Analysis Of Temperature Effects On Rice Flowering And Yield Traits Through QTL Approach And Identification Of A Novel Rice Plant Height Gene

Heading (flowering) date is one of the most important adaptive characteristics of plants, which has a major impact on grain yield in crop species. In rice, photoperiod and temperature are two crucial exogenous signals that control heading date. Extensive research on photoperiod effects has identified two crucial flowering pathways. However, very little is known about temperature effects. Field observations indicate that low temperature delays the flowering, but the molecular mechanism underlying this process has not yet been identified. The main objective of this study was to dissect the genetic basis of rice flowering regulation by temperature, apart from the photoperiod. For this, we have conducted phenotypic and genotypic analysis on two Oiyza sativa L. indica varieties, Zhenshan 97 and Zhongzao 18, and 168 recombinant inbred lines derived from them, sowed in two different seasons in two years. Parents were also tested under different photoperiod and temperature conditions in growth chambers. The main results were as follows1) The short day (SD) promotion rates of ZS97 and ZZ18 in the high-temperature treatments were 1.56% and 2.66%, respectively, and 2.27% and 1.03% in the low-temperature treatments. The high-temperature promotion rates of ZS97 and ZZ18 under SD conditions were 25.6% and 23.9%, respectively, and 26.1% and 22.6% under long day (LD) conditions, indicating that both parents are influenced by temperature but not by photoperiod.2) The averaged effective cumulative temperatures (ECTs) necessary for Zhenshan 97 and Zhongzao 18 were fluctuated around 1110 and 1260℃, respectively, either in both field and growth chamber experiments or long day and short day conditions, indicating these values are parents’threshold ECTs, which could be the prerequisite before heading.3) Two-way analysis of variance showed there was no photoperiod effect and interaction effects on HD and ECT, but only temperature had significant effects on HD and ECT4) A major ECT QTL, qEHD10, also with a large effect on HD, was identified in the interval between markers RM1375 and RM3229 on chromosome 10, which could explain 42.2% to 57.0% of ECT variation and 39.8% to 59.4% of HD variation in four environments. 5) Comparative sequencing of photoperiod genes showed that Hdl and Ghd7 didn’t function in the parents. Thus, Hdl-mediated flowering pathways, which are controlled by photoperiod, did not function in the parents and the population. While Ehdl is functional, but the two parents did not expressed the phenotype of Ehdl, a key gene in rice photoperiod flowering pathway. Thus speculating there might be some temperature related signals which trigger the flowering.In addition, same population was sowed in three different seasons in one year to study the impact of seasonal changes on rice yield components. As temperature and photoperiod fluctuate rapidly in different seasons of the year, and analyzing their effects on rice yield components is crucial for adaptation of rice under various climatic conditions. The main results of this study were as follows6) The phenotype results in the field showed that temperatures across the three seasons played a crucial role in determining the trait effects. Spikelets per panicle (SPP), panicle length (PL) and plant height (PH) traits increased with high temperatures in middle season.7) Genetic analysis detected major quantitative trait loci (QTLs) qSPP10, qPL10 and qPH10 for SPP, PL and PH in the interval between markers RM1375 and RM3229 on chromosome 10, in all the three seasons.8) Two-way ANOVA showed that genotype by environment and QTL by environment interactions for these traits were highly significant (P<0.0001). Thus the region with a cluster of QTLs detected in all three seasons could be the preferred target to breeders in developing rice varieties that can be accustomed to different seasonal changes.Our present study also concentrated on fine mapping and candidate gene analysis of novel plant height gene ph1 detected from the introgression lines of ZS97 and Pokkali. The main results are as follows:9) A major gene ph1 gene was mapped to a region closely linked to sdl on chromosome 1; the additive effects of ph1 were more than 50 cm on the plant height and 2 days on the heading date in a BC4F2 population and its progeny.10) Sequencing and expression analysis confirmed that sdl has no function in these parents. 11)phl was then fine mapped to BAC AP003227. Gene annotation indicated that LOC_OS01g65990 encoding a chitin-inducible gibberellins-responsive protein (CIGR), which belongs to the GRAS family, might be the right candidate gene.12) A higher expression level of phl was detected in all the tested tissues in tall plants compared to those of short plants, phl showed a tremendous genetic effects on plant height which is distinct from sdl and could be a new resource for breeding semi-dwarf varieties.