Molecular genetic mapping of quantitative trait loci for milling quality in rice (Oryza sativa L.)

Identification and mapping of genomic regions controlling quantitative trait loci (QTLs) was undertaken to determine the genomic regions associated with milling traits in rice to facilitate breeding of new rice varieties with high milling quality. The recombinant inbred (RI) population used was derived from cross of a japonica variety, ‘Asominori’, with an indica variety, ‘IR24’ through 289 RFLP markers. Three milling traits, namely, brown rice percentage (BRP), milled rice percentage (MRP), and milled head rice percentage (MHP), which are the main indicators of milling quality in rice, were estimated for each RI line and their parental varieties. Continuous distributions and transgressive segregations of three milling traits were observed in the RI population, showing that the three traits were quantitatively inherited. Two QTLs (qBRP-9 and qBRP-10) for BRP were identified and mapped to chromosomes 9 and 10, and explained 7.2 and 21.3% of the total phenotype variation, respectively. Two QTLs (qMRP-11 and qMRP-12) governing MRP were detected and mapped to chromosomes 11 and 12, accounted for 12.2 and 7.7% of total phenotype variation, respectively. In addition, three QTLs (qMHP-1, qMHP-3 and qMHP-5) controlling MHP were observed and mapped to chromosomes 1, 3 and 5, and explained 16.0, 22.1 and 8.7% of the total phenotype variation, respectively. Among them, five QTLs (qBRP-9, qBRP-10, qMRP-11, qMHP-3 and qMHP-5) from japonica parent, Asominori, and two QTLs (qMRP-12, qMHP-1) from indica IR24 can improve milling quality in rice. The results and the tightly linked molecular markers that flank the QTL will be useful in breeding for improvement of milling quality in rice.     

Molecular mapping of quantitative trait loci for zinc toxicity tolerance in rice seedling (Oryza sativa L.)

Excess zinc harms the growth of rice plants and zinc toxicity can easily occur in acid soils. The aim of the study was to map quantitative trait loci (QTLs) in rice for tolerance to zinc toxicity, using a recombinant inbred (RI) population derived from the cross of a japonica variety (Asominori: relatively tolerant to Zn²⁺ toxicity) with an indica variety (IR24, relatively susceptible), through 289 RFLP markers. The index scores of damage (representing Zn²⁺ toxicity tolerance), after irrigating rice seedlings with a 1000-ppm Zn²⁺ solution for 20 successive days, were examined for each RI line and its parental varieties. Continuous distributions and transgressive segregations of the index scores were observed in the RI population, suggesting that Zn²⁺ toxicity tolerance was a quantitatively inherited trait. Three QTLs for Zn²⁺ toxicity tolerance were detected on chromosomes 1, 3 and 10 and explained 21.9, 8.9 and 7.6%, respectively, of the total phenotypic variation. The results and the tightly linked molecular markers that flank the QTLs, detected in this study, will be useful in improving Zn²⁺ tolerance in rice. In addition, the genomic positions between QTLs for Zn²⁺ toxicity tolerance and the QTLs for other metal (Fe²⁺, Mn²⁺, Al³⁺) toxicity tolerances, from previous studies, are discussed.     

Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.)

Direct seeding instead of transplanting for rice (Oryza sativa L.) has increasingly been used in northern and eastern China because of labor and cost saving. However, poor germinability is still one of the major problems faced in the adoption of direct seeding under low temperature (low temperature germinability: LTG) and anoxia (anoxia germinability: AG) condition. To gain an understanding of the genetic control of seed germinability under these unfavourable conditions, two rice lines, USSR5 (japonica type) and N22 (indica type) and F₂ individuals derived from the cross USSR5 × N22 were tested for LTG and AG. USSR5 and N22 differ significantly for both LTG and AG. The LTG of the F₂ individuals ranged from 0 to 100% after a 10 days incubation. AG ranged from 0.0 to 4.0 cm shoot length. Based on segregation in the F₂ population, a linkage map was constructed using 121 SSR markers. The map covered 1821.5 cM, with a mean inter-marker distance of 16.7 cM. Eleven putative QTLs for LTG were detected, one on each of chromosomes 3–5, 7, 9–11, and four on chromosome 5. The USSR5 alleles in all these QTLs acted to increase LTG. Two QTLs for AG were located on chromosomes 5 and 11, respectively, at both of which the USSR5 alleles acted to increase AG. We propose that USSR5 could make a major contribution to improving LTG and AG in rice breeding programs.     

Studies on culture ability of Glabrous rice(Oryza sativa L.)

Glabrous rice is characterized by its smoothand hairness leaves and husks,mainly dis- tributed in America,Africa,and Yunnan andGuizhou provinces of China.It has the charac- teristics of strong stem,high endurance tolodging,good compatibility,high grain quali-ty,and high yield,and is propitious to themachanized harvest.The Glabrous rice hasbeen proved to be plant population of superior- ity,which could be used as germplasm re-     

Localization,validation and characterization of plant-type QTLs on chromosomes 4 and 6 in rice (Oryza sativa L.)

Improvement of rice (Oryza sativa L.) plant type is a major breeding objective. This study aimed to precisely localize and characterize key genomic regions for plant type using near-isogenic individuals. Selfing of partially heterozygous F₅ recombinant inbred (RI) individuals [parental varieties Milyang 23 (M23) and Akihikari (AK)] developed heterogeneous inbred families (HIFs) composed of 108 and 93 F₇ progenies, which segregated at molecular marker loci on the long arms of chromosomes 4 and 6, respectively. The progeny lines (F₈) were evaluated for traits composing plant type in Los Baños, Philippines, to locate quantitative trait loci (QTLs) using interval mapping and to evaluate the effects of the QTL region by phenotypic comparison between the genotypes. QTLs for the traits were detected in 17 cM across XNpb12 on chromosome 6. The M23 homozygote for the QTL region resulted in a >7% increase and decrease in plant length and tiller number at heading, respectively, relative to the AK homozygote. Consequently, culm length (CL) and traits determining flag-leaf and panicle sizes increased 5–56% by the M23 homozygote, together with a 15% decrease in panicle number. For a QTL region detected in 6 cM across XNpb235 on chromosome 4, the AK homozygote had similar effects on these traits, except CL. The directions and magnitudes of their effects agreed with those previously estimated in the RI line population, thus increasing confidence in primary QTL analyses for plant type. Analyzing the HIFs validated and characterized the two QTL regions greatly involved in determining varietal plant type from an early growth stage to maturity, providing information useful for empirical and marker-assisted breeding towards rice improvement.     

水稻重要农艺性状的两年QTL剖析

 利用水稻汕优63（珍汕97 × 明恢63）重组自交系群体241个株系，对株高、生育期、产量及其产量构成因子等9个重要农艺性状进行了年度间的QTL定位和比较。结果表明，9个性状的表现型在两年均为连续分布，且都存在一定数量的双向超亲遗传类型。两年共检测到64个QTL，分布于水稻除第4染色体外的其余11条染色体，其中1999年检测到45个，2000年检测到35个，两年相同的QTL共16个。2000年检测到的QTL贡献率介于283%~1499%，且大多低于1999年。不同环境可以影响QTL的表达，但表达差异并不全是QTL×环境(QE)互作结果，也可能是由于该性状的遗传力偏低、QTL本身效应偏低或QE互作等原因共同造成的。另外，检测到8个显著的QE互作，但其互作效应明显低于对应的QTL效应。     

发育时期对水稻耐低磷胁迫有关性状QTLs检测的影响

 选用水稻窄叶青8号(籼稻)、京系17(粳稻)以及F1花药培养产生的127个DH株系，在磷素不同处理时期检测根表面积和干物重性状的数量性状基因(QTL)。结果表明，对于相对根表面积性状，处理10 d（3叶期）时检测到一个微效QTL，而在30 d时未检测出控制位点。在两个发育时期都检测到了控制干物重性状的QTL，但它们在染色体上的位置和贡献率均不一致。通过对根表面积和干物重性状QTL的定位，进一步证实发育时期与基因型表现存在互作效应，而最后反映在QTL定位的差异上。通过相关分析与检测性状控制位点贡献率的大小，初步认为在本试验条件下，对于根系形态等适应机制的评价应在早期进行；对水稻耐低磷胁迫敏感度（相对干物重为指标）的评价在磷素处理30 d时为佳。     

Effect of rice establishment methods on weedy rice (Oryza sativa L.) infestation and grain yield of cultivated rice (O. sativa L.) in Sri Lanka

Weedy rice is a great threat to rice production in Sri Lanka. Selective herbicides to manage weedy rice in conventional rice cultivars are not available in Sri Lanka. In the absence of appropriate chemical control measures, cultural approaches may help to achieve effective control of weedy rice. A study was conducted in two consecutive seasons in farmers' fields at three sites (Atalla, Samanthurai, and Girithale villages) in Sri Lanka to evaluate the effect of different establishment methods (farmers' practice, random broadcast, row seeding, seedling broadcast, and transplanted rice) on weedy rice infestation and rice yield. The farmers' practice had a higher number of weedy rice panicles (60–80 m⁻²) than the random broadcast (39–48 panicles m⁻²), seedling broadcast (3–15 panicles m⁻²), and transplanted rice (1.3–3.0 panicles m⁻²) methods. The use of clean rice seeds in the random broadcast method reduced weedy rice seed production by 29–41% compared with the farmers' practice (0.6–2.0 t ha⁻¹). Compared with the farmers' practice, the seedling broadcast method reduced weedy rice seed production by 71–87% and transplanted rice by 95–98%; and increased rice yield by 27–49% (7.5–9.1 t ha⁻¹). At all three sites, the farmers' practice resulted in the lowest grain yield (5.1–6.7 t ha⁻¹). Compared with the farmers' practice, the random broadcast and row seeding methods increased rice yield by up to 21% and 31%, respectively. The findings suggest that the use of clean rice seeds, the use of a row-seeded crop, and the adoption of different rice planting methods may help to suppress the spread of weedy rice.     

Glutelin is partially degraded in globulin-less mutants of rice (Oryza sativa L.)

Multigenic glutelins and monogenic globulin are major storage proteins accumulating in vacuole-derived protein body (PB-II) of rice (Oryza sativa L.) seeds. Because their interplay in PB-II formation was scarcely known, the effect of globulin-less mutation on glutelin accumulation was investigated. In globulin-less mutants, no phenotypic defect was found in seed and plant growth, while PB-II was deformed and apparent glutelin composition was changed, producing new glutelin α polypeptides X1–X5. 2D-PAGE of different combinations of globulin-less and glutelin subunit mutations suggested that the X1/X2, X3, and X4/X5 were derived from glutelin GluB1/GluB2/GluB4, GluA3, and GluA1/GluA2 subunits, respectively. Western blot with glutelin GluB4 subunit-specific and its variable region discriminable antibodies indicated at least in part the new spots X1/X2 are partially degraded products of GluB4 α polypeptides by the removal of 2–39 residues from C-terminus. Time course experiments with maturing seeds indicated the partial degradation of GluB4 occurred earlier (from 7 days after flowering) and higher than that of GluA1/GluA2. Considering the above results together with the fact that globulin accumulates at the periphery of PB-II and its absence produces deformed PB-II, globulin protects glutelins from proteinase digestion and thereby facilitates stable glutelin accumulation.     

Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.)

Background

Root system architecture is an important trait affecting the uptake of nutrients and water by crops. Shallower root systems preferentially take up nutrients from the topsoil and help avoid unfavorable environments in deeper soil layers. We have found a soil-surface rooting mutant from an M₂ population that was regenerated from seed calli of a japonica rice cultivar, Nipponbare. In this study, we examined the genetic and physiological characteristics of this mutant.

Results

The primary roots of the mutant showed no gravitropic response from the seedling stage on, whereas the gravitropic response of the shoots was normal. Segregation analyses by using an F₂ population derived from a cross between the soil-surface rooting mutant and wild-type Nipponbare indicated that the trait was controlled by a single recessive gene, designated as sor1. Fine mapping by using an F₂ population derived from a cross between the mutant and an indica rice cultivar, Kasalath, revealed that sor1 was located within a 136-kb region between the simple sequence repeat markers RM16254 and 2935-6 on the terminal region of the short arm of chromosome 4, where 13 putative open reading frames (ORFs) were found. We sequenced these ORFs and detected a 33-bp deletion in one of them, Os04g0101800. Transgenic plants of the mutant transformed with the genomic fragment carrying the Os04g0101800 sequence from Nipponbare showed normal gravitropic responses and no soil-surface rooting.

Conclusion

These results suggest that sor1, a rice mutant causing soil-surface rooting and altered root gravitropic response, is allelic to Os04g0101800, and that a 33-bp deletion in the coding region of this gene causes the mutant phenotypes.     

Estimation of combining ability for yield and yield components in rice (Oryza sativa L.) cultivars using diallel cross

In order to estimate combining ability and gene action of a number of rice cultivars, a 5 x 5 half a diallel cross genetic design has been used. Parents and their hybrids have been evaluated in a randomized complete block design with 3 replicates for yield and 6 yield components in 2007 in Rice Research Station of Iran-Amol. Mean squares of genotypes for all traits were highly significant (p < 0.01). Significant mean squares of combining ability for all traits showed additive and non-additive effects in control of the related traits. Having nonsignificant MS(GCA)/MS(SCA) ratio for all traits but 1000-grain weight show higher importance of nonadditive effects in comparison with additive effects of controlling genes. High relative importance of specific combining ability indicated that all traits but 1000-grain weight are highly affected by impacts of specific combining ability. Generally, Dasht, Neda and Binam were the best parents for general combining ability and Binam x IR62871-175-1-10 and Mashhad Domsiah x Binam were the best hybrids for grain yield and its components.     

A potential method to fix heterosis of rice(Oryza sativa L.)with autoployploid

By crossing homologuos triploid plants derivedfrom twin-seedlings with diploid plants,manykinds of aneuploid were produced as expectedbecause the abnormal chromosome pairing oc- curred in triploid itself and F_1.In the mean- time,we also obtained a few normal developeddiploid F_1 plants.The self progeny(F_2)showed agronomic stability,checked withSSLP and RFLP markers.It was found thatthe F_1 was non-segregated hybrid.In thisstudy,the triploid served as male parent andthe diploid indica rice variety R725 served as     

Competitiveness of rice (Oryza sativa L.) cultivars against Echinochloa crus-galli (L.) Beauv. in water-seeded production systems

Developing more competitive rice cultivars could help improve weed management and reduce dependency on herbicides. To achieve this goal, an understanding of key traits related to competitiveness is critical. Experiments were conducted at Gelemen and Bafra districts of Samsun province in Turkey between 2008 and 2009 to measure the competitiveness of rice cultivars against Echinochloa crus-galli, a problematic weed in rice fields. Five rice cultivars (Osmancık, Kızılırmak, Karadeniz, Koral and Neğiş) and five E. crus-galli densities (0, 5, 10, 20, and 30 plants m⁻²) were used. Koral produced significantly more tillers than the other cultivars irrespective of E. crus-galli densities and reduced E. crus-galli tiller production by about 29.5% at Gelemen and 15.8% at Bafra at the highest weed density. E. crus-galli interference reduced rice height and there was a density dependent relationship. Koral was the most competitive cultivar; it maintained high biomass accumulation in early growth stages and suffered smaller reductions in plant height in the presence of E. crus-galli, compared to the other cultivars. In the absence of weed competition, Koral and Neğiş produced the highest yields at both locations. Stepwise regression analyses of the combined data from both years showed tillering capacity, early growth crop biomass, and plant height were critical traits related to competitiveness. These traits should be considered by plant breeders in their efforts to develop rice cultivars with enhanced competitiveness against weeds. Development of such cultivars could substantially reduce herbicide and labor inputs for rice production.     

Growth and yield formation of rice (Oryza sativa L.) in the water-saving ground cover rice production system (GCRPS)

A new water-saving ‘Ground Cover Rice Production System’ (GCRPS) was evaluated in 2001 and 2002 near Beijing, North China. Using GCRPS, lowland rice was cultivated without a standing water layer during the entire growth period and plots were irrigated when soil water tension was below 15 kPa (approximately 90% water holding capacity). In order to prevent soil evaporation, the soil surface was covered with 14 μm thick plastic film (GCRPS_Plastic) or mulched with straw (GCRPS_Straw). In a third GCRPS treatment the soil was left uncovered (GCRPS_Bare). These treatments were compared with lowland rice cultivated under traditional paddy conditions (Paddy control). In an additional treatment with bare soil, one aerobic rice variety was cultivated. Compared to Paddy control, only 32–54% of irrigation water was applied in GCRPS treatments. Plants in GCRPS were smaller, developed fewer panicles and had a smaller leaf area index compared to Paddy control. Yield was significantly less in GCRPS_Bare and GCRPS_Straw compared to Paddy control in both years, while yield in GCRPS_Plastic was only 8% less than the Paddy control yield in 2002. Water-use efficiency (WUE, gram grain yield per litre water input) in GCRPS_Plastic was higher (0.35) than in Paddy control (0.23). Grain yield was highly significantly correlated with maximum leaf area index and leaf area index duration. Among yield components, the number of productive tillers had the greatest positive effect on yield, while the number of grains per panicle, thousand-grain weight and harvest index remained almost unaffected. Under uncovered condition, the aerobic rice variety had a significantly higher harvest index (HI), yield, and WUE compared to the lowland rice variety (GCRPS_Bare). The experiment demonstrates that GCRPS has potential to save substantial amounts of water at relatively minor yield penalties, if stress factors such as low soil temperature, water deficit, and nutrient deficiencies during the vegetative growth stage are avoided by suitable management practices.     

Genetic architecture, inter-relationship and selection criteria for yield improvement in rice (Oryza sativa L.)

This study has been conducted to determine the extent of genetic association between yield of Rice (Oryza sativa L.) and its components. The present experiment was carried out with 40 Rice (Oryza sativa L.) genotypes which were evaluated in a randomized block design with 3 replications during wet season of 2007 and 2008. Results showed that sufficient amount of variability was found in the entire gene pool for all traits studied. Higher magnitude of genotypic and phenotypic coefficients of variation was recorded for seed yield, harvest index, biological yield, number of spikelets per panicle, flag leaf length, plant height and number of tillers indicates that these characters are least influence by environment. High heritability coupled with high genetic advance as percent of mean was registered for seed yield, harvest index, number of spikelets per panicle, biological yield and flag leaf length, suggesting preponderance of additive gene action in the expression of these characters. Grain yield was significantly and positively associated with harvest index, number of tillers per hill, number of panicle per plant, panicle length, number of spikelet's per panicle and test weight at both genotypic and phenotypic levels. Path coefficient analysis revealed that harvest index, biological yield, number of tillers per hill, panicle length, number of spikelets per panicle, plant height and test weight had direct positive effect on seed yield, indicating these are the main contributors to yield. From this study it may be concluded that harvest index, number of tillers per hill, panicle length and number of spikelet per panicle and test weight are the most important characters that contributed directly to yield. Thus, these characters may serve selection criteria for improving genetic potential of rice.     

Critical nitrogen concentrations: implications for high-yielding rice (Oryza sativa L.) cultivars in the tropics

The critical nitrogen concentration of a plant can be defined as the minimum nitrogen concentration required for maximum growth rate at any time. It has been suggested that the relationship between the critical N concentration and dry matter per unit ground area for a wide range of crops is the same and is independent of climatic zone. Results presented in this paper support the concept of a critical N-dilution curve for yield of rice (Oryza sativa L.), which may be independent of climatic zone. The similarity between the nitrogen dilution curves for temperate and tropical environments indicates that there is no intrinsic difference in the ratio of carbon-to-nitrogen capture in those environments even though the final aboveground biomasses differed. Both the rate and duration of resource capture are probably limiting yields in tropical environments. In order to break through the current ceiling-yield barrier of approximately 10 t grain ha⁻¹ in the tropics, superior germplasm must be lodging resistant and capable of acquiring 144 kg N ha⁻¹ (N_0.5) in the first 35 days following transplanting. An examination of the rates of nitrogen acquisition indicated that more emphasis must be placed on providing sufficient nitrogen during the early stage of crop growth if higher yields are to be obtained. The time course of nitrogen accumulation by the aboveground biomass was calculated for weights greater than 1 t ha⁻¹; at weights less than this there were insufficient data to make calculations. At weights of aboveground biomass greater than 1 t ha⁻¹, the rate of nitrogen acquisition per unit ground area declined. The decline probably reflected a lowering in crop demand for soil nitrogen caused by the internal cycling of nitrogen from aging to young developing tissues; roots' age may also play a part in the decline. The estimated rate of demand for nitrogen by the panicle exceeded the rate at which the aboveground biomass acquired it, emphasizing the importance of having a large `reservoir' of nitrogen in vegetative tissues. Such a reservoir would ensure that the nitrogen demand of the panicle could be met without causing the photosynthetic capacity of the crop to prematurely lose its ability to meet the carbohydrate demand of the panicle.     

Effect of SWD irrigation on photosynthesis and grain yield of rice (Oryza sativa L.)

A study was conducted with the objective to determine the influence of (shallow water depth with wetting and drying) SWD on leaf photosynthesis of rice plants under field conditions. Experiments using SWD and traditional irrigations (TRI) were carried out at three transplanting densities, namely D1 (7.5 plants/m²), D2 (13.5 plants/m²) and D3 (19.5 plants/m²) with or without the addition of organic manure (0 and 15 t/ha). A significant increase in leaf net photosynthetic rate by SWD was observed with portable photosynthesis systems in two independent experiments. At both flowering and 20 DAF stages, photosynthetic rate was increased by 14.8% and 33.2% with D2 compared to control. SWD significantly increased specific leaf weight by 17.0% and 11.8% over the control at flowering and 20 DAF stages, respectively. LAI of D2 under SWD was significantly increased by 57.4% at 20 DAF. In addition, SWD with D2 significantly increased the leaf dry weight (DW) at both growing stages. At all the three densities, SWD increased the leaf N content and the increase was 18.9% at D2 density compared with the conventional control. In SWD irrigation, the leaf net photosynthetic rate was positively correlated with the leaf N content (R² = 0.9413), and the stomatal conductance was also positively correlated with leaf N content (R² = 0.7359). SWD enhanced sink size by increasing both panicle number and spikelet number per panicle. The increase in spikelet number per panicle was more pronounced in the 15 t ha⁻¹ manure treatment than in the zero-manure treatment. Grain yield was also significantly increased by SWD, with an average increase of 10% across all treatments. SWD with D2 had the highest grain yield under the both cultivars with or without 15 t ha⁻¹ manure treatment, which was 14.7% or 13.9% increase for Liangyoupeijiu and 11.3% or 11.2% for Zhongyou 6 over the control, respectively.