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Rice blast poses a significant threat to food security in Bangladesh, particularly in irrigated lowland (boro rice), which constitutes over 50% of the country's total rice production. While using resistant varieties is an effective method to control rice blast, developing durable resistance is challenged by the pathogen's high variability. To address this, the current study examined the distribution of rice blast reaction types in the major rice‐growing ecosystem of Bangladesh, the irrigated lowland. Two surveys were conducted and 80 blast isolates were evaluated for pathogenicity against differential varieties (DVs). The results revealed that the high frequency of virulence (over 80%) for blast resistant genes, such as Pib, Pit, Pia, Pik‐s, Pi12(t), Pi19(t) and Pi20(t), whereas Pish, Pik‐m, Pi1, Pik‐h, Pi9 and Pita‐2 genes had the least virulence frequency. These low virulence frequency genes demonstrated promising potential for the development of blast resistant varieties in Bangladesh. The isolates were further categorized into two distinct cluster groups based on their reaction patterns to DVs, with theones coming from the eastern region predominantly in Cluster I, while the ones from the northern regions belonged mainly to Cluster II. Additionally, the isolates were classified based on five reaction types, namely U, i, k, z and ta, following a new designation system. Among these, U63, i0, k100, z06 and ta403 were the most dominant reaction types. Although these reaction types were prevalent across Bangladesh, their distribution frequency varied in different major rice‐growing regions. Furthermore, the study observed that early maturing varieties in the irrigated lowland ecosystem were highly susceptible to blast. The findings of this study will be crucial for developing a comprehensive and long‐lasting blast protection system in Bangladesh, focusing on broad‐spectrum resistance strategies. [ABSTRACT FROM AUTHOR]

Twenty‐one near‐isogenic lines (NILs) for 18 resistance genes—Pia, Pii, Pi3, Pi5(t), Pik‐s (two lines from two donors), Pik‐m, Pi1, Pik‐h, Pik, Pik‐p, Pi7(t), Pi9(t), Piz, Piz‐5, Piz‐t, Pita‐2, Pita (three donors) and Pi20(t)—to blast disease were developed through introduction into the genetic background of a semi‐dwarf susceptible rice line, US‐2, by recurrent backcross breeding. US‐2 is derived from a cross between an Indonesian Tropical Japonica Group cultivar, 'Kencana', and an improved high‐yielding and semi‐dwarf Indica Group cultivar, 'Takanari', bred in Japan. The reactions of US‐2 NILs to standard differential blast isolates were clearly defined than previous differential varieties (DVs) such as monogenic lines. US‐2 and its NILs are adapted well to wide environmental conditions from temperate to subtropical regions. They will be useful and easier to handle and manage as the first DV set with genetic background of Indica Group rice for pathology studies and as gene sources for rice breeding programme. [ABSTRACT FROM AUTHOR]

The total spikelet number (TSN) per panicle is an essential factor involved in grain yield among yield components in rice. IR64-NIL12 carrying qTSN12.2-YP4, which was detected on chromosome 12 for TSN per panicle, has been developed in a previous study. It is important to characterize the environment of gene function to increase yields. Thus, we attempted to evaluate IR64-NIL12 grown under no, low, and high fertilizer conditions in 2019 and 2020. Grain yields of IR64-NIL12 were significantly higher than that of IR64 in all conditions. The average grain yield of each condition for IR64 and IR64-NIL12 ranged from 387 to 616 g m−2. Therefore, qTSN12.2-YP4 would have an increasing effect on grain yield within this range. The ratio of fertility improved in IR64-NIL12. This rice line exhibited modified traits, such as tiller number and plant height (during the vegetative stage), as well as panicle number (at maturity), which may confer an advantage in terms of light-intercepting characteristics. We also focused on the number of unproductive tillers and dry weight per tiller at the heading stage to investigate the mechanism of the increasing effect of qTSN12.2-YP4 on TSN per panicle. There is a significant difference in dry weight per tiller at heading between IR64 and IR64-NIL12, but not in the percentage of unproductive tillers. Therefore, this result indicated that qTSN12.2-YP4 contributes to increasing dry weight per tiller until the heading stage and, consequently, TSN per panicle. [ABSTRACT FROM AUTHOR]

Roots are important plant organs that absorb water and nutrients. Root length responses are influenced by the plants' sources of nitrogen (N), such as ammonium (NH4+) and nitrate (NO3−) ions and their concentrations. Here, to determine the genetic resources with the potential to improve the root system of rice (Oryza sativa L.), the root development traits of a core set of 334 introgression lines (ILs) were assessed in plants grown in hydroponic culture medium containing low (5 μM) or high (500 μM) concentrations of N in the form of NH4+ or NO3−. ILs were classified into three clusters. The mean value of maximum root length (MRL) in cluster I was significantly higher than that in the other two clusters under all conditions. Root number (RN) differed significantly between clusters IIa and IIb, with the mean RN being higher in cluster IIa. In addition, the order of the mean total root length of the clusters was cluster I > IIa > IIb. Therefore, ILs in cluster I are considered genetic resources for improving root development traits under all tested N conditions. Among the ILs, YTH187 – which is derived from YP5 as a donor – had a longer MRL under all conditions. Quantitative trait loci (QTL) analyses, performed using recombinant inbred lines derived from a cross between IR 64 and YTH187, revealed that qRL5.3-YP5 and qRL6.5-YP5 were detected under all N conditions. In contrast, qRL4.1-YP5 was detected only under low KNO3 concentrations, whereas qRL8.1-YP5 was detected under high concentrations of NH4Cl and KNO3. YP5 alleles at these QTLs increased MRL. QTLs for root length in rice grown in hydroponic culture have not previously been detected in the vicinity of qRL8.1-YP5; thus, this may be a novel QTL that controls root length in rice. Moreover, qRL8.1-YP5 and qRL4.1-YP5 could be useful QTLs to determine the mechanism of root elongation under KNO3 conditions because such QTLs have not yet been detected under these conditions in rice. In future studies, further fine-mapping and characterization of qRL8.1-YP5 could reveal the mechanism of root elongation under high KNO3 concentration conditions. [ABSTRACT FROM AUTHOR]

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. Highlight: The gs3 allele transfer from large‐grain japonica rice cultivar, Akita 63, into normal‐grain japonica rice cultivar, Notohikari, increases yield and improves nitrogen‐use efficiency. [ABSTRACT FROM AUTHOR]

Summary: 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 NH4Cl, 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. [ABSTRACT FROM AUTHOR]

Genetic variations in the root traits of rice remain unexplored in relation to varietal groups and diverse ecosystems. Therefore, we evaluated 257 Bangladeshi accessions, which included landraces and improved varieties belonging to four ecotypes (Aus, Aman, Boro and Jhum), to understand genetic variations in the total root length (TRL), maximum root length and root number under different concentrations of ammonium and nitrate nitrogen in hydroponic culture. There were large variations in all traits across all nitrogen levels. Active elongation of individual roots of the landrace type across all nitrogen conditions suggested a higher potential for the uptake of nutrients by extending roots distribution in any nitrogen environment, while the active development of primary root primordia in the improved type in the presence of nitrate suggested a higher potential for the uptake of nitrate from the soil surface by extending roots distribution around soil surface. Cluster analysis classified the examined accessions into two groups according to their TRL: cluster I with a longer TRL and cluster II with a shorter TRL across all nitrogen conditions. Each of these groups was further divided into two sub-clusters: sub-cluster Ia, in which the longer TRL resulted from active development of primary root primordia, sub-cluster Ib, in which the longer TRL resulted from active elongation of individual roots, sub-cluster IIa, in which the shorter TRL resulted from severe reduction of the elongation of individual roots, and sub-cluster IIb, in which the shorter TRL resulted from a moderate reduction in the elongation of individual roots. Further investigation revealed a difference in the composition of these four sub-clusters among the four ecotypes, indicating that Aman was the most diverse ecotype, followed by Aus. The root traits of these promising accessions could be exploited in the future to understand genetic and physiological mechanism(s) of adaptation to diverse ecosystems. [ABSTRACT FROM AUTHOR]

Wide variations of typhoon-induced spikelet sterility and days to heading (DH) were found among 317 introgression lines (INLs) originating from new-plant-type varieties with a genetic background of Indica Group rice variety IR 64. Sterility was induced by continuous dry winds from the typhoon. The most seriously affected were 194 INLs with DH ranging from 83 to 86 days. Positive correlations with the spikelet sterility score (SSS) were found for culm length (CL), panicle length (PL), and panicle weight (PW). Based on these traits and DH, the 194 INLs were classified into three groups: A1, A2, and B. The means of SSS and four traits (CL, PL, culm and leaf weight (CW), and panicle weight (PW)) were the lowest in group A1, and highest in group B. PN was significantly higher in group B than those in the others. Seven quantitative trait loci (QTL) for SSS were detected on chromosomes (chr.) 1, 2, 4, 7 (two), 8, and 11. Among them, the QTL of chr. 4 was located in the same regions as those of DH, CL, PL, CW, and panicle number (PN). Thus, the region on chr.4 might induce sterility in the INLs by modifying plant architecture, such as large panicles or high plant height with the minor effect of many tillers. The relationships among traits, and the QTLs will be useful information for genetic improvement of tolerance to typhoon damage in rice. [ABSTRACT FROM AUTHOR]

Nitrogen (N) is an important nutrient influencing the growth and yield in rice. Root plasticity is a key trait in the higher uptake of nutrient from the soil, especially in conditions where some major nutrients such as N is under optimal. In this study, a total of 168 BC1F4 mapping population from a cross between Malay 2 and US-2 and their parents were grown in hydroponics with deficient (5 µM) and sufficient (500 µM) N for 8 days to identify putative quantitative trait loci (QTLs) associated with root elongation. Eighty-three (83) markers were used in QTL detection using composite interval mapping. Results showed that US-2 had significantly greater shoot length and number of nodal roots than Malay 2 under N-deficient conditions. Around 19.6 and 26.8% of the population in N-deficient and N-sufficient conditions, respectively, had either longer or similar seminal root length compared with US-2. For the allele distribution, 43.1% of the population had homozygous allele for Malay 2, 20.9% had homozygous allele for US-2, and 8.4% had heterozygous allele for both parents. A total of eight putative QTLs associated with seminal root length (qSRL11.1 and qSRL2.1); number of nodal roots (qNNR6.1, qNNR11.1, and qNNR11.2); root dry weight (qRDW11.1 and qRDW11.2); and shoot length (qSL2.1) in chromosome 2, 6, and 11 regions were detected under both N treatments. [ABSTRACT FROM AUTHOR]

Summary: 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 m m 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. [ABSTRACT FROM AUTHOR]

We characterized 333 introgression lines (INLs) harboring chromosome segments from new plant type (NTP) and Japonica-type cultivars with the genetic background of the elite Indica-type rice ( Oryza sativa L.) cultivar IR 64, by evaluating yield components and dry matter production under irrigated lowland (IL) and upland (UP) culture in 2011 and 2012; and elucidated the relationships between the traits and chromosome segments introduced from the donors. The panicle weight (PW), PW/total plant weight (PW/TW), number of fertile spikelets (FS), and FS/total number of spikelets per panicle (FS/TS) of the INLs increased, while the culm weight (CW) and panicle number (PN) decreased. Most INLs produced more dry matter in the UP than in the IL culture. The INLs were clustered into three groups (A–C) according to their traits in the UP culture, and four groups (I–IV) according to their traits in the IL culture. They were then sorted into six groups (A-I, A-II, B-II, B-III, C-III, and C-IV) according to the relationships between culture conditions. The INLs of group A-II had increased panicle length (PL), PW, PW/TW, FS, and TS, and these traits were stable in both IL and UP culture. In the other groups, the trait values changed with the conditions and season. Association analyses using trait phenotype and genotype data of SSR markers detected 166 quantitative trait loci (QTLs) for 10 traits, distributed on all chromosomes except 3 and 10. Of these, 81 QTLs for DH, CL, PL, CW, PW, PW/TW, PN, FS, TS, and FS/TS were newly detected. The INLs were characterized under different conditions, and dramatic trait modifications in IR64 rice were associated with these QTLs, through introgression from the donor cultivars. Thus, these INLs and QTLs will be useful in genetic studies to identify the gene(s) that modified IR64, and as breeding materials for genetic improvement of Indica-type cultivars. [ABSTRACT FROM AUTHOR]

Highlights: [•] Reliable growth conditions for nitrogen deficiency were successfully established in rice. [•] Rice root elongation was promoted by nitrogen deficiency, but inhibited by oxygen deficiency. [•] Nitrogen deficiency extensively enhanced porosity and aerenchyma formation in roots. [•] Patterns of aerenchyma formation in nitrogen deficiency differed from those in oxygen deficiency. [ABSTRACT FROM AUTHOR]

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 M 2 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 F 2 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 F 2 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. [ABSTRACT FROM AUTHOR]

Zea nicaraguensis (teosinte), a wild relative of maize (Zea mays ssp. mays), constitutively forms aerenchyma, which contributes to plant waterlogging tolerance, in the root cortex in drained soil, whereas maize (inbred line Mi29) does not. One with highest logarithm of odds (LOD) among quantitative trait loci (QTLs) that control constitutive aerenchyma formation in Z. nicaraguensis is Qaer1.05-6 on chromosome 1. Here, we attempted to identify genes in Qaer1.05-6 by comparing cDNA libraries from Mi29, Z. nicaraguensis and a line BC4F1 #62 carrying Qaer1.05-6. We first confirmed that constitutive aerenchyma formation was apparently observed in the order Z. nicaraguensis > BC4F1 #62 > Mi29. Contigs were assembled from cDNAs pooled from the three lines. We identified 1,868 contigs in the region on chromosome 1 that contained Qaer1.05-6. These contigs were screened for contigs that were predominantly composed of cDNAs from BC4F1 #62 and Z. nicaraguensis (no more than 10% of cDNAs from Mi29). Twenty-one such contigs were found and the genes they encoded were identified. In a real-time reverse transcription-polymerase chain reaction (RTPCR) analysis, expression of six of these genes in BC4F1 #62 was at least double that in Mi29, making them candidates for genes associated with constitutive aerenchyma formation. [ABSTRACT FROM AUTHOR]

To understand genetic adaptation of rice to environmental nitrogen status, this study mapped and verified the quantitative trait locus/loci for root elongation in response to exogenous concentration. Significant inhibition of root elongation by increasing concentration in hydroponic culture was observed in seedlings of Oryza sativa cv Taichung 65 (japonica variety) but not in O. glaberrima line IRGC 104038. A total of 161 backcross recombinant lines between these species were employed to map the quantitative trait locus/loci controlling root length of seedlings grown hydroponically with a low (5 µM) or sufficient (500 µM) supply. Five quantitative trait locus/loci were detected: two on chromosome 1 and three singles on chromosomes 2, 3, and 6. The quantitative trait locus/loci qRL1.1 was significant under sufficient supply. Progeny analysis using heterogeneous inbred-type family nearly isogenic lines (HIF-NILs) for the candidate region of qRL1.1 revealed that seminal roots of IRGC 104038-fixed genotypes were significantly longer (12.4 or 11.6%) than those of Taichung 65-fixed genotypes when grown with 500 µM , but not without or with 5 µM . qRL1.1 was confirmed and delimited within a 4-Mbp-long region on the long-arm region of chromosome 1. Comparative mapping with genes for uptake and nitrogen metabolism showed the apparent location of the aspartate aminotransferase gene (OsAAT2) within the candidate region of qRL1.1. Together, the results suggest that qRL1.1 is an adaptive quantitative trait locus/loci for rice root elongation in response to sufficient supply of external and OsAAT2 may be a candidate gene responsible for qRL1.1. [ABSTRACT FROM PUBLISHER]

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 μM 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’. [ABSTRACT FROM AUTHOR]

Immunocytological studies in this laboratory have suggested that NADH‐dependent glutamate synthase (NADH‐GOGAT; EC 1.4.1.14) in developing organs of rice (Oryza sativa L. cv. Sasanishiki) is involved in the utilization of glutamine remobilized from senescing organs through the phloem. Because most of the indica cultivars contained less NADH‐GOGAT in their sink organs than japonica cultivars, over‐expression of NADH‐GOGAT gene from japonica rice was investigated using Kasalath, an indica cultivar. Several T0 transgenic Kasalath lines over‐producing NADH‐GOGAT under the control of a NADH‐GOGAT promoter of Sasanishiki, a japonica rice, showed an increase in grain weight (80% as a maximum), indicating that NADH‐GOGAT is indeed a key step for nitrogen utilization and grain filling in rice. A genetic approach using 98 backcross‐inbred lines (BC1F6) developed between Nipponbare (a japonica rice) and Kasalath were employed to detect putative quantitative trait loci (QTLs) associated with the contents of cytosolic glutamine synthetase (GS1; EC 6.3.1.2), which is probably involved in the export of nitrogen from senescing organs and those of NADH‐GOGAT. Immunoblotting analyses showed transgressive segregations toward lower or greater contents of these enzyme proteins in these BC1F6. Seven chromosomal QTL regions were detected for GS1 protein content and six for NADH‐GOGAT. Some of these QTLs were located in QTL regions for various biochemical and agronomic traits affected by nitrogen recycling. The relationships between the genetic variability of complex agronomic traits and traits for these two enzymes are discussed. [ABSTRACT FROM AUTHOR]

Studies quantitative trait loci associated with cytosolic glutamine synthetase and NADH-glutamate synthase using plant genome mapping in rice. Factors essential in the determination of nitrogen recycling velocity; Correlation between enzyme contents and allelic polymorphism; Genes responsible for the regulation of gene products.

Hybrid sterility is a reproductive barrier that prevents gene flow between species. In Oryza species, some hybrid sterility loci, which are classified as gamete eliminators, cause pollen and seed sterility and sex-independent transmission ratio distortion (siTRD) in hybrids. However, the molecular basis of siTRD has not been fully characterized because of lacking information on causative genes. Here, we analyze one of the hybrid sterility loci, S2, which was reported more than forty years ago but has not been located on rice chromosomes. Hybrids between African rice (Oryza glaberrima) and a near-isogenic line that possesses introgressed chromosomal segments from Asian rice (Oryza sativa) showed sterility and siTRD, which confirms the presence of the S2 locus. Genome-wide SNP marker survey revealed that the near-isogenic line has an introgression on chromosome 4. Further substitution mapping located the S2 locus between 22.60 Mb and 23.54 Mb on this chromosome. Significant TRD in this chromosomal region was also observed in a calli population derived from cultured anther in hybrids of another cross combination of African and Asian rice species. This indicates that the pollen abortion caused by the S2 locus occurs before callus induction in anther culture. It also suggests the wide existence of the S2-mediated siTRD in this interspecific cross combination. Chromosomal location of the S2 locus will be valuable for identifying causative genes and for understanding of the molecular basis of siTRD. [ABSTRACT FROM AUTHOR]

(Jpn. J. Soil Sci.Plant Nutr., 77, 337–342, 2006) [ABSTRACT FROM AUTHOR]

We developed 21 near-isogenic lines (NILs) in the genetic background of the Indica Group rice (Oryza sativa L.) cultivar IR64, with each containing one of the 11 blast resistance genes: Pish , Piz , Piz-5 , Pi9 (t), Pii , Pi3 , Pik , Pik-h , Pik-p , Pi1 , and Pi7 (t). The NILs were confirmed to harbor these genes by their reaction patterns to standard differential blast isolates and by analyses for graphical genotypes using DNA markers located on the same chromosome regions as the target resistance genes. The agronomic traits of these NILs, such as days to heading and yield components, were also investigated and found to be very similar to those of IR64, even when grown under the dramatically different environmental conditions of the temperate and subtropical regions of Japan. These NILs and their genetic information will be used as gene sources for Indica Group rice breeding programs, to improve resistance to blast disease, and as a multiline variety that will also be useful as an alternative approach to the development of the durability of rice resistance to blast disease in tropical areas, especially in irrigated lowland ecosystems. [ABSTRACT FROM AUTHOR]

Glutamine synthetase (GS; EC 6.3.1.2) is a key enzyme of nitrogen assimilation, catalyzing the synthesis of glutamine from ammonium and glutamate. In Arabidopsis, cytosolic GS (GS1) was accumulated in roots when plants were excessively supplied with ammonium; however, the GS activity was controlled at a constant level. The discrepancy between the protein content and enzyme activity of GS1 was attributable to the kinetic properties and expression of four distinct isoenzymes encoded by GLN1;1, GLN1;2, GLN1;3 and GLN1;4, genes that function complementary to each other in Arabidopsis roots. GLN1;2 was the only isoenzyme significantly up-regulated by ammonium, which correlated with the rapid increase in total GS1 protein. GLN1;2 was localized in the vasculature and exhibited low affinities to ammonium (Km = 2450 ± 150 µM) and glutamate (Km = 3.8 ± 0.2 mM). The expression of the counterpart vascular tissue-localizing low affinity isoenzyme, GLN1;3, was not stimulated by ammonium; however, the enzyme activity of GLN1;3 was significantly inhibited by a high concentration of glutamate. By contrast, the high affinity isoenzyme, GLN1;1 (Km for ammonium < 10 µM; Km for glutamate = 1.1 ± 0.4 mM) was abundantly accumulated in the surface layers of roots during nitrogen limitation and was down-regulated by ammonium excess. GLN1;4 was another high affinity-type GS1 expressed in nitrogen-starved plants but was 10-fold less abundant than GLN1;1. These results suggested that dynamic regulations of high and low affinity GS1 isoenzymes at the levels of mRNA and enzyme activities are dependent on nitrogen availabilities and may contribute to the homeostatic control of glutamine synthesis in Arabidopsis roots. [ABSTRACT FROM AUTHOR]

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., (Copyright © 2023 by JAPANESE SOCIETY OF BREEDING.)

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 F 2 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 Akita63NIL GS3 -Koshihikari. Compared with Akita63NIL GS3 -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., (Copyright © 2022 by JAPANESE SOCIETY OF BREEDING.)

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.