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Genetic Segregation Analysis and QTL Mapping as Well as Association Analysis for Panicle Angle Trait in Japonica Rice (Oryza Sativa L.)

Author: NiuFuAn
Tutor: HongDeLin
School: Nanjing Agricultural College
Course: Crop Genetics and Breeding
Keywords: Japonica rice Panicle angle Growing environment Mixed inheritance model QTL mapping Mapping analysis
CLC: S511.22
Type: Master's thesis
Year: 2011
Downloads: 17
Quote: 1
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Abstract


Rice plays an important role in grain production in China. The planting area of rice in china is 33 million hectares each year, of which indica rice is about 25 million hectares and japonica rice is about 8 million hectares. Currently most of japonica rice in china are conventional varieties. The proportion of the planting area for hybrid japonica rice is only 3%, far behind the hybrid indica rice (70%). Therefore, great space exists for developing japonica hybrid rice. Competition heterosis in yield of japonica rice is not obvious than indica rice, and utilization of erect panicle (EP) is one of the important reasons for conventional varieties keeping competition advantages in yield. Previous research suggests that varieties with EP have high yielding potential and EP is considered to be another important change for rice plant type after Semi-dwarf rice breeding. So combination of the EP trait and heterosis utilization is possible to achieve the breakthrough of rice production, and it is a feasible way for hybrid japonica rice out of the current predicament. Discovering elite alleles for panicle angle trait can provide genetic information for improving hybrid japonica varieties. In the present study, genetic segregation analysis for panicle angle trait was first performed by using 254 recombinant inbred lines (RILs) and their parents, Xiushui79 and C Bao, which are both japonica rice cultivars. A new SSR genitic map was then constructed using the RIL population according to the former linkage map constructed by our laboratory. QTL analysis by QTLNetwork 2.0 and WinQTLcart 2.5 softwares were performed based on the map. Finaly, association mapping analysis between panicle angle trait and SSR markers was performed in the natural population composed of 95 japonica varieties in Taihu Lake valley. All results were as follow:(1) In the RIL population, E-2-0 was determined as the best-fitted inheritance model for the panicle angle trait in all the four growing environments, showing that this trait followed the mixed inheritance of two major genes with additive-epistatic effects plus polygene with additive-epistatic effects. The heritability of major genes were 77.47%、73.59%、72.15% and 65.27%, while the heritability of polygenes were 21.00%、25.18%、 22.93% and 29.39% in the four growing environments, respectively, which implied that panicle angle trait was mainly controlled by major genes.(2) A new SSR genitic map composed of 111 markers was constructed, and then twelve additive effect QTLs were detected by two QTL identification methods in the RIL population based on the map. Twelve additive QTLs were detected by WinQTLCart2.5 software, explaining 2.83%~30.60% of the phenotypic variation. Eight additive QTLs were detected by QTLNetwork2.0 software, explaining 0.01%~39.89% of the phenotypic variation. Eight additive QTLs were both detected by the two softwares. The five QTLs, qPA4.1、qPA6.1、qPA9.2、qPA9.5 and qPA9.7, which were all detected at least in three environments by WinQTLCart2.5 software, were also detected by QTLNetwork2.0 software. qPA9.2 and qPA9.5 were two major QTLs, explaining 38.65% and 39.89% of the phenotypic variance at most, respectively. The negative effect alleles of all the QTLs detected came from Xiushui 79 except qPA11.Another eight epistatic interaction QTL pairs were also detected, but their explaining phenotypic variation was very small. No significant interaction between QTLs and environments was found.(3) In the natural population, association analysis between SSR markers and panicle angle trait was performed by TASSEL GLM program. The results showed that the natural population was composed of ten subpopulations. Of the 94 pairs of SSR primers used in this study, six were detected to be associated with panicle angle trait. Ten elite alleles and their typical carrier materials were further screened out. Five elite alleles with larger reducing phenotypic effects were all came from XiushuiO4 or Xiushui 79.

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CLC: > Agricultural Sciences > Crop > Cereal crops > Rice > Meters of sticky points > Japonica
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