Dissection Of The Genetic Bases Of The Number Of Spikelets Per Panicle And Fine Mapping Of Its Major QTLs

The number of spikelets per panicle or the number of grains per panicle is an important component of rice yield. It has a theoretical and practical significance to study spikelets per panicle. However, this trait is inherited in a quantitative manner and typically controlled by a number of major and minor quantitative trait loci (QTL) and affected by environment, which causes a challenge to characterize it. With the QTL analysis based on molecular makers, the spikelets per panicle QTL can be detected. Many reports have provided the evidences for very complicated genetic bases of yield traits, which are affected by QTL, epistasis and environments simultaneously in primary mapping populations. By developing near isogenic lines (NILs) which can avoid genetic background noise, the QTL can be visualized as a Mendelian factor, and make QTL fine mapping and cloning become easier. In this study, utilizing two sets recombinant inbred lines (RILs) Zhenshan 97/Teqing and Minghui 63/Teqing, their genetic linkage map were constructed. Collecting two years' phenotype data of two sets RILs, nine traits QTLs were detected. Eight QTL containing six spikelets per panicle QTL and two. grains per panicle QTL were developed for NILs. Genetic effects for Four QTLs' were re-estimated in NIL background and three QTLs were fine mapped. On the basis of map Based cloning strategy, the SPP7b candidate gene was cloned.1. The genetic linkage map of Zhenshan 97/Teqing population was constructed based on 176 loci, which covered a total of 1432.1 cM with an average interval of 8.1 cM between adjacent loci; the genetic linkage map of Minghui 63/Teqing population was constructed based on 133 loci, which covered a total of 1371.4 cM with an average interval of 10.3 cM between adjacent loci. There were 50 common SSR makers between two RILs with maker orders on chromosomes well according to that published in previous reports.2. Collecting two years' phenotype data of two sets RILs, all nine traits' QTL containing spikelets per panicle, grains per panicle et al were detected on basis of composite interval mapping. Totally, 26 QTLs were detected in Zhenshan 97/Teqing in both the years 2004 and 2006, of which 13 QTLs were commonly detected in two years. 24 and 28 QTLs were detected in Minghui 63/Teqing in 2005 and 2006 where 13 QTLs are commonly detected in two years.3. Combining the grains per panicle and heading date phenotype data, the conditional QTL analysis was executed in two RILs. The result showed that 5 QTL of 8 GPP QTL in Zhenshan 97/Teqing were affected by heading date of rice. The other 3 QTL in Zhenshan 97/Teqing and all 5 GPP QTL in Minghui 63/Teqing were not influenced by rice flowering time. Hence, the panicle size QTL can be differentiated two types: the type I only controls grain per panicle, and type II is a flowering time affecting QTL which increase grains per panicle by elongation of life cycle.4. Eight NILs of panicle size QTL containing 6 spikelets per panicle QTL and 2 grains per panicle QTL were developed. And all NILs BC4F2 material was attained.5. The genetic effect of SPP3b was re-estimated in NIL background. In the BC₃F₂ population and BC₃F₃ progeny test population, a main effect QTL were detected, which have a LOD value of 12.8 and 8.8, additive effect of 11.89 and 7.85, and contribution of 29.1% and 20.2% of phenotype variance, respectively. Also, a main effect QTL controlling 1000-grain weight were detected in this NILs, which have a LOD value of 26.2 and 17.0, additive effect of -1.81 and -0.89, and contribution of 50.4% and 34.5% of phenotype variance, respectively. The co-segregation between the spikelets per panicle and 1000-grain weight was found by progeny test analysis, and this two QTLs considering as a maker were exactly map in the locus 1.6 and 1.0 cM away from markers RM15855 and W3D16, respectively. These results suggested that it is possible that the SPP3b was pleiotropic QTL controlling panicle size and 1000-grain weight.6. Analysing the genetic effect of SPP1 in NILs of F₂ and F₃ progeny population showed that a main effect QTL was detected, which have a LOD value of 23.95 and 35.52, additive effect of 22.05 and 10.81, and contribution of 51.1% and 63.4% of phenotype variance in F₂ and F₃ respectively. Utilizing a segregating population which has 2200 individuals, the SPP1 was fine mapped to a 107 kb region which contains 17 putative genes by bioinformatics predicting.7. In SPP6 NILs F₂ pouplation, three traits containing heading date, plant height, spikelets per panicle were co-segregated. The QTL for plant height, spikelets per panicle explained 81.2% and 50.9%of phenotype variance with a LOD value of 72.58, 29.96 and an additive effect of 7.72, 22.14 in F₂, respectively. The co-segregation among the three traits including heanding date, plant height and spikelet number per panicle was found by progeny test analysis, and this four QTLs considering as a maker were exactly map in the locus 3.1 and 3.4 cM away from markers RM19746 and RM19795, respectively. Theses results suggested that it is possible that the SPP6 was pleiotropic QTL controlling these three traits. Utilizing a segregating population which has 3300 individuals, the SPP6 was fine mapped to a 1 Mb region which contains Hd1, a cloned gene for heading date of rice. Due to the dominance of flowering in Hd1, which was counter to SPP6, it was a novel gene which is different from Hd1.8. There is a segregation of heading date, plant height and spikelets per panicle in NILs of SPP7b. By re-estimating the genetic effects of QTLs for these three traits, the main effect QTL were detected which explained 76.9%, 50.2%, 45.3% of phenotype variance with a LOD value of 59.33, 24.73, 19.22 and an additive effect of 3.91, 3.13, and 18.86 in F₂, respectively. Also in F3 progeny test population, main effect QTLs were detected which explained 51.5%, 45.0%, 50.6% of phenotype variance with a LOD value of 30.83, 24.37, 29.68 and an additive effect of 3.52, 3.22 and 17.04, respectively. Utilizing a segregating population which has 8018 individuals, the SPP7b was delimited to a 19-kb region which contains 3 putative genes by bioinformatics predicting. Sequencing comparison of 19-kb region between Zhenshan 97 and Teqing, the candidate gene of SPP7b was ascertained as Loc_Os07g48989. By RT-PCR, the result showed that Loc_Os07g48989 was expressed in Teqing genome as a real gene. A BAC clone 12D18 which contained the 19-kb region was screened to the Teqing BAC clone library. By utilizing the vector pCAMBIA 1301, the candidate gene of SPP7b was cloned.