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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]

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]

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]

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.

Von Hippel-Lindau disease (VHL disease) is an inherited neoplasia syndrome. VHL disease which frequently complicates pancreatic lesions is rarely diagnosed by existence of pancreatic involvements. We report two cases of VHL disease with pancreatic lesions. The first patient was a 40-year-old woman. Adrenal pheochromocytoma, spinal hemangioblastoma and pancreatic endocrine tumor were resected. The second case was a 68-year-old woman with past surgical histories included cerebellar and spinal hemangioblastoma. Subtotal pancreatectomy was performed for multiple serous cystadenoma. IPMN which has been never reported as pancreatic involvement of VHL disease were documented by imaging diagnosis in the first case, and by histological examination in the second case. We considered VHL disease from coexistent multiple tumors include pancreatic involvements and finally diagnosed by genetic examination in both cases. Care should be taken regarding the patient's right for treatment against for the genetic disease. We hold a genetic conference composed of multidisciplinary team. Consequently we detected another VHL disease patient from patient's family.

A 56-year-old man, who had epigastralgia and abnormal liver function test, was admitted to our hospital. ERCP showed common bile duct dilation and stones. We therefore performed endoscopic lithotripsy after endoscopic sphincterotomy. Ten months later, MRCP showed recurrent CBD stones. After rehospitalization, resection of the dilated bile duct was carried out. This case was diagnosed Todani's type Ib congenital cystic dilatation of common bile duct. Todani's type Ib is rare type of congenital dilatation of bile duct, and is interesting embryologically.

A 72-year-old woman with multilocular liver cysts was admitted. This lesions seemed to be an alveolar hydatid disease. Two methods of Western blotting were used for serologic diagnosis. One method recognizes antigens of crude extracts of Echinococcus multilocularis (EM). The other method recognizes a purified antigen (Em18) of EM. Her serum only reacted with the former method and never reacted with Em18 antigen. Eighteen months after first admission, she had an operation. The resected specimen was diagnosed with simple cysts. Western blotting using Em18 antigen could greatly facilitate the differential diagnosis of simple liver cyst and alveolar hydatid disease.