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.     

Mapping quantitative trait loci (QTLs) for seedling-vigor using recombinant inbred lines of rice (Oryza sativa L.)

Seedling-vigor is important for optimum stand establishment and increasing weed competitive ability in rice cropping systems. In the current study, three seedling-vigor-related traits, seed germination rate, seedling shoot length and dry matter weight, were investigated by the paper-roll tests with rice recombinant inbred lines derived from a cross between Lemont (japonica) and Teqing (indica). The phenotype data, together with a linkage map consisting of 198 marker loci, was used to conduct composite interval mapping by QTLMapper 1.0 to simultaneously map both main-effect and epistatic QTLs for seedling-vigor in rice. Totally, 13 putative main-effect QTLs and 19 pairs of epistatic loci with R² ≥ 5% were identified. Almost all of these QTLs or interactions individually explained only around 5–10% of the phenotypic variation. The majority (68%) of these main-effect and epistatic loci were clustered in seven chromosome regions, each spanning 12–28 cM (centi-Morgan) and containing three or more detectable loci. When detectable for the multiple seedling-vigor-related traits, either the main-effect QTLs or the epistatic interactions sharing the same map location had their additive or epistatic effects in the same direction, which agreed well with the positive correlations among the traits. The results demonstrated that seedling-vigor in rice could be controlled by many loci, most of which had small effects, but, relatively, epistasis as a genetic factor was much more important than main-effects of QTLs. Along with the results reported previously, this study revealed the extensive genetic diversity for seedling-vigor in rice. In addition, the QTL q^SV-7 on chromosome 7 was found to have the largest main-effects on multiple seedling-vigor-related traits and therefore could be used as a potential target to be genetically manipulated by marker-assisted selection in rice seedling-vigor breeding programs.     

大豆苗期耐盐性的遗传及QTL定位分析

利用重组自交系群体NJRIKY进行大豆苗期耐盐性的遗传及QTL定位分析。以每个家系的平均存活时间为耐盐指标,采用主基因+多基因混合遗传模型进行RIL遗传分析,结果表明,NJRIKY群体的耐盐性遗传符合F-3模型,即由3对主基因控制,没有多基因修饰,主基因遗传率是64.4%。利用Cartographer V.2.5进行QTL定位。结果显示,共检测到3个耐盐QTL,它们分别位于B1、G和K三个连锁群上,分别解释8.4%、17.9%和11.3%的表型变异。     

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-     

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.     

Physiological traits of hybrid rice (Oryza sativa L. ) associated with iron toxicity

Iron toxicity, a physiological disorder of rice, is widely spread in tropical and subtropical areas and causes severe rice yield reduction.     

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.     

Quantitative trait loci for seedling vigor in rice under field conditions

Previous QTL studies on seedling vigor in rice (Oryza sativa L.) were conducted all based on laboratory germination tests. In the current study, a set of recombinant inbred lines derived from a rice cross were assessed for seedling vigor related traits in natural field environments including two treatments (drained soil and flooded soil). Composite interval mapping identified nine QTL for seedling vigor traits that correlated positively with each other. Individual QTL explained 4–14% of the total trait variation. Among the QTL, three and four were specific to the drained and flooded treatments, respectively, while two others were common between the two treatments. Four QTL (qFV-1-1, qFV-3-2, qFV-5-1 and qFV-10) each simultaneously showed effect on two or more traits with additive effects always in the same direction. The QTL qFV-5-1 could be further resolved into at least two linked loci, qFV-5-1a controlling seedling height and qFV-5-1b controlling seedling dry weight while the QTL qFV-10 could be a single locus with a pleiotropic effect on both seedling height and dry weight. The QTL qFV-1-1 and qFV-3-2 expressed specially under the flooded conditions, each pleiotropically controlling both coleoptile and seedling emergence. These two QTL were completely different from that affecting seedling emergence in the drained conditions. Comparison of the QTL indicated that the QTL mapping results based on field assessments could to some extent coincide with those based on lab tests but the discrepancy between the two kinds of experiments could not be overlooked.     

Physiological traits of hybrid rice (Oryza sativa L. ) associated with iron toxicity

Iron toxicity, a physiological disorder of rice, is widely spread in tropical and subtropical areas and causes severe rice yield reduction.     

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.     

Adaptation of rice (Oryza sativa L.) genotypes in the rainfed lowlands of Lao PDR

Genotype by environment (G×E) interactions for grain yield were investigated in 14 rice genotypes across eight rainfed lowland field environments in Lao PDR, in order to identify stable adapted cultivars for improved farmer livelihood and food security. G×E accounted for 20.3% of the total variance, with three vectors from ordination analysis accounting for 75.1% of the G×E-SS, in 6 genotype?×?6 environment groups. PCA1 indicated water-limited yield potential, PCA2 pre-flowering stress and PCA3 post-flowering stress. Genotype groups (G1–G6) differed in adaptation to these environments. G5 (VT450-2 and TSN9) were widely adapted and high-yielding. G6 (TDK11 and TDK37) were also high-yielding, topping the rankings in three environment groups, but yielded less in Phalanxay 2012 and Phalanxay 2011, where their phenology was unstable under stress. Other genotype groups showed specific adaptations, but failed to exceed yields of G5 and G6. Hence, VT450-2 and TSN9 (G5) were the preferred genotypes for rainfed lowland in southern Lao PDR, due to their high and stable grain yields. Stability in flowering time and high yield in rainfall deficit were desirable traits for improved farmer livelihood and food security.     

Weed management challenges in rice (Oryza sativa L.) for food security in Bhutan: A review

Rice is the most important and staple cereal in Bhutan, currently grown over an area of 19,549 hectares with a total production of 77,038 tonnes. However, its yield is limited in certain regions due to weed competition with losses of up to 50% reported through infestation from both annual and perennial weeds. In this article, we describe the current weed management practices in rice in Bhutan and identify challenges and prospects to guide future weed control research given that weed science in Bhutan is in its infancy. Generally, the most common form of weed control is hand weeding. However, herbicide use is also increasing as farmers face labour shortages on farms and realize the benefits of herbicides, especially in reducing the time taken to weed crops. But the continued use of the single chemical butachlor is a concern given the possible development of herbicide resistance. Research priorities for weed management in rice in Bhutan include a systematic assessment of crop yield losses; prioritization of weed importance and species shifts; mechanical and cultural alternatives to hand weeding; herbicide resistance testing and management; collective community approaches to area-wide management; and weed management options to suit alternative rice production systems. The ecology and management of the perennial semi-aquatic Potamogeton distinctus needs serious attention owing to its prevalence in major rice areas and potential alone to cause significant yield losses of up to 37%. The successful experiences and challenges in neighbouring Asian countries should also help to guide future weed control research in Bhutan.     

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