Genetic Bases Of Important Agronomic Traits And Fine Mapping Of Plant Type QTL In Rice

The main contents in this study is 1) to develop a highly informative microsatellite (SSR) marker framework for rice (Oryza sativa L.) genotyping by using fifteen rice cultivars including 6 indica varieties (He-tian-xiang-dao, Kasalath, Habataki, IR36, R99, IR3) and 9 japonica varieties (Hitomebore, Toyonishiki, Sasanishiki, Nipponbare, Akitakomachi, Shen-nong265, Liaojing263, Liaojing294,02428),2) to comparative analysis of genetic information between two populations (F2 and RIL) and to detect and compare QTL for panicle related traits, grain related traits, flag leaf traits, plant height and its components and chlorophyll content at the stages of tillering, heading and maturity by employing RIL population derived from the cross between Shennong 265 and Lijiangxintuanheigu and its genetic linkage map and 3) to fine map the important plant type related quantitative trait locus qPCL9, which controlling flag leaf length, internode length and flag leaf length. The main results are as follow:(1) Six indica varieties and nine japonica varieties were used to analyze the polymorphism information content (PIC) value of 489 SSR markers. The PIC value of each chromosome were ranged from 0.4039 (chromosome 2) to 0.5840 (chromosome 11). Between the two rice subspecies, indica (0.3685～0.4952) gave a larger PIC value than japonica (0.1326～0.3164) and displayed a higher genetic diversity. A SSR framework including 141 highly informative markers for genotyping was selected from 199 SSR markers (PIC>0.50). Ninety-three SSR markers distributed on 12 chromosomes were found to be related to indica-japonica differentiation. Of these SSR primers,17 pairs were considered to be as core primers (all the japonica varieties have the same specific alleles, while the indica varieties have another specific alleles),48 pairs as second class primers (all the japonica (or indica) varieties have the same specific alleles, while the indica (or japonica) varieties have two or more other specific alleles) and 28 pairs as third class primers (all the japonica and indica varieties have two or more alleles, but the specific alleles are difference between japonica and indica). Thirty-two SSR markers were selected to be highly informative and useful for genetic diversity analysis of japonica varieties.This work provides a lot of useful information of SSR markers for rice breeding programs, especially for genotyping, diversity analysis and genetic mapping. (2) Comparative analysis of genetic information and QTL controlling flag leaf related traits including flag leaf length, flag leaf width and specific leaf weight between two populations (F2 and RIL) derived from a same cross between two japonica rice cultivars, 'Shennong265'and'Lijiangxintuanheigu' were studied.1) Most markers had same sequence along chromosomes, but the genetic distance between two markers was different. Thirty and thirteen markers showed genetic distortion significantly and extremely significantly in F2 population, separately. Nineteen and eleven markers deviated toward SN265 and LTH, separately. Sixty two and thirty eight markers showed genetic distortion significantly and extremely significantly in RIL population, separately. Forty three and nineteen markers deviated toward SN265 and LTH, separately. These distortional markers formed ten segregation distortion regions (SDR). Six of them were detected in both F2 and RIL populations.2) RIL population had more powerful detective ability than F2 population. Seven QTL controlling flag leaf related traits including two controlling leaf length, four controlling leaf width and one controlling specific weight were detected in F2 population. While seventeen QTL for these traits (seven for leaf length, five for leaf width and five for specific leaf weight) were detected in RIL population. Four QTL were detected in both populations including qFLL9 controlling flag leaf length on chromosome 9, qFLW4 controlling flag leaf width on chromosome 4, qFLW12.1controlling flag leaf width on chromosome 12 and qSLW6 controlling specific leaf weight on chromosome 6. Among them, qSLW6 (Additive effect=1.956mg/cm2) for specific leaf weight has a high research and application value.(3) 12 panicle related traits and 3 grain related traits showed a continuous normal distribution in the RIL population and transgressive segregation was also identified in all 15 traits.39 QTL were identified for panicle related traits including four for panicle length, five affecting primary branch number per panicle, three controlling secondary branch number per panicle, two affecting spikelet number per panicle, two controlling grain number per panicle, five for spikelet number of primary branch, five for spikelet number per primary branch, five controlling spikelet number of secondary branch, five affecting spikelet number per secondary branch, four controlling percent seed set, two for percent seed set of primary branch and two controlling percent seed set of secondary branch. They showed cluster forms on chromosome 2, 4,7,11 and 12. Clusters of QTL in genome would be the important genetic basis of the correlation among panicle related traits.13 QTL were detected for grain related traits (4 for 1000-grains weight,5 for grain length and 4 for grain width). The region between RM205 and RM207 on chromosome 2 controlled both phenotypes of grain length and width. The middle of chromosome 3 affected grain length and 1000-grains weight. The region between RM24412 and H90 controlled grain length, grain width and 1000-grains weight on chromosome 9.(4) QTL affecting plant height and its component factors were analyzed by employing 126 recombinant inbred lines (RIL) derived from a cross between two japonica rice cultivars, Shennong265 and Lijiangxintuanheigu. And then compared them with the genes involved in gibberellins and brassinosteroid biosynthesis and transduction. Plant height and its component factors showed a continuous normal distribution in the RIL population. The plant height showed a high positive correlation with its component factors, respectively. The correlation between plant height and its component factors descended from upper to lower. The correlation between adjacent plant height components was positively significant while the significance of the correlation between non-adjacent plant height components was less even negative. Further result indicated that the plant height is mainly affected by the length ofⅠinternode andⅣinternode.A total of 21 QTL controlling plant height and its components were identified on chromosomes 1,2,3,5,6,7,8,9,11 and 12, respectively. QPH9b (EP1, DEP1 or qPE9-1) on chromosome 9 plays a very important role in affecting plant height through controlling theⅠinternode andⅡinternode length from top. Its molecular function was different from the other genes controlling plant height be identified previously. So, it would be provided a novel mechanism for plant height. Comparison between 21 QTL and genes controlling gibberellins and brassinosteroid biosynthesis and transduction indicated that the genetic basis of plant height is extremely complex in this RIL population. And possible molecular mechanism for plant height was proposed by result of the comparison.(5) We analyzed the QTL controlling chlorophyll content at the stages of tillering, heading and maturity. Five, seven and ten QTL controlling chlorophyll contents at tillering stage, heading stage and maturity stage were detected, respectively. They were distributed on all rice chromosomes except chromosome 5.Comparison of the QTL and the genes underlying the key enzymes of chlorophyll biosynthesis and degradation revealed that relatively more QTL detected at earlier stage co-located with the genes related to chlorophyll biosynthesis and degradation. With the growth stage going on, more QTL were detected but only a few of them involved in chlorophyll biosynthesis and degradation. The results suggested that the expression level of most genes related to chlorophyll biosynthesis (degradation) had no difference at earlier stage but specific key genes increased at later stage. And two possible genetic bases for stay-green were proposed.(6)qPCL9, which controlling panicle length, culm length and flag leaf length, was identified on chromosome 9 in both F2 and RIL populations. In order to eliminate the influence of other loci, one single residual heterozygous plant for qPCL9 region, RHL-qPCL9 was selected based on MAS. We did not obtain any recombination among these three traits.This result revealed that these three traits were controlled by a same gene. We found that the heterozygous RHL-qPCL9 plant had short panicle, cuhn and flag leaf, and the segregation ratio between short plants and long plants in the segregating population was 658:231=2.85:1.00, fitting well to the 3:1 ratio (χ2=0.4593,P>0.05). These results revealed that the length of panicle, culm and flag leaf was controlled by a single gene,and it is a recessive trait in this population. Using this segregating population, this region was narrowed down to an interval between RM24423 and RM24434. According to the rice annotation project database, there are seventeen predicted genes in the 198-kb target region. Considering the organ specificity in gene expression and the molecular function information from a protein knowledgebase,AK107584 (similar to cytochrome P450 monooxygenase CYP92A1),AK111616 (similar to elicitor-inducible cytochrome P450) and J065094C22 (similar to cytochrome P450) might be the most likely candidate genes for qPCL9, but does not rule out the possible of the ten other candidate genes.