Construction Of Rice (Oryza Sativa L.) Genetic Map And QTL Analysis

Using 180 PA64S × Nipponbare F₂ descendants as mapping population, we constructed rice SSR linkage map, and positioned a group of new SSR markers. Using interval mapping protocol, quantitative trait loci (QTLs) with 18 agronomic traits including tiller number, effective tiller number, percentage of tillering, plant height, heading date, days to heading etc, were positioned and analyzed. The results were as the following:1. Using the population of PA94SxNIPP-F₂(180 lines), we constructed a molecular genetic map containing 93 pairs of SSR markers. They covered 1602.5 cM of rice genome, and the average distance between two markers were spanned to 17.23 cM.2. The 48 novel markers on the map were positioned on the 1,2,3,4,5,6,8,9,11,12 chromosome, respectively. Most of markers distributed on chromosome 1,3, 11, were 12, 7, 7 markers, respectively, whereas 2,4,5,2,4,2,3 markers were positioned on chromosome 2,4,5,6,8,9,12, respectively.3. Forteen traits, including tiller number, effective tiller number, plant height, effective panicle number, flag leaf length, grain number, filled grain number, seed setting, grain weight, density of panicle, grain length, grain width, grain thickness, and ratio of grain length and width, showed more divergent between two parents, and among the F₂ offspring; 4 traits, including percentage of tillering, heading date, days to heading, panicle length, showed little divergent, but larger in F₂ population. Most of traits fitted for normal distribution. Complex correlativity presented among different traits.4. Using the molecular linkage map constructed with PA64s × Nipponbare, by the interval plotting method, QTLs of rice agronomy traits were positioned and analyzed with the data collected from two sites for two years. 28 QTLs controlled 14 of 18 traits were found in F₂ population, and they distributed in 15 intervals on 9 chromosomes. However, no QTLs were detected in 4 traits including heading date, days to heading, panicle length and grain thickness. Using the repeated QTL position, after analyzing 7 of 18 traits in F_2:3 population, 11 QTLs which control 5 traits were found (among of them, 3 QTLs on the plant-height were found again), but no QTLs that control heading date and days to heading were detected in 9 intervals on 8 chromosomes. Among of 35 QTLs, contribution percentage of 8 QTLs named as tn1, ph1, ph2, ph4, ph5, f12, rlw4, rlw5 were larger (exceeding 20%); They are major alleles, the contribution of the rest of 27 QTLs are little (0-19.9%), are minor alleles.(1) QTL position relevant to tillering: 2 QTLs which control tillering -tnl, tn(4)l -are located on chromosome 12. The contribution of tnl and tn(4)1 are 54.9% and 7.7%, respectively; Two QTLs which control effective tillering - etn1,etn(4)l, are located on chromosome 5 and 4, respectively; The percentage of contribution were 7.6% and 12.4%, respectively; Three QTLs which control tillering rate - ptl, pt(4)l, pt(4)2 - are located on chromosome 5, 2, 8, respectively, with little percentage of contribution, which are 7.7%, 8.1%, 6.4%, respectively.(2) QTLs relevant to plant height: Five QTLs which control plant height - phi, ph2, ph3, ph4 and ph5 - were detected in F2 population, and the five loci can cover to 59.30% in the total variation related to the plant-height. In F2.3 population, 6 QTLs which control plant height - ph(4)l,ph(4)2, ph(4)3, ph(4)4, ph(4)5, ph(4)6, they cover for 76.90% variation. The ph(4)l with phi, and ph(4)6 with ph5, respectively, then the ph(4)3 or ph(4)4 with ph4, is in same allele. Colligating the F2 and F23 populations, 7 QTLs designed as phi, ph2,ph3,ph4,ph5,ph(4) 2, ph(4)5 are related to the plant height, and repsectively located on chromosome 1,1,4,6,12,1,10, with percentage of contribution of 8-57.6%.(3) QTLs related to flag leaf length, panicle length and panicle number: 2 QTLs related to flag leaf length -fll,fl2 - are located on chromosome 1, 12, and with percentage of contribution of 6%, 55.2%, respectively, but no QTLs related to panicle length detected in F2 population. The QTL of main panicle length, mp 1(4)1, showed a percentage of contribution of 5.6%, and are detected in F2.5 population. In F2 population, the QTL related to panicle number, pnl, is located on chromosome 5, and had a percentage of contribution of 11.3%.(4) QTLs related to spikelets per panicle, filled grain number per panicle and density of panicle: 3 QTLs related to spikelets per panicle - sppl, spp2, spp3 - are located on chromosome 1, 9, 10, respectively. They showed percentage of contribution of 5-7.6%, and the total percentage of contribution is 16.2%, in F2 population. One QTL of filled grain number per panicle, gppl, is located on chromosome 5, Its percentage of contribution was 10.2%. 2 QTLs of seed setting - ssl, ss2 - are located on chromosome 5 and 6, respectively, the percentages of contribution were 6.3-7%, and the total co-explaining variation accounts for 12.0%. 2 QTLs of density of panicle - dpi, dp2 - are located on chromosome 1,10, the percentage of contribution showed as 13.4%, 5.4%, respectively, and the percentage of combined variation accounts for 5.4% of total.(5) QTL related to grain weight and grain shape: one QTL of grain weight - kwl - is located on chromosome 5. Its percentage of contribution was 7.5%. One QTL of grain length - gll- is located on chromosome 3, and had a percentage of contribution of 0. Another 2 QTLs of grain width - gwl, gw2 - are located on chromosome 2, 5, respectively, the percentage of contribution were also 0. NoQTLs of grain thickness are detected. 5 QTLs of ratio of grain length and width -rlwl, rlw2, rlw3, rlw4, and rlw5 - are located on chromosome 2,3,5,6,10, respectively, and showed phenotypic percentage of contribution of 7.8-47.5%.5. Due to the traits in F2 and F23 population were inspected at Chengdu and Hainan of which environment have greater diverged, the traits of parents and offspring showed larger difference. The tnl, etnl, ptl are not detected in F23 offspring, and 4 different QTLs - tn(4)l, etn(4)l,pt(4)l,pt(4)2 - are detected on chromosome 12, 4, 2, 8, respectively. The 3 QTLs - phi, ph4, ph5 of 5 QTLs which control plant height - phi, ph2, ph3, ph4, ph5, are detected in F23 population. In addition, 2 different QTLs of plant height - ph(4)2,ph(4)5 - are detected on chromosome 2,10, respectively.6. Bioinformatics analysis on the 7 QTLs with 0 distances among markers showed that marker RP3 locates within gene PO678F11.20, and we speculate that the site has a coding gene, which might play a role in increasing grain number, whereas the gene in which marker OSR28 locates might play a role in decreasing grain number, and then the gene in which marker RM592 locates may play a role of increasing grain number. The marker OSR33 locates in the intergenic region between OSJNBa0078001.11 and OSJNBa0078001.26, the proximal 2 genes might play the role in decreasing the density of panicle. RM526 amplified a fragment of 239 bp in the genomic and the mRNA sequence from Nipponbare, so we speculate the genes near the marker might play the role in increasing grain width and decreasing percentage of tillering. Due to RM491 amplified a fragment of 263 bp from genomic and an 1684-bp-long mRNA sequences from Nipponbare, so we guess that its gene might play the role in increasing tillering.On the other hand, in this paper we also discussed on the construction of genetic linkage map, the factor effecting QTL, and function analysis of QTL etc.