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The main objective of this study was to dissect the genetic basis of rice flowering regulated by temperature. We used two indica varieties Zhenshan 97 and Zhongzao 18, and 168 recombinant inbred lines (RILs) derived from them to estimate temperature effects on heading date (HD). Tests under four different photoperiod and temperature conditions in growth chambers showed that HD of both parents was accelerated at high temperatures, indicating that both parents were strongly thermo-sensitive. The averaged effective cumulative temperatures (ECTs), 1,120 and 1,263 °C necessary for Zhenshan 97 and Zhongzao 18 respectively, could be the prerequisite in a given condition before heading. QTL analysis was conducted with the RILs grown in both long day and short day conditions in 2 years. A total of 4 ECT QTLs corresponding to 4 HD QTLs were mapped. The major ECT QTL, qEHD10, was repeatedly identified on chromosome 10, which could explain 42.2–57.0 % of ECT variation and 39.8–59.4 % of HD variation in four environments. Overall these novel findings would improve the knowledge of temperature on rice flowering.

Improvement of rice grain yield (YD) is an important goal in rice breeding. YD is determined by its related traits such as spikelet fertility (SF), 1,000-grain weight (TGW), and the number of spikelets per panicle (SPP). We previously mapped quantitative trait loci (QTLs) for SPP and TGW using the recombinant inbred lines (RILs) derived from the crosses between Minghui 63 and Teqing. In this study, four QTLs for SF and four QTLs for YD were detected in the RILs. Comparison of the locations of QTLs for these three yield-related traits identified one QTL cluster in the interval between RM3400 and RM3646 on chromosome 3. The QTL cluster contained three QTLs, SPP3a, SF3 and TGW3a, but no YD QTL was located there. To validate the QTL cluster, a BC4F2 population was obtained, in which SPP3a, SF3 and TGW3a were simultaneously mapped to the same region. SPP3a, SF3 and TGW3a explained 36.3, 29.5 and 59.0 % of phenotype variance with additive effect of 16.4 spikelets, 6 % SF and 1.8 g grain weight, respectively. In the BC4F2 population, though the region has opposite effects on TGW and SPP/SF, a YD QTL YD3 identified in this cluster region can increase 4.6 g grains per plant, which suggests this QTL cluster is a yield-enhancing QTL cluster and can be targeted to improve rice yield by marker aided selection.

Transgressive segregation is a common phenomenon in plant species. In this study, transgressive segregation for kilo-grain weight (KGW) was observed in a recombinant inbred line (RIL) population derived from the cross between an indica variety, Teqing, and a wide compatible japonica variety, 02428, in three environments. A genetic linkage map with 154 single sequence repeat markers (SSR) was developed. Effects on KGW of quantitative trait loci (QTLs), digenetic epistasis, and their environmental interaction (QE) were determined using a mixed linear model approach. 13 QTLs with additive effects and 8 digenetic interactions involving 16 loci were identified. Eight QTLs were involved in interactions. Two QTLs and one epistasis showed QE. 30.0 and 14.0% of variation was explained by the additive effects and epistasis, respectively, which were much greater than the 4.4% of variation explained by QE. According to the model used, predicted KGW values of extreme phenotypes in the RIL population were very close to their observed values. This indicated that complementary action of additive QTLs and epistasis can adequately account for the important genetic bases of transgressive segregation for KGW in the rice RIL population.

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. To study the effects of seasonal changes on yield components, 168 recombinant inbred lines derived from a cross between two Oryza sativa L. indica varieties, Zhenshan 97 and Zhongzao 18 were grown for phenotype collection, in three different seasons, within a year. The results implied 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. 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. Two-way ANOVA showed that genotype by environment and QTL by environment interactions for these traits were highly significant (P < 0.0001). 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.

Seed dormancy (SD) is controlled by its own complicated genetic factors and environmental factors. SD is an important trait affecting grain yield and quality in cereal crops. A population comprising 240 recombinant inbred lines (RIL) was used for detecting quantitative trait locus (QTL) for SD in rice. To minimize the effect of environment, data for lines for which the optimum temperature during the late ripening stage is either below 20°C or above 30°C were excluded from the analysis, which left 185 lines. In a dynamic germination test of the parents of the population, Minghui 63 showed clear SD and Zhenshan 97 showed none. The seeds of each RIL, harvested 32 days after heading, were divided into two lots: seeds in one lot were sown immediately, without any treatment to break their dormancy, whereas seeds in the other lot were sown after they had been exposed to dry heat (50°C) for 72 h. Composite interval mapping showed the presence of qDGE1, qDGR5a, qDGR5b, and qDGR7 in the first lot whereas only qDGR7 was detected in the second lot––which had been treated to break SD––indicating the strong influence of qDGR7 in controlling SD. A recently cloned Sdr4 is also located in the qDGR7 region. Coincidently, three rice homologues of Arabidopsis SD gene DOG1 were found in qDGE1 and qDGR5b regions where no SD QTL had been reported so far. These results indicate that the QTL found in this study are reliable, and that it would be worthwhile to clone qDGE1 and qDGR5b.

The ability to detect quantitative trait loci (QTLs) in a bi-allelic population is often limited. The power of QTL detection and identification of the most beneficial allele at each QTL could be greatly improved by comparing QTLs among different populations derived from connecting multi-parents. In this study, three sets of connected recombinant inbred lines (RILs) derived from the crosses between Zhenshan 97 and Minghui 63 (PZM), Zhenshan 97 and Teqing (PZT), and Minghui 63 and Teqing (PMT), respectively, were used. QTL analyses for the number of spikelets per panicle (SPP) and 1,000-grain weight (TGW) were performed in PZT, and five SPP QTLs on chromosomes 1, 6, and 7 and two TGW QTLs on chromosome 1 were detected. QTL for SPP was also identified in PMT, and six QTLs were detected on chromosomes 1, 2, 3, 6, and 7 in this population. In an earlier study, we identified five SPP QTLs and four TGW QTLs in PMT and nine TGW QTLs in PZM. Comparison of the QTL mapping results of these two studies showed that one QTL was common to the three populations, 11 QTLs were detected in two populations, and six QTLs were found in only one population. Comparison of genetic effect and the action direction of the QTLs detected in the three populations showed that additive effects of QTLs estimated in different populations were also expressed additively among three parental alleles. Additive effects of SPP7a estimated in three near-isogenic line F2 populations supported this finding. Based on these results, we suggest that pyramiding the most beneficial alleles among the three parents could efficiently improve rice yield.

Chilling injury is one of the most important limiting factors affecting rice production in temperate and high-elevation areas. In this study, 146 microsatellite markers were employed to identify quantitative trait loci (QTL) conferring cold tolerance at seedling stage (CTS) .The mapping population consisted of 193 doubled haploid (DH) lines, which derived from a cross between a cold-tolerant japonica variety (AAV002863) and a cold-sensitive indica cultivar (Zhenshan97B). Tolerance to cold was assessed by the survival percentage of seedlings after cold treatment. In a climate chamber, after treatment at 6°C/10°C for 7 d, the measurement was taken on the sixth day of the recovery stage at room temperature. The phenotypic distribution of the DH population approximately fitted normality with skewness and kurtosis less than 0.3, and the difference among the three repetitions was not significant. Five main effect QTLs were identified with LOD > 4.0 on chromosomes 1, 2, 8 using a composite interval mapping approach. The accumulated contribution of the five QTLs was 62.28%, and a major QTL (LOD = 15.09) was identified on chromosome 2 flanked by RM561 and RM341, which explained 27.42% of the total phenotypic variation. Four significant epistatic interactions were also detected with a total contribution of 20.14%.

The genetic dissection of morphological traits can helpful to evaluate their potential values as markers for rice genetic improvement. In this study, a RI population derived from a cross from Zhenshan97 and IRAT109 was used to dissect the genetic bases of seven morphological traits such as leaf sheath color (LSC), grain apiculus color (GAC), grain hairiness density (GHD), grain awn length (GAL), ratio of leaf length to width (RLW), leaf erectness (LER) and natural leaf rolling status (NLR). Totally, 26 main-effect QTLs and 22 epistatic QTLs were detected. Of them, 11 main-effect and 3 epistatic QTLs expressed environmental interactions. GAC controlled by a single gene could be regarded as the most useful marker. LSC controlled by two major interacted main-effect QTLs, but with no environmental interaction, is suitable to become morphological marker. LSC will be a very efficient morphological marker for identification of hybrid plants at rice seedling stage when the two major QTLs are introduced into male sterile line and restorer line separately. GHD controlled by a major QTL and a few minor QTLs with comparative low QEIs could also be used as marker. The traits GAL, NLR, RLW and LER, which were controlled by a number of minor effect QTLs and affected by environmental conditions could not be used as marker. But the QTLs with large effects, such as nrl8, can be targeted for corresponding trait improvement through marker-aided selection in rice breeding.