Development Of Chromosome Segments Substitution Lines Derived From Japonica (Koshihikari)/Indica (9311) And QTL Mapping For Rice Quality

Rice is the major staple food crop in the world. There is growing concern about rice quality because of social-enconomic development and ever increasing living standard of China. In this study, using SSR marker-assisted selection, we developed a CSSLs populations derived from crossing and back-crossing of two rice cultivars:Koshihikari, a japonica cultivar as the donor and 9311, an indica cultivar as recipient, Using this population, QTL controlling agronomic and quality traits of rice were identified. The main findings are shown as follows.1) A total of 626 SSR primers were employed to screen the polymorphisms of two parents, japonica cultivar Koshihikari and indica cultivar 9311. A total of 189 polymorphic SSR primers were obtained, with the ratio of polymorphism being 30.88%. The proportion in chromosome 11 is the lowest, only 17.50%. By contrast, the proportion in chromosome 2 and 10 were 41.49% and 41.18%. A linkage map consisting of 108 co-dominant maekers was constructed. As calculated over the 108 co-dominant SSR markers,138 out of the total 208 were shown to substitute one or more chromosome segment from Koshihikari. The resulting CSSLs cover about 89% of rice genome. Most of chromosome segment substitution lines cover segments from donor parent were less than five, the number of single segment substitution lines was 51 and its coverage of CSSLs was 36.95%.2) QTL mapping for agronomic traits and appearance quality was performed using CSSLs derived from Koshihikari/9311. A total of 27 QTL for five traits were identified by single marker analysis. Among these 3,17 2,4, and 2 QTLs are involved in plant height(PH), panicle length(PL), grain number per panicle(SPN), grain length(GL), length-width ratio(LW), respectively. A Total of 13 additives QTL for five traits were identified by likelihood ratio test based on step wise regression for additive QTL (RSTEP-LRT-ADD). Among these,3,2,3,4,1 were involved in PH, PL, SPN, GL and LW, respectively. Most of these QTLs have been reported previously, but qGL-4 had not been reported before. Twenty-eight pairs of epistasis QTL for four traits were found based on likelihood ratio test based on stepwise regression for digenic epistasis (RSTEP-LRT-EPI).3) QTL mapping for cooking and eating quality was performed using CSSLs derived from Koshihikari/9311. A total of nine QTL for six traits were identified on chromosome 2, 4 and 7 by single marker analysis, with contributions of 8.08%-15.42%. A total of ten additive QTL for six traits were identified by RSTEP-LRT-ADD, with contributions of 8.13%-13.08%. Ten QTLs were identified on chromosome 1,2,3,4,5 and 9 using composite interval mappig. Most of these QTLs have been reported previously, but qBDV-1, qPT-4.1, qPT-4.2, and qCSV-3 had not been reported before. The qHPV-2 in an interval of RM341-RM525 and qBDV-2 in an interval of RM341-RM525 were involved in amylopectin synthesis. Sixteen pairs of epistasis QTL controlling PT, AC and PC were found based on likelihood ratio test based on RSTEP-LRT-EPI.A set of chromosome segment substitution lines were identified, and QTLs affecting rice quality was detected initially, providing ideal material for improvement of rice quality. Further, this study demonstrated the potential of CSSLs derived from "Koshihikari/9311" in QTL analysis.