Construction Of Chromosome Segment Substitution Lines Between Two Sequenced Rice Varieties And Preliminary Mapping Of Important QTLs

Rice is one of the most important crops, and now also as one of the model organisms for plant molecular biology. It is important and useful for both breeding and biological study to understand the genes'function in rice. But, like other cereals, many traits in rice are controlled by quantitative trait loci (QTLs). So it is difficult for us to analyze and map a QTL via traditional genetic methods. It will be more easy to detect QTLs by using Chromosome Segmen Substitution Lines (CSSLs), as which has little background noise and does not require complex statistical analysis.So more and more rice geneticists and breeders are paying more attention in it now. Especially, it would be moer effective to identify target QTLs as well as research in functional genomics by using a set of chromosome single segment substitution lines (SSSLs) covered the whole genome in sequenced rice varieties. In this study, the main purpose is to develop a set of CSSLs from the cross between two sequenced rice varieties and idetify important genes between subspecies. The indica rice cultivar 93-11 and japonica rice cultivar Nipponbare are used as the donor and the recipient varieties, respectively, and molecualr markers were employed to assistantly select the target CSSLs. The main results were as followings:1.With an aim to use a convenient method for CSSL construction, the agarose gel electrophoretic technology was chose to validate the polymorphism of molecular markers.. Among 375 SSR markers derived from the public database, 134, 35.73% of totals, showed polymorphism between the two parents Nipponbare and 93-11. Besides, 75 and 25 polymorphism molecular markers were selected and designed, respectively, according to the information from the polymophism databases which had been constructed and reported by others. Based on the published pseudomolecules of Nipponbare, we located the validated polymorphism markers on 12 rice chromosomes. Finally, a molecular map was developed, and which contains 140 markers distributed evenly on all 12 chromosomes, the average distance btween two flanking markers was about 3.2 Mb.2. After selection assisted with the polymorphism markers, a set of CSSLs were developed from the advanced backcross population BC4F2 and BC5F1. In which, the indica rice 93-11 and japonica rice Nipponbare was used as the donor and recurrent parents, respectively. 102 CSSL plants were preliminary identified to contain a single segment, and 26 of them, combined with other 14 CSSL plants carried 2-4 substituted segments, were selected to construct the graphical genotypes. Among these 40 select CSSL plants, a total of 60 chromosome segments from the donor were introgressed, which cover about 96% of the whole rice genome. The length of the 60 introgressed segments ranged from 1.4 Mb to 27.4 Mb, with an average of 10.12 Mb, and their total length was about 607.3 Mb, equal to 1.5 folds of the genome of 9311.3. By using the developed CSSLs, a QTL which controlled the heading date of rice was preliminary mapped on the long arm of chromosome 3, near the molecular marker CS0330 & CS0333. The data of further studies showed that the marker CS0333 is closed to a cloned QTL Hd6, which also controls rice heading date. After detected with a genic marker of Hd6, we found that CSSL plants with a longer heading date carrys the gene Hd6 derived from 9311. Besides, another QTL affecting the tiller angle of rice was mapped in the region near the marker RM278 and RM205 on chromosome 9, and the data from sequence analysis implied that our mapped QTL might be the same locus of the reported TAC1 gene, which also controlled tiller angle in rice.4. After analysis of several CSSL plants showed semi-sterility, a QTL qS12 causing rice semi-sterility was mapped around the marker RI05618 and RM247 on chromosome 12. The data from genetic analyses suggested that qS12 could be activated when it was heterozygous, and it maybe have a false linkage with the S5 locus.5. The gelatinization temperature of mature seeds from some CSSL plants was carefully analysed through three ways, alkali digestion test, RVA analysis and DSC analysis, and the results revealed that two CSSL plants have a lower gelatinization temperature than the recipient parent Nipponbare. Based on the genetic background of these two plants, we considered that four substituted segments in these two plants may carry QTLs controlled rice gelatinization temperature.