Development Of The Chromosome Segment Substitution Lines Derived From Super Hybrid Rice (PA64S)/(9311) And The Study Of Yield Related Traits

Rice?Oryza sativa L.?,one of the most important crops in the world,is the staple food for more than 60%of China's population.In the past ten years,as the urbanization process accelerating,the cultivated area of our country is diminishing.Meanwhile,environmental pollution aggravating,and global climate changing,especially extreme weather occurs frequently,all of these problems of food security have become a key factor for social stability.China's rice planting area accounts for nearly 1/3 of the sown area of grain,and rice total output accounts for about 41%of the total grain yield.The yield per unit area is about 46%higher than the average yield of grain crops.One of the most important factors is the planting of hybrid rice in large areas.It is well known that the yield of hybrid rice is about 10-20%higher than the conventional rice yield But rice yield related traits are usually controlled by multiple genes.These traits are conventionally detected by segregating populations derived from direct hybridation of both parents,such as simple F2 and backcross BC1F₁ populations,Some progress have been made in analyzing the number of quantitative trait loci and their genetic effects of rice yield related traits using these populations.However,parental genetic background of such populations is complex,the obtained locus are often less accurate,especially that some locus wtih smaller effects will be very difficult to detect.Chromosome segment substitution line population?CSSLs?is a set of lines with one parent as the recurrent parent,the replacement of a serie of chromosome fragments of donor parent,covering the complete donor genome.The genetic background of the CSSLs population is simple and the substituted fragements are relatively small,which makes it easy to.perform multiple years of repeated verification test.Thus,more and more attentions have been paid in rice genetic research and breeding.In addition,chromosome segment substitution lines population can not only improve the mapping accuracy of complex quantitative traits,but also can fine-map and map-based cloning of target site through establishing a secondary large segregating population.This research using the super hybrid rice Liangyoupeijiu which applied on large areas of China and both parents:photo thermo-sensitive genic male sterile line Peiai 64S?PA64S?as the female parent,and the sequenced the excellent restorer lines of indica rice 9311 as male parent.Through the cross,backcross and self-cross,and the construction of the DNA pool in high generation,using molecular marker assisted selection,the chromosome segments of male sterile line PA64S were introgressed into 9311 genetic background.These fragments cover the whole genome of PA64S.We want to provide research materials for the cloning of genes/QTLs controlling the important yield related traits of super hybrid rice.At the same time,some of the substitution lines can be used as the intermediate breeding materials for utilizing heterosis in hybrid rice breeding.The results are as following:1.975 pairs of SSR primers were screened from primers reserved in our laboratory,138 markers exhibited polymorphism between both parents.The polymorphism ratio is 14.15%.The distribution of polymorphic molecular markers on each chromosome also exists certain difference.Chromosome 9 has the highest proportion of polymorphic molecular marker,which amounts to 25%.Whereas chromosome 12 has only 10.98%polymorphic markers.Subsequently,123 makers relatively evenly distributed on 12 chromosomes were selected for the construction of the linkage map,covering the whole genome of 1573.4 cM.The average distance between markers was 12.13 cM.During the construction of "PA64S/9311" CSSLs,all these markers were used to analyze individuals in each backcross generation.Through marker assisted selection?MAS?strategy.Target individuals were selected for further backcross or self-cross to obtain the desired subsitituion lines.During the process of CSSLs construction,detection of whole genome with all markers was mainly from the beginning of BC3F4 generation,and the selection standard was that every plant contains as few as possible donor chromosome fragment,especially lines containing a single fragments of donor parent.When target lines have multiple fragments,then backcross hybridization and self cross were peformed to obtain several lines with only one single fragment,eventually all the substituted fragments contained in each line can cover the whole genome of the donor parent "PA64S".Genetic component analysis shows that each substitution lines contained a fragment accounting for 4.76%of the whole rice genome.The total length of fragments of 156 lines of this population is 2586.3 cM,equivalent to 1.8 times of the total length of rice genome,which can well represents the whole rice genome.Compared with the substitution lines reported,our CSSLs will be better for analysis,gene mapping and map-based cloning.2.Heterosis is a phenomenon that particular inbred lines can produce hybrids with favorable phenotypes over their parents,such as higher yields and stronger tolerance for stresses.Here,a set of 156 chromosome segment substitution lines?CSSLs?carrying overlapping segments of PA64s in a genetic background of 93-11 were constructed and planted in six different environments.Three major agronomic traits,viz.panicle length?PL?,heading date?HD?,and plant height?PH?,and five yield-related traits,viz.grain weight per panicle?GWP?,number of grains per panicle?GPP?,1000-grain weight?TGW?,seed set?SS?,and number of panicles of per plant?PPP?,were evaluated in three years.Quantitative trait loci?QTL?analysis was conducted using a likelihood ratio test based on the stepwise regression.A total of 46 putative QTLs distributed on 11 chromosomes were detected in more than one year.Remarkably,GWP of four lines carrying positive yield QTL outperformed the recurrent parent 93-11 by 15%in at least two environments.There are 12 main effect QTLs repeatedly detected at heading stage in at least two environments,namely QTL-qHD8.1 and qHD8.2,QTL-qPH2 and qPH5 in plant height,number of grains per panicle QTL-qGPP2.1,the number of panicles of per plant QTL-qPPP2.1,and 1000-grain weight QTL-qTGW7,qTGW10 and qTGW12,and grain weight per panicle of QTL-qGWP2.1.At the same time,yield related QTLs were discovered by chromosome segment substitution lines population,which can provid reference information to reduce the negative effect loci and pyramid positive loci for breeding by molecular marker assisted selection.3.The 156 CSSLs which can completely cover the donor parent PA64S genome s and the background parent plant 9311 and a set of 156 hybrid combination group?CSSLHs?were selected for analysis.QTL IciMapping V2.2 software was adopted for CSSLs and CSSLHs to analyze yield and Yield Related Traits in 2010?El?and 2011?E2?years.A total of 40 yield and yield related traits were found in two sites.These results indicate the CSSLs are effective in identifying the yield-associated traits,and the lines harboring yield-increased QTL will be a rich source in future molecular breeding programs.For the CSSL population,in the environment of E1,15 yield and yield related QTLs were detected;in the environment of E2,17 yield and Yield Related QTL were detected.Among them,there are 8 related to yield traits of QTL in the CSSLs were detected in two years.For the F₁ hybrid population,in the environment of E1,8 yield and yield related QTL were detected;in the environment of E2,15 yield and Yield Related QTL were detected.Among them,there are 3 related to yield traits of QTL in the Fi hybrid population were detected in two years.Only one QTL was detected both in the CSSL and F₁ population.13 QTLs showed over dominant effects,accounting for about 32.5%of all QTLs;14 QTLs showed partial dominant effects,accounting for about 35%of all QTLs;7 QTL showed additive effects accounted for about all 17%QTLs;6 QTLs showed complete dominance,accounting for about 15%.The above analysis shows that in the single locus level,the over-dominant effects plays an important role in the formation of heterosis in the super hybrid rice of Liangyoupei9.At the same time,because of the complexity of the yield components,partial dominance of quantitative trait loci may also be an important factor in the formation of heterosis in this super hybrid rice.