Genomic Analysis And Mapping Of QTLs For Panicle Length In Oryza Longistaminata

Rice（Oryza sativa L.） is one of the most important crops in the word and more than half of the population in China lives on rice. Oryza longistaminata, originated in Africa, is a kind of wild rice, and it belongs to AA genome just like cultivated rice. Oryza longistaminata has a good resistance to bacterial blight and rice blast, and it also has a lot of good agronomic traits. And it can be emptoyed to breed a new variety of cultivated rice with good quality and high yield. Panicle length（PL） is a component of yield, which determines panicle architecture and affects the yield of rice. Although there are a lot of studies on genes or QTL which controls the rice panicle length, this trait has not been well studied, especially for wild rice.In this study, a clonally propagated F2 population（F2CP）, derived from the cross of cultivated rice Huanghuazhan and Oryza longgistaminata（Huanghzzhan/Oryza longgistaminata）, has been built and has been used for QTL mapping. The genome of Huanghuazhan and Oryza longgistaminata have been analysed by sequencing the whole genome. The results are as follows:1. Comparing the whole genome sequencing data with the reference genome （Oryza_indica₉311_ensembl_release22）, the result is that the amount of Oryza longistaminata reads mapped to that of the reference is 614435516, and the mapped reads ratio is 96.17%.; The amount of Huanghuazhan reads mapped to that of the reference is 2845636628, and the mapped reads ratio is 98.96%. At the same time, a lot of SNP and InDel exist in Oryza longistaminata and Huanghuazhan. The amount of SNP and InDel is 7451883 and 79854 respectively. They can be employed to develop polymorphic markers between these two parents.2. A clonally propagated F2 population（F2CP）, including 130 lines, has been built, and F2 seeds are derived from the cross of Huanghuazhan/Oryza longgistaminata on medium.3. A linkage map has been constructed by using 147 polymorphic markers, and it coversl2 chromosomes of rice. The total length is 1389.3 cM, and the average distance between the two markers is 12.55 cM.4. The panicle length of Huanghuazhan （26.94cm on average） shows significant differences from that of the Oryza longistaminata （39.65cm on average）. The analysis of the F2 population genetic shows that there is a transgressive segregation in panicle length, and the quantitative trait is controlled by multiple genes.5. Six QTLs of panicle length have been mapped in two different environments. The results show that they located on the chromosome 4、9、10 and 11, with the LOD values ranges from 2.52 to 5.54. The additive effect ranges from-6.03 to 6.13, and the range of individually explaining phenotypic variation is from 2.32%to 7.76%. They were designated as qPL4、 qPL9.1、qPL9.2、qPL10、qPLll.l and qPL11.2.