Effects of planting methods on yield and quality of different types of japonica rice in northern Jiangsu plain, China

Mechanical transplanting with carpet seedlings(MC) and mechanical direct seeding(MD) are newly developed planting methods, which increase in popularity and planted area each year. Knowing the difference for yield and rice quality under different planting methods is of great importance for the development of high quality and yield cultivation techniques under mechanical conditions. Therefore, three kinds of japonica rice including hybrid japonica rice, inbreed japonica rice, and soft rice were adopted as materials. And the differences in the quality of processing, appearance, cooking and eating quality, nutrition, and the rapid viscosity analyzer(RVA) profile were studied to reveal the effects of planting methods on yield and quality of different types of japonica rice. Results showed that the milled rice and head rice rates under MC was significantly higher than those under MD, and the processing quality of inbreed japonica rice was the most stable. Compared with MC, length/width ratio of rice under MD was significantly increased, and chalkiness rate, size, and degree were significantly decreased. The protein content under MD was lower than that under MC. MC showed higher peak viscosity and breakdown value than MD. The taste value was the greatest for soft rice, followed by inbreed japonica rice, and then by japonica hybrid rice, with no significant differences resulting from planting methods. Compared with MC, MD significantly improved the appearance quality, though processing quality and nutritional quality were decreased. And there was no significant difference in cooking and eating quality between MC and MD. Under different planting methods, the appearance quality of inbreed japonica rice changed the most and the processing quality was the most stable. The nutritional, cooking and eating quality of soft rice changed the least. Therefore, according to the different planting methods and market needs, selecting the appropriate rice varieties can reduce the risks in rice production and achieve good rice quality.

Top-dressing nitrogen fertilizer rate contributes to decrease culm physical strength by reducing structural carbohydrate content in japonica rice

Lodging is an important factor limiting rice yield and quality by bending or breaking stem in japonica rice（Oryza sativa L.） production. The objectives of this study were to determine the mechanism of lodging resistance in japonica rice as affected by carbohydrate components, especially its related arrangement in culm tissue and response to top-dressing nitrogen（N） fertilizer. Field experiments were conducted in Danyang County, Jiangsu Province, China, by using two japonica rice varieties Wuyunjing 23（lodging-resistance variety） and W3668（lodging-susceptible variety） with three top-dressing N fertilizer rates（0, 135 and 270 kg N ha^（-1）） in 2013 and 2014. Lodging related physical parameters, morphological characteristics and stem carbohydrate components were investigated at 30 d after full heading stage. Results showed that with increasing N fertilizer rates, the lodging rate and lodging index increased rapidly primarily due to significant reduction of breaking strength in two japonica rice varieties. Correlation analysis revealed that breaking strength was significantly and positively correlated with bending stress, but negatively correlated with section modulus, except for significant correlation at W3668 in 2014. Higher stem plumpness status and structural carbohydrate contents significantly enhanced stem stiffness, despite of lower non-structural carbohydrate. With higher N fertilizer rate, the culm wall thickness was almost identical, and culm diameter increased slightly. The structural carbohydrates, especially for lignin content in culm, reduced significantly under high N rate. Further histochemical staining analysis revealed that high N treatments decreased the lignin deposition rapidly in the sclerenchyma cells of mechanical tissue, large vascular bundle and small vascular bundle region, which were consistent with reduction of bending stress, especially for W3668 and thus, resulted in poor stem strength and higher lodging index. These results suggested that structural carbohydrate plays a vital role for improving stem strength in japonica rice. N rate decreased lodging resistance primarily due to poor stem stiffness, by reducing structural carbohydrate content and lignin deposition in the secondary cell wall of lower internode culm tissue.

Relationship Between Lodging Resistance and Chemical Contents in Culms and Sheaths of Japonica Rice During Grain Filling

To understand the relationship between lodging resistance and chemical component contents in culms and leaf sheaths of rice, the physical strength and maximum bearing capacity of culm, and the contents and amounts of potassium （K） silicon （Si） and soluble sugars in culms and leaf sheaths were investigated using four japonica rice varieties with different lodging resistance characteristics during grain filling. There were significant differences in the total amounts of K, Si and soluble sugars in culms and leaf sheaths among the tested rice varieties. The difference in the total amount of Si was greater than that of K or soluble sugars. The physical strength and maximum bearing capacity of culm continuously decreased from heading to ripening, with a rapid decrease at the dough stage. However, the contents and total amounts of K and Si in culms and the Si content in leaf sheaths gradually increased and an accumulation of K and Si in culms was exhibited, whereas the content and total amount of K and the total amount of Si in leaf sheaths gradually decreased and an exportation of K and Si in leaf sheaths was presented. The physical strength was positively and significantly correlated with the total amounts of K and Si in culms during grain filling except that at the heading stage, the total amount of soluble sugars in culms at the heading and milky stages, the total amounts of Si and soluble sugars in leaf sheaths at the heading stage, the total amount of K in leaf sheaths at the heading and milky stages, and the maximum bearing capacity during grain filling. It is suggested that the lodging resistance of japonica rice would be improved by increasing the amount of soluble sugars in plants at the early filling stage, and enhancing the amount of Si in plants during grain filling through topdressing Si fertilizer at the early filling stage.

Effect of Biochar on Relieving Cadmium Stress and Reducing Accumulation in Super japonica Rice

It is of great importance to solve the threats induced by cadmium pollution on crops. This paper examined the effect of biochar on cadmium accumulation in japonica rice and revealed the mechanism underlying the response of protective enzyme system to cadmium stress. Biochar derived from rice straw was applied at two application rates under three cadmium concentrations. Shennong 265, super japonica rice variety, was selected as the test crop. The results indicated that cadmium content in above-ground biomass of rice increased with increasing soil cadmium concentrations, but the biochar application could suppress the accumulation of cadmium to some extent. Under high concentrations of cadmium, content of free proline and MDA （malondialdehyde） were high, so did the SOD （superoxide dismutase）, POD （peroxidase） and CAT （catalase） activity in the flag leaf of rice. However, the protective enzyme activities remained at low level when biochar was added.

Identification of Quantitative Trait Loci for Grain Traits in Japonica Rice

Quantitative trait loci（QTLs） of grain traits were detected to provide theoretical basis for fine mapping and molecular marker-assisted breeding of grain traits in japonica rice.Using an F2 population including 200 individuals derived from a cross combination between two japonica rice DL115 with large grain and XL005 with small grain,the grain length,grain width,grain thickness,ratio of grain length to width and 1 000-grain weight were evaluated in Beijing;and the quantitative trait loci for above five grain traits were identified by composite interval mapping using SSR markers.The results showed that the five grain traits exhibited a normal continuous distribution in F2 population,indicating they were quantitative traits controlled by multiple genes.A total of 16 QTLs conferring the five grain traits were detected on chromosomes 2,3,5 and 12,respectively.Eight QTLs,namely qGL3a,qGW2,qGW5,qGT2,qRLW2,qRLW3,qGWT2 and qGWT3,were major QTLs and explained 15.42,40.89,13.54,33.43,13.82,13.61,12.51 and 10.1% of the observed phenotypic variance,respectively.Among them,qGW2,qGT2,qRLW2 and qGWT2 were mapped in same interval RM12776-RM324 on chromosome 2.The marker interval RM12776-RM324 on chromosome 2 was common marker intervals of four major QTLs,and the two SSR markers RM12776 and RM324 would be used in molecular markerassisted breeding in japonica rice.The modes of gene action were mainly additive and partial dominance.Four QTLs＇ alleles were derived from small grain parent XL005,and other 12 QTLs＇ alleles were derived from large grain parent DL115.The alleles from larger parent were showed significant effects to grain length,grain width,grain thickness and 1 000-grain weight.

Cluster Analysis on Japonica Rice(Oryza sativa L.) with Good Eating Quality Based on SSR Markers and Phenotypic Traits

Diversity of 60 conventional japonica rice accessions with good eating quality at home and abroad was analyzed using SSR molecular markers, agronomic traits and taste characteristics. A total of 290 alleles were detected in the 60 accessions at 72 SSR loci with the high similarity coefficients varying between 0.600 and 0.924. The loci on chromosome 5 showed the greatest value in average allele number. Additionally, most of the SSR loci could detect 3 to 4 alleles. An UPGMA dendrogram based on the cluster analysis of the genetic similarity coefficients showed that the grouping trend of part of the rice accessions was geographic-related and most of the rice accessions in Jiangsu Province, China were clustered together. Furthermore, many domestic accessions from south and north origins in China were close to the foreign japonica rice varieties, as proved by their pedigree origin from the foreign high-quality sources. For taste characteristics, part of the accessions with excellent taste were clearly clustered into one category though they came from different geographical regions, which indicates that taste characteristics of some varieties were mainly genetically determined. In addition, the agronomic traits of japonica rice with good taste might be closely related with their geographical origins, but the relationship between superior taste characteristics and agronomic traits should be further clarified.

Analysis on Genetic Similarity of Japonica Rice Variety from Different Origins of Geography in the World

The genetic similarity and genetic difference among improved japonica rice varieties from different countries （or regions and organizations） were detected. The aim is to provide genetic basis to the breeding of japonica rice varieties. The genetic similarity and cluster of 313 improved japonica varieties from 20 countries （or regions and organizations） were analyzed using the SSR marker. With 34 SSR primers which were polymorphic and uniformly distributed in rice genome, totally 198 alleles were detected among these improved varieties with the average number of alleles per pair of primers of 5.8235. RM320, RM531, RM1, RM21, and RM336 located more alleles, which were 16, 13, 12, 10, and 10 respectively. RM320, RM336, RM286, RM531, and RM21 showed higher genetic diversity indexes, which were 2.3668, 2.0041, 1.9684, 1.9508, and 1.7203, respectively. The genetic similarity for improved japonica varieties among different countries （or regions and organizations） were ranged from 0.279 to 0.918, and the mean value was 0.653. The rice varieties from countries whose latitude and geography position were all nearer were clustered together with higher genetic similarity indexes. The rice varieties from countries who had more different latitude and far geography position were clustered separately with lower genetic similarity indexes. The results indicated the genetic similarity indexes among improved japonica varieties had a close relationship with the geographical position, especially with the latitude.

Comparison of agronomic performance between inter-sub-specific hybrid and inbred japonica rice under different mechanical transplanting methods

Mechanical transplanting has been applied to rice cultivation to save labor costs and ease labor shortages in Asian countries, especially in China. However, little information is available related to the characteristics of agronomic performance when comparing inter-sub-specific hybrid rice(IHR) and inbred japonica rice(IJR) under mechanical transplanting method. In 2013 and 2014, field experiments were conducted using IHR(Yongyou 2640) and IJR(Wuyunjing 24) under two cultivation patterns, that is, pot seedlings mechanically transplanted(PS) and carpet seedlings mechanically transplanted(CS). Grain yield, yield components, leaf area index(LAI), leaf area duration(LAD), aboveground biomass, crop growth rate(CGR), nitrogen(N) uptake, and N accumulation were investigated. When compared with CS, PS displayed significantly increased grain yield for both varieties because the larger sink size allowed higher N accumulation from panicle initiation to maturity. Moreover, total aboveground biomass under PS increased significantly compared with that under CS; that is, higher photosynthetic productivity resulted from a greater LAI and higher LAD during the grain filling stage. Higher N absorption capacity in the middle and late growth periods resulted in significantly enhanced total N uptake under PS. When compared with IJR for both treatments, IHR generated 75.2% more grain yield. However, the characteristics creating high yield of IHR were different from those of IJR. Greater aboveground biomass production as well as higher N uptake and accumulation created higher grain yield in IHR than in IJR. These results suggest higher yield could be achieved using PS with IHR, attributing to exploit both yield superiority and productive potential.

Effect of side deep placement of nitrogen on yield and nitrogen use efficiency of single season late japonica rice

Side deep placement of nitrogen plays an important role in improving rice yield and nitrogen use efficiency.Few studies have examined the effects of reducing the times of nitrogen(RTN)application and reducing the nitrogen rate(RNR)of application on rice yield and nitrogen use efficiency under side deep placement of nitrogen in paddy fields.Therefore,a field experiment of RNT and RNR treatments was conducted with nine fertilization modes during the 2018–2019 rice growing seasons in a rice–wheat cropping system of the lower reaches of the Yangtze River,China.Rice yield and nitrogen use efficiency were investigated under side deep placement of nitrogen.We found that under the same nitrogen application rate,the yield of RTN3 increased by 9.64 and 10.18%in rice varieties NJ9108 and NJ5718,respectively,compared with the farmers’fertilizer practices(FFP).The nitrogen accumulation of RTN3 was the highest at heading stage,at 11.30 t ha^(–1)across 2018 and 2019.Under the same nitrogen application rate,the N agronomic use efficiency(NAE),N physiological efficiency(NPE)and N recovery efficiency(NRE)of RTN3 were 8.1–21.28%,8.51–41.76%and 0.28–14.52%higher than those of the other fertilization modes,respectively.RNR led to decreases in SPAD value,leaf area index(LAI),dry matter accumulation,nitrogen accumulation,and nitrogen use efficiency.These results suggest that RTN3 increased rice yield and nitrogen use efficiency under the side deep placement of nitrogen,and RNR1 could achieve the goals of saving cost and increasing resource use efficiency.Two fertilization modes RTN3 and RNR1 both could achieve the dual goals of increasing grain yield and resource use efficiency and thus are worth further application and investigation.

Genetic Diversity of Seed Storage Proteins in Different Ecotype Varieties of japonica Rice and Its Application

One hundred and fifteen varieties （including cultivars and lines） with different ecotypes in japonica rice （Oryza sativa L.） were analyzed for endosperm storage proteins by sodium dodecyl sulfate polyacrylamide gel electrophoresis （SDS-PAGE） to estimate their genetic diversity for the purpose of genetic improving and variety identification. Nineteen types of profile were identified according to 1） presence/absence of 65 kDa bands, 2） staining intensity of 70, 60, 57, 37-39, 22-23, 13 and 10 kDa bands, 3） migration velocity of 35 kDa （α-4） and 4） band number at 57 kDa location. An unweighted-pair group average method with arithmetic mean （UPGMA） dendregram based on the cluster analysis of genetic similarity of the protein bands showed a small genetic variation among the tested materials, with the similarity coefficients varying between 0.75 and 1.00. Three distinct groups were identified from the cluster analysis of the rice varieties studied at the similarity coefficient level of 0.894. The first group included eight varieties with high amylose content, the second group contained fifteen varieties with high protein content, and the third group had the remaining ninety-two varieties, which accounted for 80% of the total materials. Clear relationship between ecotypes distinguished by maturity and groups revealed by cluster analysis was not found in this study. Only the group of high amylose linked with medium-maturity medium japonica ecotype. The bands of 70 kDa and 65 kDa can be used as protein markers to identify F1 seed purity of japonica hybrid rice Liuyanyou 422.

Transgenic japonica rice expressing the cry1C gene is resistant to striped stem borers in Northeast China

Rice production and quality are seriously affected by the lepidopteran pest,striped stem borer(SSB),in Northeast China.In this study,a synthetic cry1 C gene encoding Bacillus thuringiensis(Bt)δ-endotoxin,which is toxic to lepidopteran pest,was transformed into a japonica rice variety(Jigeng 88)in Northeast China by Agrobacterium-mediated transformation.Through molecular detection and the Basta resistance germination assay,a total of 16 single-copy homozygous transgenic lines were obtained from 126 independent transformants expressing cry1 C.Finally,four cry1 C-transgenic lines(JL16,JL23,JL41,and JL42)were selected by evaluation of the Cry1 C protein level,insect-resistance and agronomic traits.The cry1 C-transgenic lines had higher resistance to SSB and higher yield compared with non-transgenic(NT)control plants.T-DNA flanking sequence analysis of the transgenic line JL42 showed that the cry1 C gene was inserted into the intergenic region of chromosome 11,indicating that its insertion may not interfere with the genes near insertion site.In summary,this study developed four cry1 C-transgenic japonica rice lines with high insect resistance and high yield.They can be used as insect-resistant germplasm materials to overcome the problem of rice yield reduction caused by SSB and reduce the use of pesticides in Northeast China.

Construction of SSR Linkage Map and Analysis of QTLs for Rolled Leaf in Japonica Rice

Genetic analysis of rolled leaf is important to rice ideotype breeding. To detect loci controlling rolled leaf of japonica restorer lines, SSR marker genotypes and phenotypes of flag leaf rolling index （LRI） were investigated in Xiushui 79 （P1, a japonica rice variety）, C Bao （P2, a japonica restorer line） and 254 recombinant inbred lines derived from the cross between P1 and P2 , and in two environments. A genetic map of this cross was constructed, QTLs for LRI were detected and their interactions with environments were analyzed. Among 818 pairs of SSR primers, 90 primers showed polymorphism between P1 and P2, and 12 markers showed highly significant correlation with LRI in both environments based on single marker regression analysis. The genetic map containing 74 information loci has a total distance of 744.6 cM, with an average of 10.1 cM between two adjacent loci. Three QTLs （qRL-1, qRL-7 and qRL-8-1） were detected with two softwares： WinQTLCart 2.5 and QTLNetwork2.0. qRL-8-1 was a new locus, accounting for 15.5% and 12.8% of phenotypic variations in the two environments, respectively. The phenotypic variation explained by additive effect was 6.6%. No interaction was found between qRL-8-1 genotype and environments.

Transcript Profiling Reveals Abscisic Acid,Salicylic Acid and Jasmonic-Isoleucine Pathways Involved in High Regenerative Capacities of Immature Embryos Compared with Mature Seeds in japonica Rice

Induced pluripotent cell mass plays a role in genetic transformation mediated by Agrobacterium. Mature seeds are more recalcitrant to the induction of suitable calli than immature embryos in rice, but the exact molecular mechanisms involved remain elusive. In this study, the morphological structure of calli induced from mature seeds and immature embryos were observed under a scanning electron microscope using a paraffin embedded technique. Meanwhile, a total of 2 173 up- and down-regulated genes were identified in calli induced from mature seeds and immature embryos by RNA-seq technique and furtherly confirmed by quantitative real-time PCR. The results revealed the remarkable morphological differences in calli induced from mature seeds and immature embryos, and plant hormone signal transduction and hormone biosynthesis pathways, such as abscisic acid, salicylic acid and jasmonic-isoleucine, were found to play roles in somatic embryogenesis. This study provided comprehensive gene expression sets for mature seeds and immature embryos that were served as an important platform resource for further functional studies in plant embryogenesis.

New Stably Expressed Loci Responsible for Panicle Angle Trait in Japonica Rice in Four Environments

Panicle angle （PA） of 254 recombinant inbred lines derived from a cross between two japonica varieties Xiushui 79 and C Bao was investigated under four environments,and a genetic linkage map including 111 SSR markers was constructed.Genetic analysis was conducted by mixed major gene plus polygene inheritance models,and quantitative trait loci （QTLs） identification by the QTLNetwork 2.0 and the composite interval mapping approach of WinQTLCart 2.5 software.Results showed that the PA trait was controlled by two major genes plus polygenes,mainly by major genes.Eight QTLs for PA were detected by the QTLNetwork 2.0 software,and each locus explained 0.01% to 39.89% of the phenotypic variation.Twelve QTLs for PA were detected by the WinQTLCart 2.5 software,with each locus explaining 2.83% to 30.60% of the phenotypic variation.Two major QTLs （qPA9.2 and qPA9.5） distributed between RM3700 and RM3600 and between RM5652 and RM410,respectively,and a moderate QTL （qPA9.7） distributed between RM257 and OSR28,were both detected by the two methods in all of the four environments.The negative effect alleles of the three QTLs were from Xiushui 79.In addition,eight pairs of epistatic QTLs with minor effects were also detected.QTL × environment interactions were not significant for additive QTLs and epistatic QTL pairs.

Mining Elite Alleles of Growth Duration and Productive Panicle Number per Plant by Association Mapping with Conditional Phenotypic Value in Japonica Rice

To provide genetic information and materials for breeding hybrid japonica rice with wide adaptability and strong competitive advantage of yield, elite alleles and their carrier varieties of growth duration （GD） and productive panicle number per plant （PN） were detected. A natural population composed of 94 japonica varieties was phenotyped for the GD, PN and plant height （PH） in two environments. The conditional phenotypic data were transferred by the linear model method in software QGAStation 1.0, and association mapping based on the unconditional and conditional phenotype values of GD and PN was analyzed by using general linear model in software TASSEL. A total of 34 simple sequence repeat （SSR） marker loci associated with GD and PN were detected in the two environments. Among them, 15 were associated with GD, and 19 were associated with PN. Four elite alleles of RM8095-120bp, RM7102-176bp, RM72-170bp and RM72-178bp were associated with GD, and their carrier varieties were Hongmangshajing, Nipponbare, Hongmangshajing and Nannongjing 62401, respectively. These elite alleles from the carrier varieties can shorten GD by 2.03-9.93 d when they were introduced into improved materials. RM72-182bp associated with PN was an elite allele, and its carrier variety was Xiaoqingzhong. It can increase PN by three when introduced into improved materials. Moreover, these elite alleles can be used to improve target traits without influencing another two traits.

Moderate drought alleviates the damage to grain quality at high temperatures by improving the starch synthesis of inferior grains in japonica rice

In agricultural production,temperature and moisture are important factors affecting grain yield and quality.Although moderate drought at the grain-filling stage can effectively alleviate the damage caused by high temperature,the specific regulatory mechanism driving the effect of moderate drought at the high temperature on starch synthesis is still unclear.To explore the effects and mechanisms of high temperature and moderate drought on rice starch synthesis at the grainfilling stage,the activities of enzymes and expression levels of the genes involved in starch synthesis under four different treatments involving high temperature and/or water stress(CK,HT,WS,and HT+WS)were investigated in this study.The starch synthesis of a japonica inbred rice was measured under the four treatments during the grain filling.The results show that the effects of high temperature and moderate drought on grain filling mainly occur in the inferior grains of rice.Through the regulation of enzymes involved in starch synthesis and the expression levels of their main genes,the synthesis of rice starch can be affected.Therefore,the high temperature and moderate drought were antagonistic,and moderate drought can alleviate the damage to grain quality at a high temperature by improving the starch synthesis of inferior grains in japonica rice.This study provides a basis for stress-resistance cultivation and breeding strategies of rice with high temperature tolerance.

Development of lepidopteran pest-resistant transgenic japonica rice harboring a synthetic cry2A* gene

A synthetic cry2A^＊ gene enco ding Bacillus thuringiensis（Bt） δ-endotoxi n that resi st ance to lepidopteran pest was transformed into japonica rice variety Jijing 88, which is the most widely cultivated variety in Jilin Province, Northeast China, by Agrobacterium-mediated transformation. A total of 106 independent transformants overexpressing cry2A^＊ gene driven by ubiquitin（Ubi） promoter was produced. Three single-copy homozygous transgenic lines were finally selected based on the results of PCR analysis, se gregation ratio of Bast a resistance, and Southern hybridiza tion analyse s. RT-PCR and enzyme linke dimmune sorbent assay（ELISA） revealed that cry2A^＊ transcripts and protein were highly expressed in these lines. The high level of Cry2A^＊ protein expression resulted in high resistance to rice striped stem borer as evidence d by insect feeding bioassays. Our results demonst rate that cry2A^＊ transgenic japonica rice confers resistance to the rice striped stem borer in the laboratory conditions.

QTL Analysis for Seven Quality Traits of RIL Population in Japonica Rice Based on Three Genetic Statistical Models

QTL mapping for seven quality traits was conducted by using 254 recombinant inbred lines （RIL） derived from a japonica-japonica rice cross of Xiushui 79/C Bao. The seven traits investigated were grain length （GL）, grain length to width ratio （LWR）, chalk grain rate （CGR）, chalkiness degree （CD）, gelatinization temperature （GT）, amylose content （AC） and gel consistency （GC） of head rice. Three mapping methods employed were composite interval mapping in QTLMapper 2.0 software based on mixed linear model （MCIM）, inclusive composite interval mapping in QTL IciMapping 3.0 software based on stepwise regression linear model （ICIM） and multiple interval mapping with regression forward selection in Windows QTL Cartographer 2.5 based on multiple regression analysis （MIMR）. Results showed that five QTLs with additive effect （A-QTLs） were detected by all the three methods simultaneously, two by two methods simultaneously, and 23 by only one method. Five A-QTLs were detected by MCIM, nine by ICIM and 28 by MIMR. The contribution rates of single A-QTL ranged from 0.89% to 38.07%. All the QTLs with epistatic effect （E-QTLs） detected by MIMR were not detected by the other two methods. Fourteen pairs of E-QTLs were detected by both MCIM and ICIM, and 142 pairs of E-QTLs were detected by only one method. Twenty-five pairs of E-QTLs were detected by MCIM, 141 pairs by ICIM and four pairs by MIMR. The contribution rates of single pair of E-QTL were from 2.60% to 23.78%. In the Xiu-Bao RIL population, epistatic effect played a major role in the variation of GL and CD, and additive effect was the dominant in the variation of LWR, while both epistatic effect and additive effect had equal importance in the variation of CGR, AC, GT and GC. QTLs detected by two or more methods simultaneously were highly reliable, and could be applied to improve the quality traits in japonica hybrid rice.