| Rice is one of the most important crops. It is important for both breeding and biological study to look for useful genes. But, in rice, many traits are controlled by quantitative trait loci (QTLs). It is very difficult to analyze and map these QTLs by using traditional genetic materials and methods. Due to the little background noise, the chromosome segmen substitution lines (CSSLs) are very useful to map and clone QTLs. Using the CSSLs covering the whole genome in sequenced rice varieties, we can not only detect new genes or alleles between indica and japonica subspecies, but also can study the function of detected genes/QTLs. In this study, the indica rice cultivar 93-11 and japonica rice cultivar Nipponbare are used as the donor and the recipient varieties respectively to develop the CSSLs. Besides, by using these CSSLs, we attemp to map the QTLs controlling important agronomic traits. The main results were as followings.1. By using the indica variety 9311 as donor and japonica variety Nipponbare as recipient paren, we developed a set of novel population with 57 candidate CSSLs through backcross and marker-assisted selection (MAS). Each of the CSSLs contains a single or few indica introgresed chromosomal segments within the uniform japonica genetic background. Among these CSSLs, 32 lines may have only one introgresed segment from the donor, 11 CSSLs may contain two segments and the other 14 CSSLs have three or more segments. Each CSSL contains 1.8 segments. The length of these 104 introgressed segments ranged from 0.075 Mb to 24.07 Mb, with an average of 3.95 Mb. Their total length could cover 76.5% of the rice genome and was equal to 1.2 folds of the genome of 9311.2. These CSSLs containing homologous segment(s), as well as their heterologous lines (homozygous CSSLs crossed with Nipponbare), were used to analyze and map the QTLs controlling important agronomic traits, such as heading date, plant height and related traits, yield and related traits. Based on mapping theory with CSSL, totally 58 related QTLs were mapped on all 12 chromosomes. Among these mapped QTLs, 12 QTLs were for the heading date (qHd), which located on 9 rice chromosomes (except chromosome 10,11 and 12). 14 QTLs were for the plant height and related traits (qPh, qLfi) on 9 chromosomes (except chromosome 4,5 and 12). Besides, 32 QTLs were for yeild and related traits (qGw, qSs, qPbn and qSbn) which mapped on 11 chromosomes (except chromosome 9). Several QTLs, such as qHd-4,qPh-1,qLfi-2,qGw-4-2,qSs-3,qPbn-2-1 and qSbn-10, were identified as new loci in rice. These results were very helpful to fine map and further clone useful genes/QTLs between the indica and japonica subspecies.3. Among these analyzed CSSLs, several CSSLs, such as CS-40, CS-41, CS-10 and CS-14, were detected to contain several QTLs cotrolled different agronomic traits located on the same introgressed segment. It was presumed that the QTL in such individual CSSL would have the multiple effects on agronomic traits, or there were several genes/QTLs on the same segments. Thus, we wish to pyramid these useful QTLs together though marker-assisted selection (MAS) in the same genetic background, which would be very helpful to molecular breeding by design in rice.
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