectroscopy (NIRS).The results showed that the coefficient of determination(R～2) for cross validation amounted to 0.90, and the root of mean square errors for calibration(RMSECV) was 0.52.The results indicated that NIRS technique could be applied to screen rice germplasm resources effectively and to rice breeding for quality improvement.2) Amylose content (AC), protein content (PC) of a RI population with 187 lines from the cross between Zhenshan97B and IRAT109, were investigated under water stress and non-stress conditions. The result showed that PC under water stress was significantly lower than that under non-stress condition, but the difference in AC was not significant.3) A total of 22 main effect QTLs and 66 pairs of epistasis were associated with AC or PC. QTL related to AC:Total 10 main-effect QTLs were detected.Under stress water conditions,6 QTLs were detected which locate on chromosome 2,7,9,11.They showed percentage of contribution of 5.20%～31.10%,and the total percentage of contribution is 53.4%; while under normal water condition, 4 QTLs were detected which locate on chromosome 1,8,9.They showed percentage of contribution of 4.70%～25.60%,and the total percentage of contribution is 35.34%.QTLs relevant to PC: Total 12 main-effect QTLs were detected.Under stress water conditions 8 QTLs were detected which locate on chromosome 1,3,6,9,10.They showed percentage of contribution of 4.70%～11.40%,and the tatal percentage of contribution is 58.10%. while under normal water condition, 4 QTLs were detected which locate on chromosome 3,6,7,.They showed percentage of contribution of 5.05%～15.20%,and the total percentage of contribution is 37.33%.The accumulated contribution of digenic epistasis on AC and PC were 66.74%, 57.49% under non-stress condition and 48.65%, 36.59% under water stress condition.
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