| Rice is one of the most important crops in the world. Indica and Japonica are two subspecies of Asian cultivated rice and show high genetic differentiation. Great heterosis also exists in the inter-subspecific crosses between Indica and Japonica rice cultivars. The genetic effect of alleles from japonica (or indica) in a genetic background of indica (or japonica) and the efficiently utilization of inter-subspecific heterosis between Indica and Japonica has its important theory meaning and practical meaning. In the aforementioned studies, F2, F3 populations and the populations derived by backcrossing recombinant inbred lines (RILs) with the parents were usually used. Due to genetic background noise in these mapping populations, QTL location and its effect was not easily and precisely estimated. Especially, the identity of some minor QTL with a low LOD score could be ignored. Chromosome segment substitution lines (CSSLs), with each line carries a single or fewer defined chromosome segment of donor genome, have a pure genetic background from a recurrent genotype. Additionally, CSSLs are directly used in breeding programs when their genetic background is an elite cultivar. Moreover, secondary F2 population can be derived from a further backcross between a selected CSSL and the recurrent parent, and then be used in the fine mapping. For these reasons, the development of series of chromosome segment substitution lines (CSSLs) has been an effective way to isolate useful genes.In order to breed a set of CSSL population for fine mapping of quantitative trait loci, map-based cloning and heterosis analysis, the present study used C418 and 9311, which are elite indica and japonica cultivars respectively, as the materials, to develop a set of chromosome segment substitution lines by using molecular marker aided selection. The main results are as follows:1) A total 1000 pairs of SSR primers and 40 pairs of new developed in/del markers were used to detect the polymorphism between the parents, among them,158 pairs, which account for 14.25% of the total SSR markers, showed polymorphism. The frequency of the polymorphism markers varied from chromosomes, with the highest of 24.39% on chromosome 9 and the lowest of 11.1% on chromosome 3 and 6. The marker linkage map was built according to marker distance report by Temnykh et al., McCouch et al. and the International Rice Genome Sequencing Project, which is consisted of 136 molecualr loci, spanned a total of 1,480.9 cM on all 12 chromosomes with an average interval of 10.89 cM between adjacent markers. The candidate substitution lines were marker assisted selected from the progenies with these molecular markers.2) The genotype of the BC3F4 lines and its consecutive progenies derived from "C418/9311" were analyzed with the 136 molecular markers. Eventually, the chromosome segment substitution lines, which were composed of 108 lines and chosen from BC3F8 and SF2 progenies, were developed with the following criterias:a) a high number of purely recurrent linkage groups;b) a wide coverage of the genome by the donor substituted segments.3) The average percent of substitution markers in the 108 lines is 4.76%, with a range of 1 to 15, among them,5.96 and 0.59 markers exhibited homologous donor and heterozygous type, respectively.The substitution genome length was 2586.3 cM, about as many as 1.7 times of the rice genome. The 12 chromosomes’genome was substituted by 108 lines, the most substitution lines were on chromosome 2, including 16 substitution lines;next were chromosomes 4 and 7, including 11 substitution lines;the least substitution lines were on chromosomes 5 and 10,6 and 5 respectively, the average substitution lines were 9.4) The CSSLs were used to detect the quantitative trait locus (QTL) for kernel traits in two contrasting environments, and led to the identification of 70 quantitative trait loci (QTL), distributing on 11 chromosomes. Out of these QTL affecting kernel traits,11 QTL were simultaneously identified in both environments:1000-grain weight QTL-qTGW6.1, qTGW7; grain length QTL-qGL5;grain width QTL-qGW5, qGW6.1 and qGW7.2;grain length and width ratio QTL-qLW5.1 and grain volume QTL-qGV2, qGV7.4, qGV8.1 and qGV9. More detailed mapping of qTGW7 showed that it was co-segregated with RM22034 on the short arm of chromosome 7. These results indicated that the CSSLs were effectively to identify quantitative trait loci associated with important agronomy traits, and provided rich resource for rice molecular breeding synchronously.5) 64 lines from these CSSLs were crossed one by one with the recipient parent to generate a set of corresponding CSSL hybrids (CSSLHs). These materials were field-tested over two years for yield and yield-related traits. A total of 87 (in 2008) and 93 (in 2009) QTL were detected. In 2008,62.1%(54) of the QTL were over-dominant, in 2009, this proportion was 61.3%(57), indicating that over dominance was a major contributor to heterosis. Some of the CSSLs harboured QTL associated with heterosis in both years;these should represent potential candidates as parents of F1 hybrids along with cv.9311 or other indica lines. Moreover, few of these yield-related QTL were detected in both CSSLs and CSSLHs, indicating that the main yield-related traits and heterosis were formed by two different genetic mechanisms. |
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