A unique genetic variation with respect to blast (Pyricularia oryzae Cavara) resistance in rice (Oryza sativa L.) varieties in Vietnam.

A unique genetic variation with respect to blast resistance was clarified in 201 rice accessions from Vietnam. These accessions were classified into three clusters-A, B1, and B2-based on their reactions to 26 standard differential blast isolates selected in Vietnam. Cluster A was the dominant cultivar group in Vietnam and the most susceptible of the three clusters. Cluster B1 was the smallest group and the most resistant. Cluster B2 was the second-most dominant group and of intermediate resistance between clusters A and B1. The percentages of accessions comprising each cluster varied by region and area. Accessions in cluster A were distributed widely throughout Vietnam and had the highest frequencies in both the Central and North regions. Accessions in cluster B2 were found with highest frequencies in the mountainous and intermediate areas of the North region. Accessions in cluster B1 were found with highest frequencies in the Central region and Red River Delta area (North region). These results suggest that rice accessions in Vietnam were basically susceptible (cluster A) or of intermediate resistance (cluster B2), and that high-resistance cultivars were mainly distributed in the low altitude areas, such as the Red River Delta area and Central region.

Contribution of the grain size QTL GS3 to yield properties and physiological nitrogen-use efficiency in the large-grain rice cultivar 'Akita 63'.

The development of crop varieties with high nitrogen-use efficiency (NUE) is thought to be important in achieving sustainable cereal crop production. The high yield large-grain rice cultivar Oryza sativa L. 'Akita 63' (temperate japonica) has high physiological NUE (PNUE) for grain yield (GY). Our previous study revealed that a large-grain allele of GS3 is present in 'Akita 63'. Here, we verified the influence of GS3 on the yield properties and PNUE for GY in 'Akita 63'. The frequency distribution of brown rice length in F2 crosses of 'Iwate 75' and 'Akita 63' showed a continuous distribution that could be explained by GS3. A near-isogenic line was developed to substitute the GS3 segment of 'Koshihikari', which harbours a normal-sized grain allele, in the genetic background of 'Akita 63' and the line was designated as Akita63NILGS3-Koshihikari. Compared with Akita63NILGS3-Koshihikari, 'Akita 63' exhibited a significantly increased grain length, single brown grain weight and GY, although no significant differences were observed in the nitrogen content and above-ground biomass per unit of cultivated area. These results indicate that the GS3 large-grain allele is a contributing factor to high PNUE for GY in 'Akita 63'. These findings will facilitate the development of nitrogen-efficient rice varieties.

The gs3 allele from a large-grain rice cultivar, Akita 63, increases yield and improves nitrogen-use efficiency.

The Green Revolution allowed a large amount of nitrogen (N) fertilization to increase crop yield but has led to severe environmental pollution. Therefore, increasing the crop grain yield must be achieved without such considerable input of N fertilization. A large-grain japonica rice cultivar, Akita 63, significantly increased grain yield and improved N-use efficiency (NUE) for yield per amount of N absorbed by plants. This study found that the nonsense mutated GS3 gene, the gs3 allele of Akita 63, has a superior yield production with enlarged grain size. The gs3 allele increased the yield with improvements in harvest index and NUE for yields per plant N content by analyzing the near-isogenic line of rice plants with a large grain (LG-Notohikari), which was developed by introducing the gs3 allele of Akita 63 into normal-grain japonica cultivar, Notohikari. Thus, the gs3 allele would be promising for further yield increase without additional large input of N fertilization in non-gs3-allele rice varieties.

Rice amino acid transporter-like 6 (OsATL6) is involved in amino acid homeostasis by modulating the vacuolar storage of glutamine in roots.

Glutamine is a product of ammonium (NH4+ ) assimilation catalyzed by glutamine synthetase (GS) and glutamate synthase (GOGAT). The growth of NH4+ -preferring paddy rice (Oryza sativa L.) depends on root NH4+ assimilation and the subsequent root-to-shoot allocation of glutamine; however, little is known about the mechanism of glutamine storage in roots. Here, using transcriptome and reverse genetics analyses, we show that the rice amino acid transporter-like 6 (OsATL6) protein exports glutamine to the root vacuoles under NH4+ -replete conditions. OsATL6 was expressed, along with OsGS1;2 and OsNADH-GOGAT1, in wild-type (WT) roots fed with sufficient NH4 Cl, and was induced by glutamine treatment. We generated two independent Tos17 retrotransposon insertion mutants showing reduced OsATL6 expression to determine the function of OsATL6. Compared with segregants lacking the Tos17 insertion, the OsATL6 knock-down mutant seedlings exhibited lower root glutamine content but higher glutamine concentration in the xylem sap and greater shoot growth under NH4+ -replete conditions. The transient expression of monomeric red fluorescent protein-fused OsATL6 in onion epidermal cells confirmed the tonoplast localization of OsATL6. When OsATL6 was expressed in Xenopus laevis oocytes, glutamine efflux from the cell into the acidic bath solution increased. Under sufficient NH4+ supply, OsATL6 transiently accumulated in sclerenchyma and pericycle cells, which are located adjacent to the Casparian strip, thus obstructing the apoplastic solute path, and in vascular parenchyma cells of WT roots before the peak accumulation of GS1;2 and NADH-GOGAT1 occurred. These findings suggest that OsATL6 temporarily stores excess glutamine, produced by NH4+ assimilation, in root vacuoles before it can be translocated to the shoot.

Two Novel QTLs for the Harvest Index that Contribute to High-Yield Production in Rice (Oryza sativa L.).

BACKGROUND: The harvest index (HI) is a measure of the biological success of forming harvestable products. However, our understanding of the genetic basis of HI in rice (Oryza sativa L.) is limited, because it is a complex trait consisting of various yield-related traits and physiological attributes. YTH183 is a high-yielding line with large panicles and high HI derived from a cross between the Indica Group variety IR 64 and the NPT line IR 69093-41-2-3-2 (YP5). RESULTS: Here, we detected two novel QTLs for HI, designated qHI5.1 on chromosome 5 and qHI8.1 on chromosome 8, by using 155 recombinant inbred lines (RILs) derived from the cross between IR 64 and YTH183. The YTH183 allele at qHI5.1 contributed to a wide grain, resulting in heavy grain weight and panicle weight, and was consistently effective under the different environmental conditions of subtropical (Ishigaki) and temperate (Tsukuba) regions. Genetic polymorphism revealed that qHI5.1 was identical to GSE5/GW5, which is known to control the grain weight. On the other hand, although qHI8.1 functioned additively with qHI5.1 for higher HI, it did not show any significant effect on grain or panicle weight. In addition, its effects on HI were shown only in the first seasons at Ishigaki but not at Tsukuba or in the second season at Ishigaki. CONCLUSION: Our results indicate that qHI5.1 controls the grain size, regardless of whether environmental conditions are of subtropical or temperate regions, while qHI8.1 might be involved in controlling the physiological processes of source ability or the translocation of photosynthesis products from vegetative organs to grains depending on environmental conditions during the maturing stage. These QTLs will be useful genetic resources for future breeding programs to break through the ceiling of maximum yield in Indica Group varieties.

Pathogenicity of Isolates of the Rice Blast Pathogen (Pyricularia oryzae) From Indonesia.

A total of 201 isolates of Pyricularia oryzae (the causal agent of rice blast) were collected from three rice ecosystems (upland, lowland, and swampy) in five regions of Indonesia (West Java, Lampung, South Sumatra, Kalimantan, and Bali). Their pathogenicities were characterized based on the patterns of reaction of 25 differential varieties (DVs) and the susceptible control Lijiangxintuanheigu (LTH), which was susceptible to all blast isolates. A high proportion of isolates (>80.0%) were virulent to DVs for resistance genes Pib, Pit, Pia, Pik-s, and Pi12(t), and a low proportion of isolates (<12.9%) were virulent to DVs for Pik-m, Pi1, Pik-h, Pik, Pik-p, and Pi7(t). Virulence to the other DVs for Pish, Pii, Pi3, Pi5(t), Pi9(t), Piz, Piz-5, Piz-t, Pita-2 (two lines), Pita (two lines), Pi19(t), and Pi20(t) showed intermediate frequencies from 20.0 to 80.0%. These isolates were classified into three cluster groups, Ia, Ib, and II, and the frequencies of cluster groups varied between the three ecosystems and the five regions. The frequencies of cluster groups varied between ecosystems and regions, and races varied according to the ecosystems. A total of 27 standard differential blast isolates (SDBIs) were selected from the 201 isolates collected. The set of 25 DVs and these 27 SDBIs will be used as a new differential system for analysis of the pathogenicity of blast isolates and analysis of resistance genes in rice cultivars, which will contribute to building a durable protection system against blast disease in Indonesia.

High yielding ability of a large-grain rice cultivar, Akita 63.

To increase the yield potential while limiting the environmental impact of N management practices is an important issue in rice cultivation. The large-grain rice cultivar Akita 63 showed higher N-use efficiency for grain production. To elucidate this, we analyzed yield characteristics of Akita 63 in comparison with those of a maternal cultivar, Oochikara with a large grain, a paternal cultivar, Akita 39 with a normal grain, and a Japanese leading cultivar, Akitakomachi. The yields of Akita 63 were 20% higher than those of Oochikara and Akita 39, and 50% higher than those of Akitakomachi for the same N application. Akita 63 showed superior N uptake capacity. Whereas a trade-off between single grain weight and grain number was found for Oochikara, Akita 63 did not show such a relationship. The success in Akita 63 breeding was due to overcoming such a trade-off. Akita 63 had the large-grain alleles of GS3 and qSW5. Thus, an enlargement of grain size can have a great impact on an increase in yield with improved N-use efficiency. However, an enlargement of sink capacity led to source limitation. Thus, both sink and source improvements are essential for a further increase in the yield of today's high-yielding cultivars.

Transgenic rice overproducing Rubisco exhibits increased yields with improved nitrogen-use efficiency in an experimental paddy field.

The green revolution's breeding of semi-dwarf rice cultivars in the 1960s improved crop yields, with large increases in the use of nitrogen (N) fertilizer. However, excess N application has caused serious environmental problems, including acid rain and the eutrophication of rivers and oceans. To use N to improve crop yields, while minimizing the associated environmental costs, there is a need to produce crops with higher N-use efficiency and higher yield components. Here we show that transgenic rice overproducing ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco)-the key enzyme of photosynthesis-exhibits increased yields with improved N-use efficiency for increasing biomass production when receiving sufficient N fertilization in an experimental paddy field. This field experiment demonstrates an improvement in photosynthesis linked to yield increase due to a higher N-use efficiency in a major crop.

Genetic variation and QTLs related to root development in upland New Rice for Africa (NERICA) varieties.

To understand variation in the root development traits (total root length (TRL), maximum root length (MRL) and root number) of 18 New Rice for Africa (NERICA) varieties, seedlings were hydroponically grown under deficient and sufficient concentrations of two forms of nitrogen, NH4 + and NO3 -. The donor African rice variety, 'CG14' (Oryza glaberrima Steud.), showed greater TRL and MRL than three background Asian rice varieties (Oryza sativa L.). Wide distribution was observed in all traits of the 18 NERICAs. The 18 NERICAs and parental varieties were classified into three cluster groups by cluster analysis. Cluster Ia included only 'CG14'. Comparative analysis characterized cluster Ib (including 'NERICA7') as an active root elongation group, and cluster II (including 'WAB56-104') as an active primordia development group. QTL analysis of F2 plants developed from a cross between 'WAB56-104' and 'NERICA7' detected two putative quantitative trait loci (QTLs) for root elongation on chromosome 1. Of these, a major QTL, designated as qRL1.4-NERICA7, was an NH4 +-responsive QTL, which was narrowed down to a 0.7-Mbp region through progeny testing using F7 lines. qRL1.4-NERICA7 should help us understand genetic control in NERICAs, and improve root elongation in rice breeding programs.

Genetic variation of blast (Pyricularia oryzae Cavara) resistance in rice (Oryza sativa L.) accessions widely used in Kenya.

A total of 47 rice accessions collected from Kenya were investigated the genetic variations and classified into two cluster groups, A and B, by polymorphism data of 65 simple sequence repeat (SSR) markers. Clusters A and B corresponded to Japonica and Indica Groups, respectively. The number of Japonica Group accessions was limited in comparison with those of the Indica Group. Based on their patterns of reaction to standard differential blast isolates (SDBIs), these accessions and 57 control cultivars including differential varieties and several accessions harboring partial resistance genes were classified again into three cluster groups: Ia (high resistance), Ib (intermediate resistance) and II (susceptible). The rice accessions from Kenya were classified only into groups Ia and Ib. The accessions from Kenya were finally classified into three categories, A-Ia, B-Ia and B-Ib, based on the two classifications of polymorphism of SSR markers and resistance. The Indica Group accessions had wider genetic variation for blast resistance than did the Japonica Group accessions. The three leading cultivars (Basmati 217, Basmati 370 and ITA 310) categorized into Cluster group Ia were susceptible to some SDBIs from Kenya. The genetic variation for blast resistance in Kenya was demonstrated as the first report using SDBIs.

Lack of ACTPK1, an STY kinase, enhances ammonium uptake and use, and promotes growth of rice seedlings under sufficient external ammonium.

Ammonium influx into plant roots via the high-affinity transport system (HATS) is down-modulated under elevated external ammonium, preventing ammonium toxicity. In ammonium-fed Arabidopsis, ammonium transporter 1 (AMT1) trimers responsible for HATS activity are allosterically inactivated in a dose-dependent manner via phosphorylation of the conserved threonine at the carboxyl-tail by the calcineurin B-like protein 1-calcineurin B-like protein-interacting protein kinase 23 complex and other yet unidentified protein kinases. Using transcriptome and reverse genetics in ammonium-preferring rice, we revealed the role of the serine/threonine/tyrosine protein kinase gene OsACTPK1 in down-modulation of HATS under sufficient ammonium. In wild-type roots, ACTPK1 mRNA and protein accumulated dose-dependently under sufficient ammonium. To determine the function of ACTPK1, two independent mutants lacking ACTPK1 were produced by retrotransposon Tos17 insertion. Compared with segregants lacking insertions, the two mutants showed decreased root growth and increased shoot growth under 1 mm ammonium due to enhanced ammonium acquisition, via aberrantly high HATS activity, and use. Furthermore, introduction of OsACTPK1 cDNA fused to the synthetic green fluorescence protein under its own promoter complemented growth and the HATS influx, and suggested plasma membrane localization. Root cellular expression of OsACTPK1 also overlapped with that of ammonium-induced OsAMT1;1 and OsAMT1;2. Meanwhile, threonine-phosphorylated AMT1 levels were substantially decreased in roots of ACTPK1-deficient mutants grown under sufficient ammonium. Bimolecular fluorescence complementation assay further confirmed interaction between ACTPK1 and AMT1;2 at the cell plasma membrane. Overall, these findings suggest that ACTPK1 directly phosphorylates and inactivates AMT1;2 in rice seedling roots under sufficient ammonium.

Genetic variation of root angle distribution in rice (Oryza sativa L.) seedlings.

We developed a new method of using seedling trays to evaluate root angle distribution in rice (Oryza sativa. L), and found a wide genetic variation among cultivars. The seedling tray method can be used to evaluate in detail the growth angles of rice crown roots at the seedling stage by allocating nine scores (10° to 90°). Unlike basket methods, it can handle large plant populations over a short growth period (only 14 days). By using the method, we characterized the root angle distributions of 97 accessions into two cluster groups: A and B. The numbers of accessions in group A were limited, and these were categorized as shallow rooting types including soil-surface root. Group B included from shallow to deep rooting types; both included Indica and Japonica Group cultivars, lowland and upland cultivars, and landraces and improved types. No relationship between variation in root vertical angle and total root number was found. The variation in root angle distribution was not related to differentiation between the Japonica and Indica Groups, among ecosystems used for rice cultivation, or among degrees of genetic improvement. The new evaluation method and associated information on genetic variation of rice accessions will be useful in root architecture breeding of rice.

Fine mapping of a quantitative trait locus for spikelet number per panicle in a new plant type rice and evaluation of a near-isogenic line for grain productivity.

Total spikelet number per panicle (TSN) is one of the determinants of grain productivity in rice (Oryza sativa L.). In this study, we attempted to detect quantitative trait loci (QTLs) for TSN in the introgression lines with high TSN, derived from the cross of Indica Group variety IR 64 with new plant type lines. Two QTLs were detected on the long arm of chromosome 12: qTSN12.1 in the BC4F2 population of YTH63/IR 64 and qTSN12.2 in the BC4F3 population of YTH83/IR 64. TSN of the main tiller was significantly higher in near-isogenic lines (NILs) for qTSN12.1 (IR 64-NIL1; 188.6) and for qTSN12.2 (IR 64-NIL12; 199.4) than in IR 64 (141.2), owing to a significant increase in both primary and secondary branch numbers. These results suggest the critical function of these QTLs in the promotion of rachis branching at the panicle formation stage. Fine mapping of qTSN12.2 revealed six candidate genes in a 92-kb region of the Nipponbare reference genome sequence between flanking markers RM28746 and RM28753. Detailed phenotyping of agronomic traits of IR 64-NIL12 carrying qTSN12.2 showed drastic changes in plant architecture: this line had lower panicle number, longer culm, and longer and wider leaves compared with IR 64. Percentage of fertility and 1000-grain weight tended to be greater, and grain yield per square meter was also greater in IR 64-NIL12 than in IR 64. The newly identified QTLs will be useful for genetic improvement of the yield potential of Indica Group varieties. The markers tightly linked to qTSN12.2 are available for marker-assisted breeding.

Genetic variation of rice (Oryza sativa L.) germplasm in Myanmar based on genomic compositions of DNA markers.

The genetic diversity of 175 rice accessions from Myanmar, including landraces and improved types from upland and lowland ecosystems in five different areas-Western (hilly), Northern (mountainous), North and South-eastern (plateau), and Southern (plain)-was evaluated on the basis of polymorphism data for 65 DNA markers and phenol reactions. On the basis of the DNA polymorphism data, high genetic diversity was confirmed to conserve in the accessions from each ecosystem and area. And the accessions were classified into two cluster groups I and II, which corresponded to Indica Group and Japonica Group, respectively. Cluster group I accessions were distributed mainly in upland ecosystems; group II were distributed in lowland in the Southern area, and the distributions of dominant groups differed among areas. Rice germplasm in Myanmar has maintained high genetic diversity among ecosystems and areas. This information will be used for advanced studies in germplasm and rice breeding in Myanmar.

Identification of a low tiller gene from a new plant type cultivar in rice (Oryza sativa L.).

We characterized a rice introgression line, YTH34, harboring a chromosome segment from a New Plant Type (NPT) cultivar, IR65600-87-2-2-3, in the genetic background of an Indica Group elite rice cultivar, IR 64, under upland and irrigated lowland conditions in Japan. The number of panicles (as an indicator of tiller number) and number of spikelets per panicle of YTH34 were lower than those of IR 64 under irrigated lowland conditions, but both of those as well as culm length, panicle length, seed fertility, panicle weight, whole plant weight, and harvest index were dramatically reduced under upland conditions. And the low tiller of YTH34 was confirmed to start after the maximum tiller stage. In particular, the decrease of panicle number was remarkable in upland, so we tried to identify the chromosome location of the relevant gene. Through segregation and linkage analyses using F3 family lines derived from a cross between IR 64 and YTH34, and SSR markers, we found that low tiller number was controlled by a single recessive gene, ltn2, and mapped with the distance of 2.1 cM from SSR marker RM21950, in an introgressed segment on chromosome 7. YTH34 harboring ltn2 and the genetic information for DNA markers linked will be useful for genetic modification of plant architectures of Indica Group rice cultivar.

Enhancement of porosity and aerenchyma formation in nitrogen-deficient rice roots.

Root aerenchyma provides oxygen from plant shoots to roots. In upland crops, aerenchyma formation is induced mainly by oxygen or nutrient deficiency. Unlike upland crops, rice forms root aerenchyma constitutively and also inductively in response to oxygen deficiency. However, the effects of nitrogen deficiency on aerenchyma formation in rice remain unknown although nitrogen deficiency is common in most of the world's soils. We aimed to clarify the spatiotemporal patterns of aerenchyma formation induced in rice roots by nitrogen deficiency upon establishment of reliable growth conditions. Rice was grown hydroponically to evaluate porosity and aerenchyma formation induced by nitrogen and oxygen deficiency. Reliable growth conditions for nitrogen and oxygen deficiency were successfully established, because seedling root elongation was significantly promoted by nitrogen deficiency and inhibited by oxygen deficiency. Porosity was higher in whole roots grown under nitrogen and oxygen deficiency than in the controls. Root aerenchyma production was induced extensively by nitrogen deficiency but partially by oxygen deficiency. Thus the physiological roles of aerenchyma induced by nitrogen deficiency likely differ from those under oxygen deficiency. It indicates a possibility that inducible aerenchyma formation in nitrogen deficiency might promote adaptation to this deficiency by reducing respiration and remobilizing nitrogen, or both.

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.

Changes in nitrogen assimilation, metabolism, and growth in transgenic rice plants expressing a fungal NADP(H)-dependent glutamate dehydrogenase (gdhA).

In plants, glutamine synthetase (GS) is the enzyme that is mainly responsible for the assimilation of ammonium. Conversely, in microorganisms such as bacteria and Ascomycota, NADP(H)-dependent glutamate dehydrogenase (GDH) and GS both have important roles in ammonium assimilation. Here, we report the changes in nitrogen assimilation, metabolism, growth, and grain yield of rice plants caused by an ectopic expression of NADP(H)-GDH (gdhA) from the fungus Aspergillus niger in the cytoplasm. An investigation of the kinetic properties of purified recombinant protein showed that the fungal gdhA had 5.4-10.2 times higher V(max) value and 15.9-43.1 times higher K(m) value for NH(4)(+), compared with corresponding values for rice cytosolic GS as reported in the literature. These results suggested that the introduction of fungal GDH into rice could modify its ammonium assimilation pathway. We therefore expressed gdhA in the cytoplasm of rice plants. NADP(H)-GDH activities in the gdhA-transgenic lines were markedly higher than those in a control line. Tracer experiments by feeding with (15)NH(4)(+) showed that the introduced gdhA, together with the endogenous GS, directly assimilated NH(4)(+) absorbed from the roots. Furthermore, in comparison with the control line, the transgenic lines showed an increase in dry weight and nitrogen content when sufficient nitrogen was present, but did not do so under low-nitrogen conditions. Under field condition, the transgenic line examined showed a significant increase in grain yield in comparison with the control line. These results suggest that the introduction of fungal gdhA into rice plants could lead to better growth and higher grain yield by enhancing the assimilation of ammonium.

Fine-mapping of qRL6.1, a major QTL for root length of rice seedlings grown under a wide range of NH4(+) concentrations in hydroponic conditions.

Root system development is an important target for improving yield in cereal crops. Active root systems that can take up nutrients more efficiently are essential for enhancing grain yield. In this study, we attempted to identify quantitative trait loci (QTL) involved in root system development by measuring root length of rice seedlings grown in hydroponic culture. Reliable growth conditions for estimating the root length were first established to renew nutrient solutions daily and supply NH4(+) as a single nitrogen source. Thirty-eight chromosome segment substitution lines derived from a cross between 'Koshihikari', a japonica variety, and 'Kasalath', an indica variety, were used to detect QTL for seminal root length of seedlings grown in 5 or 500 microM NH4(+). Eight chromosomal regions were found to be involved in root elongation. Among them, the most effective QTL was detected on a 'Kasalath' segment of SL-218, which was localized to the long-arm of chromosome 6. The 'Kasalath' allele at this QTL, qRL6.1, greatly promoted root elongation under all NH4(+) concentrations tested. The genetic effect of this QTL was confirmed by analysis of the near-isogenic line (NIL) qRL6.1. The seminal root length of the NIL was 13.5-21.1% longer than that of 'Koshihikari' under different NH4(+) concentrations. Toward our goal of applying qRL6.1 in a molecular breeding program to enhance rice yield, a candidate genomic region of qRL6.1 was delimited within a 337 kb region in the 'Nipponbare' genome by means of progeny testing of F2 plants/F3 lines derived from a cross between SL-218 and 'Koshihikari'.

Reverse genetics approach to characterize a function of NADH-glutamate synthase1 in rice plants.

Rice plants grown in anaerobic paddy soil prefer to use ammonium ion as an inorganic nitrogen source for their growth. The ammonium ions are assimilated by the coupled reaction of glutamine synthetase (GS) and glutamate synthase (GOGAT). In rice, there is a small gene family for GOGAT: there are two NADH-dependent types and one ferredoxin (Fd)-dependent type. Fd-GOGAT is important in the re-assimilation of photorespiratorily generated ammonium ions in chloroplasts. Although cell-type and age-dependent expression of two NADH-GOGAT genes has been well characterized, metabolic function of individual gene product is not fully understood. Reverse genetics approach is a direct way to characterize functions of isoenzymes. We have isolated a knockout rice mutant lacking NADH-dependent glutamate synthase1 (NADH-GOGAT1) and our studies show that this isoenzyme is important for primary ammonium assimilation in roots at the seedling stage. NADH-GOGAT1 is also important in the development of active tiller number, when the mutant was grown in paddy field until the harvest. Expression of NADH-GOGAT2 and Fd-GOGAT in the mutant was identical with that in wild-type, suggesting that these GOGATs are not able to compensate for NADH-GOGAT1 function.