No-tillage and direct seeding for super hybrid rice production in rice–oilseed rape cropping system

No-tillage and direct seeding (NTDS) is an effective crop production method for reducing production costs and soil conservation. In order to understand performance of super hybrid rice under NTDS in rice–oilseed rape cropping system, a researcher-managed trail (2004–2010) and an on-farm research (2002–2005) were conducted to compare different tillage (conventional tillage or no-tillage) and rice establishment methods (transplanting or direct seeding) in super hybrid rice–oilseed rape cropping system. Under researcher-managed condition, grain yields of super hybrid rice under NTDS and conventional tillage and transplanting (CTTP) were equal. Compared with under CTTP, super hybrid rice under NTDS was characterized by more panicle number per m² but less spikelet number per panicle, and lower aboveground biomass production before heading but higher aboveground biomass accumulated during heading to maturity. Higher maximum tiller number per m² and lower spikelet production efficiency were responsible for the more panicle number per m² and less spikelet number per panicle under NTDS, respectively. Under farmer-managed condition, super hybrid rice under NTDS had more panicle number m² than under CTTP, which resulted in higher grain yield. Labor input under NTDS was lower than that under CTTP. Moreover, adoption of NTDS for super hybrid rice production had no significant impacts on seed yield and yield components of oilseed rape in rice–oilseed rape cropping system. Our study showed that CTTP could be replaced with NTDS to maintain yield and save labor for super hybrid rice production in rice–oilseed rape cropping system.     

Breeding of new rice cultivar ‘Tohoku 194’ with ‘Sasanishiki’-type good eating quality of cooked rice

Cooked rice of ‘Sasanishiki’ is soft and not as sticky as those of Japanese leading cultivars ‘Koshihikari’ and ‘Hitomebore’. As a method for efficient selection of a breeding line having a good eating quality like that of ‘Sasanishiki’, the use of physical properties of cooked rice and cooking quality was examined. There were differences of physical properties of the surface layer, starch-iodine blue value per solid substance weight in cooking water and volume expansion of cooked rice between ‘Sasanishiki’ and ‘Hitomebore’, these properties being considered to be usable for the selection of breeding lines. Using these traits as selection targets, one line, named ‘Tohoku 194’, which has eating quality highly similar to that of ‘Sasanishiki’ and cold tolerance derived from ‘Hitomebore’, was selected from progeny of a cross between ‘Sasanishiki’ and ‘Hitomebore’. An application for registration as a new variety has been submitted for ‘Tohoku 194’ under the Japanese Plant Variety Protection Act, and is expected to become a recommended cultivar in Miyagi Prefecture. ‘Tohoku 194’ may fulfill various demands of consumers and companies in the food industry.     

Anther culture of recalcitrant indica × Basmati rice hybrids

Fertile, green, di-haploid plants were obtained at high frequencies from several indica × Basmati rice F₁ hybrids and/or F₂ plant populations using an improved anther culture procedure. Anthers from cold-pretreated (10 ^°C for 10 d) panicles of six indica (HKR120, HKR86-3, HKR86-217, PR106, Gobind andCH2 double dwarf) and two Basmati rice (Basmati 370,Taraori Basmati) varieties and 14 heterotic indica ×Basmati F₁/F₂ hybrids were cultured in modified agarose-solidified N6M, Heh5M and RZM media. Best callus induction frequencies (2.6–78%) were obtained in RZM medium containing 4% (w/v) maltose,2,4-D, NAA and kinetin. F₂ plants compared to F₁ hybrids and parental rice varieties, were more responsive to anther culture. Androgenesis frequencies of 31–78% were obtained for indica × Basmati F₂ plants in RZM medium in just 30 d which are comparable to or higher than that reported for japonica rice varieties and hybrids involving japonica rice parent(s). Agarose (1.0% w/v)-solidified MS medium containing 3.0% maltose, kinetin, BAP, and NAA, induced green shoot regeneration in 0–51% of the anther-derived callide pending upon the genotype. High plant regeneration frequencies (67–337 green plants per 1000 anthers)were obtained from anther calli of several F₁hybrids (Gobind × Basmati 370 and HKR120 ×Taraori Basmati) and F₂ plants (Gobind × Basmati370, Gobind × Taraori Basmati, HKR86-3 × TaraoriBasmati). A sample of 498 plants obtained from the above hybrids, were transferred to pots with>90% survival; 8–78% of these plants had >5%spikelet fertility and were diploid. In addition,18% of the haploid plants could be diploidized by submerging in 0.1% colchicine solution for 16–18 h. The improved anther culture procedure reported here, resulted in several fold increase in the recovery of green plants from recalcitrant indica × Basmati rice hybrids compared to previous published procedures. The study may accelerate the introgression of desirable genes from indica into Basmati rice using anther culture as a breeding tool. This revised version was published online in July 2006 with corrections to the Cover Date.     

Correlation between α-amylase gene expression and seedling vigor in rice

Summary This report examines the relationship between seedling vigor, -amylase enzyme activity and -amylase mRNA accumulation in ten varieties of rice (Oryza sativa L.) grown at two temperatures (15°C and 30°C). A significant, positive correlation was observed between seedling vigor, -amylase enzyme activity, and the accumulation of mRNA from one rice -amylase gene (RAmy1A) at both temperature regimens. The results of this study support previous experiments which have correlated -amylase enzyme activity to seedling vigor. We have extended this correlation to the expression of one of ten genes that comprise the rice -amylase multigene family. These results suggest that the expression of -amylase gene RAmy1A is an important, and possibly rate-limiting factor in determining seedling vigor in rice.     

Physiological characteristics of a functional stay-green rice “SNU-SG1” during grain-filling period

Functional stay-green has been regarded as a promising characteristic to be introduced for improving rice yield potential. A functional stay-green rice “SNU-SG1” that was identified from japonica rice collections was compared with two regular high-yielding rice cultivars (HYVs) for the temporal change of leaf chlorophyll, soluble protein, and root activity, and nitrogen accumulation and remobilization during the grain-filling period. SNU-SG1 had slower decreasing rate and maintained higher concentration of chlorophyll and soluble protein in upper four leaves during the grain-filling period than HYVs “Suweon490” and “Andabyeo”, revealing a typical stay-green characteristic. Even though SNU-SG1 remobilized almost the same proportion of N accumulated before heading as HYVs to grain, it maintained much higher leaf N concentration due to the significantly higher N accumulation that is ascribable to the higher root activity sustenance during grain-filling period. The functional stay-green trait of SNU-SG1 seems to stem not only from the genetic control preventing chlorophyll degradation but also from the higher capacity to absorb N from soil due to the sustained strong root activity during grain-filling period. SNU-SG1 exhibited higher crop growth rate during late grain-filling period than HYVs, resulting in higher grain-filling percentage and non-structural carbohydrate re-accumulation in the stem at the final stage of grain filling. It is concluded that SNU-SG1 has a promising trait “functional stay-green” contributable to rice yield potential improvement through the improved grain filling.     

Correction: QTL mapping under salt stress in rice using a Kalarata–Azucena population

Euphytica - The color of flour and its end-use products is an important quality trait of wheat. Understanding the genetic basis of this trait is essential for improving wheat quality. In this...     

Identification of quantitative trait loci for seed storability in rice (Oryza sativa L.)

In the present study, quantitative trait loci (QTLs) controlling seed storability based on relative germination rate (%) were dissected using a saturated linkage map and a recombinant inbred lines (RILs) derived from a cross of japonica cultivar Asominori (Oryza sativa L.) and indica cultivar IR24 (Oryza sativa L.). A total of three QTLs (qRGR-1, qRGR-3 and qRGR-9) were detected on chromosomes 1, 3 and 9 with LOD score ranging from 3.45 to 6.95 and the phenotypic variance explained from 16.72% to 28.63%. The IR24 alleles were all associated with seed storability at all the three QTLs. The existence of these QTLs was confirmed using IR24 chromosome segment substitution lines (CSSLs) in Asominori genetic background (AIS). By QTL comparative analysis, the QTL, qRGR-9 on chromosomes 9 appeared to be consistent with another rice population, this region may provide an important region for isolating this responsible gene. These results also provide the possibilities of enhancing Seed storability in rice breeding program by marker-assisted selection (MAS) and pyramiding QTLs. Y. Xue and S. Q. Zhang—joint first authors.     

Development of advanced fragrant rice lines from MR269 × Basmati 370 through marker-assisted backcrossing

Fragrance in rice is an appealing attribute to consumers. The increasing demand for fragrant rice highlights the need to develop fragrant rice variety that suit the preference of local consumers in addition to reduce fragrant rice imports. Marker-assisted backcrossing (MABC) was employed to develop advanced fragrant rice lines from the cross between MR269 and Basmati 370. MR269 is a Malaysian high-yielding rice variety but non-fragrant and was used as recurrent parent whereas Basmati 370 is a well-known fragrant traditional rice variety and was used as donor parent for the fragrance gene. Two generations of backcrosses and a generation of selfing were conducted to introgress the fragrance gene and restore the recurrent parent genome in the backcross progenies. As a result, 14 advanced fragrant rice lines were developed. These advanced fragrant rice lines carried homozygous alleles for the fragrance gene, similar to Basmati 370. The average recovery of recurrent parent genome was 88.4%. Besides being fragrant, the advanced fragrant rice lines also had most of the morphological and agronomical traits similar to MR269. Grain quality of the advanced fragrant rice lines in terms of gelatinization temperature, amylose content and gel consistency are also similar to both parents. Besides, the advanced fragrant rice lines had 2-acetyl-1-pyrroline content similar to Basmati 370. MABC approach applied in this study has successfully introgressed the fragrance gene and accelerated the recovery of recurrent parent genome in advanced fragrant rice lines, therefore these lines can be delivered to the farmers and consumers for use in due time.     

Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross

Grain shape is an important trait for improving rice yield. A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F₂ mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations. In this study, we developed two advanced mapping populations (chromosome segment substitution lines [CSSLs] and BC₄F₂ lines consisting of more than 2000 individuals) in the genetic backgrounds of two improved cultivars: a japonica cultivar (Koshihikari) with short, round grains, and an indica cultivar (IR64) with long, slender grains. We compared the ability of these materials to reveal QTLs for grain shape with that of an F₂ population. Only 8 QTLs for grain length or grain width were detected in the F₂ population, versus 47 in the CSSL population and 65 in the BC₄F₂ population. These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds.     

Genetics of fertility restoration of ‘Wild Abortive’ cytoplasmic male sterility in rice,Oryza sativa L.

Summary Genetics of fertility restoration in six varieties and breeding lines of rice was studied in Wild Abortive cytoplasmic genetic male sterility system using cytoplasmic male sterile lines V 20 A and IR 54752 A. Fertility evaluation of the plants in F₂ and testcross populations of the crosses of V 20 A with PR 103, PR 106 and PAU 502-94-1, and IR 54752 A with PAU 1124-36-1 and PAU 1126-1-1 revealed that fertility restoration in PR 103, PR 106, PAU 502-94-1, PAU 1124-36-1 and PAU 1126-1-1 was controlled by two independently segregating dominant genes. The two genes appeared to have additive effects; one of them being stronger than the other in imparting fertility restoration. Data on spikelet fertility of the plants in F₂ and testcross populations of V 20 A/UPR 82-1-1 cross showed that fertility restoration in UPR 82-1-1 was controlled by two independently segregating dominant genes which exhibited recessive epistatic interaction.

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Genetic basis of multiple resistance to the brown planthopper (Nilaparvata lugens St?l) and the green rice leafhopper (Nephotettix cincticeps Uhler) in the rice cultivar ‘ASD7’ (Oryza sativa L. ssp. indica)

The rice cultivar ASD7 (Oryza sativa L. ssp. indica) is resistant to the brown planthopper (BPH; Nilaparvata lugens Stål) and the green leafhopper (Nephotettix virescens Distant). Here, we analyzed multiple genetic resistance to BPH and the green rice leafhopper (GRH; Nephotettix cincticeps Uhler). Using two independent F₂ populations derived from a cross between ASD7 and Taichung 65 (Oryza sativa ssp. japonica), we detected two QTLs (qBPH6 and qBPH12) for resistance to BPH and one QTL (qGRH5) for resistance to GRH. Linkage analysis in BC₂F₃ populations revealed that qBPH12 controlled resistance to BPH and co-segregated with SSR markers RM28466 and RM7376 in plants homozygous for the ASD7 allele at qBPH6. Plants homozygous for the ASD7 alleles at both QTLs showed a much faster antibiosis response to BPH than plants homozygous at only one of these QTLs. It revealed that epistatic interaction between qBPH6 and qBPH12 is the basis of resistance to BPH in ASD7. In addition, qGRH5 controlled resistance to GRH and co-segregated with SSR markers RM6082 and RM3381. qGRH5 is identical to GRH1. Thus, we clarified the genetic basis of multiple resistance of ASD7 to BPH and GRH.     

Whitebacked planthopper Sogatella furcifera (Horváth) (Homoptera: Delphacidae) resistance in rice variety Sinna Sivappu

Whitebacked planthopper (WBPH) along with brown planthopper (BPH) has emerged as a major pest of rice in several Asian countries. Development and cultivation of varieties resistant to both planthoppers is an ecologically acceptable strategy to manage these pests. Sinna Sivappu, a Sri Lankan landrace, was reported to be resistant to both planthoppers. While inheritance of BPH resistance has been reported, the genetics of WBPH resistance in this variety is not known. Using a mapping population of 255 F_2:3 families from Taichung Native (TN)1/Sinna Sivappu cross and 128 polymorphic simple sequence repeat (SSR) markers, genes or quantitative trait loci (QTLs) for WBPH resistance quantified in ten phenotypic tests were identified, adopting classical Mendelian segregation, correlation and QTL analyses. The inheritance pattern suggested that a single recessive gene controlled regulation of seedling damage score. Antixenosis or nymphal preference was influenced by two complementary recessive genes, whereas tolerance in terms of days to wilt was under the influence of a single dominant gene. Several of these phenotypic tests recorded high degree of positive or negative correlation between them, suggesting dependence or redundancy of the tests. QTL analysis revealed 13 loci associated with nine traits. Five major-effect QTLs were detected for damage score (chromosome 6), nymphal survival (chromosome 12), and days to wilt (three QTLs on chromosome 4). We suggest involvement of four WBPH resistance genes in Sinna Sivappu, designated as wbph9(t), wbph10(t), wbph11(t), and Wbph12(t). One of the recessive genes could be allelic to any of the recessive genes reported in cluster C on chromosome 6 which might confer resistance to both BPH and WBPH.     

Genetic effects and genotype × environment interactions for cooking quality traits in Indica-japonica crosses of rice (Oryza sativa L.)

Indica-japonica hybridization is an important approach for developing superior performing hybrids in rice (Oryza sativa L.). In view of the scanty information available on cooking quality characters in indica-japonica crosses, an investigation was undertaken to estimate genetic and genotype × environment variance and covariance components of amylose content, gel consistency and alkali digestion value, and to determine the relative importance of direct genetic effects, maternal genetic effects and cytoplasmic effects in the genetic variations of the three quality characters. Two indica photo-sensitive genic male sterile (PGMS) lines and four japonica varieties were used as parents to make crosses. Genetic model with genotype × environment interactions for triploid endosperm was used for genetic studies of the three cooking quality characters. Variance component analysis revealed that genetic variations of the three characters were mainly attributable to direct additive and maternal additive effects, and the three traits had significant direct and maternal heritabilities. Genotype × environment interactions were mainly dominance × environment (including direct dominance × environment and maternal dominance × environment) and cytoplasm × environment interactions. Environment factors could only affect the expression extent of dominant genes, without changing their directions. Predicted values of genetic effects indicated that the parental lines, ‘VI-70’ and ‘H9304-1’, appeared to be best for amylose content, ‘T 1950’ and ‘Suxuan’ appeared to be best for gel consistency and alkali digestion value. This revised version was published online in August 2006 with corrections to the Cover Date.     

Applications of polysaccharides (β-glucan) for physiological and biochemical parameters for evaluation rice tolerance under salinity stress at seedling stage

Salt stress is considered to be the most important abiotic stress and is the main problem in the interruption of the metabolic processes of plants, thereby limiting crop production. The present study was carried out to examine the effects of exogenously applied mushroom polysaccharides (β-glucan) on the growth of two rice varieties of Oryza sativa L. (MRQ74 and MR269) seedlings grown in vitro in 200 Mm sodium chloride (NaCl). Growth characteristics, including shoot and root height, and fresh and dry weight of salt-stressed rice seedlings were inhibited by sodium chloride treatment, the degree of which depends on the rice variety. The negative effects of salinity stress resulted in an imbalance of N, K⁺ Na⁺ and Na/K ratios and biochemical analysis activities a degradation of chlorophyll content in the plants. However, treatment with exogenously applied polysaccharides (β-glucan) ameliorated the stress generated by NaCl and improved the parameters mentioned above. The significance of the changes in growth and metabolism to salt stress tolerance in rice seedlings are discussed in the paper.     

Mineral nitrogen dynamics in irrigated rice–wheat system under different irrigation and establishment methods and residue levels in arid drylands of Central Asia

Increasing water shortage and low water productivity in the irrigated drylands of Central Asia are compelling farmers to develop and adopt resource conservation technologies. Nitrogen (N) is the key nutrient for crop production in rice–wheat cropping systems in this region. Nitrogen dynamics of dry seeded rice-(aerobic, anaerobic) planted in rotation with wheat (well drained, aerobic) can differ greatly from those of conventional rice cultivation. Soil mineral N dynamics in flood irrigated rice has extensively been studied and understood, however, the impact of establishment method and residue levels on this dynamics remains unknown. Experiments on resource conservation technologies were conducted between 2008 and 2009 to assess the impact of two establishment methods (beds and flats) in combination with three (R0, R50 and R100) residue levels and two irrigation modes (alternate wet and dry (AWD) irrigation (all zero till), and a continuously flooded conventional tillage (dry tillage)) with water seeded rice (WSR) on the mineral N dynamics under dry seeded rice (DSR)-surface seeded wheat systems. N balance from the top 80 cm soil layers indicated that 32–70% (122–236 kg ha⁻¹) mineral N was unaccounted (lost) during rice cropping. The amount of unaccounted mineral N was affected by the irrigation method. Residue retention increased (p < 0.001) the unaccounted mineral N content by 38%. With AWD irrigation, the N loss was not different among dry seeded rice in flat (DSRF), dry seeded rice in bed (DSRB), and conventional tillage WSR. Under different irrigation, establishment methods and residue levels, unaccounted mineral N was mainly affected by plant N uptake and soil mineral N content. Major amounts (43–58%) of unaccounted mineral N from DSR field occurred between seeding and panicle initiation (PI). During the entire rice and wheat growing seasons, NH₄N consistently remained at very high levels, while, NO₃N remained at very low levels in all treatments. In rice, the irrigation method affected NH₄N content. Effect of residue retention and establishment methods were not significant on NH₄N and NO₃N dynamics in both crops and years. Further evidence of the continuously fluctuating water filled pore spaces (WFPS) of 64% and the microbial aerobic activity of 93% at the top 10 cm soil surface during rice growing season indicates soil in the DSR treatments was under frequent aerobic–anaerobic transformation, a conditions very conducive for higher amounts of N loss. In DSR treatments, the losses appeared to be caused by a combination of denitrification, leaching and N immobilization. When intending to use a DSR management strategies need to be developed for appropriate N management, irrigation scheduling, and residue use to increase mineral N availability and uptake before this practices can be recommended.     

Assessing the importance of genotype × environment interaction for root traits in rice using a mapping population III: QTL analysis by mixed models

The phenotypic analysis of field experiments includes information about the experimental design, the randomization structure and a number of putative dependencies of environment and design factors on the trait investigated. In QTL studies, the genetic correlation across environments, which arises when the same set of lines is tested in multiple environments, plays an important role. This paper investigates the effect of model choice on the set and magnitude of detected root QTL in rice. Published studies on QTLs for root traits indicate that different results are obtained if varying genetic populations are used and also if different environmental conditions are included. An experiment was conducted with 168 RILs of the Bala × Azucena mapping population plus parents as checks under four environmental conditions (low light, low nitrogen, drought and a control environment). We propose a model that incorporates all relevant experimental information into a composite interval mapping approach based on a mixed model, which especially considers the correlation of genotypes in different environments. An extensive sequential model selection procedure was applied based on the phenotypic model, using the AIC to determine an appropriate random structure and Type 3 Wald F-tests for selection of fixed effects. In a first step we checked whether any of the fixed effects and random (nested) design effects could be dropped. Secondly, an appropriate covariance structure was chosen for genotype × environment interaction. In a third step Box-Cox transformations were applied based on residual analysis. We compared profiles of composite interval mapping scans with and without the inclusion of genotype × environment interaction and the experimental design information. Some distinct differences in profiles indicate that insufficient modeling of the non-QTL part can lead to an overly optimistic interpretation of QTL main effects in interval mapping. It is concluded that mixed model QTL mapping offers a reasonable way to separate environmental and genetic influences in the evaluation of quantitative genes and especially enables a more realistic assessment of QTL and QTL × environment effects than standard approaches by including all relevant effects.     

Mapping quantitative trait loci (QTL) for grain size in rice using a RIL population from Basmati × indica cross showing high segregation distortion

Grain size is one of the three productivity related traits in rice and hence a major target for genetic improvement. Since understanding genetic variation in grain size between Basmati and indica genotypes is important for rice improvement, a recombinant inbred population was developed from a traditional aromatic cultivar ‘Basmati 370’ and a non-aromatic indica genotype ‘IRBB60’. This population was phenotyped in two locations for grain length (GL), grain breadth (GB), GL/GB ratio (LBR) and grain weight (GW). Though the RIL population reported in the current study exhibited segregation distortion (SD) for 54 % of the markers, they were utilized in analysis using an appropriate statistical package, PROC QTL in the SAS environment. Interval mapping revealed a total of 15 QTLs for GL, seven for GB, 15 for LBR and two for GW. Among them 13 were not reported earlier and thus novel. For a known major QTL identified in the study, GW8 for GB, a PCR based functional marker was designed and validated. This is the first report wherein a very high proportion of markers (>50 %) exhibiting SD have been successfully used for QTL mapping.