Inheritance of two endosperm protein loci in rice (Oryza sativa L.)

Summary Previous studies indicated two types of phenotypic protein markers as two minor bands of SDS-PAGE for rice storage protein. A variant derived from a Pakistani variety, Dular, was found to show a mobility variant with Band 11, a relatively faster-moving band as compared to Band 10, while most of the other cultivated rices exhibited Band 10 at a molecular weight of around 100–110 K. Band 11 was also observed in several wild rice species. How this variant occurred is not known. Another marker is characterized by the presence of either Band 56 (slower-migrating band) or Band 57 (faster-migrating band) in most cultivars at a molecular weight of about 28–27 K. Most indica varieties developed in Taiwan have Band 57 and japonica varieties have Band 56. Genetic analysis of F₁, F₂ and F₃ seeds from interstrain crosses indicated that Band 10 versus Band 11 and Band 56 versus Band 57 are due to codominant alleles at two loci. Tests of independent inheritance between these two loci (Band 10/11 versus Band 56/57) indicated that there is no linkage between them. Both of these two protein loci encode for endosperm proteins and mostly belong to the minor polypeptide subunits of the glutelin fraction of rice seed proteins. Studies on reciprocal crosses indicate dosage effects as exhibited in band patterns. Variations in band intensity were frequently observed when the maternal genotype was different.     

Molecular cloning, expression analysis and chromosomal mapping of salt-responsive cDNAs in rice ( Oryza sativa L.)

By using differential display PCR (DD-PCR) technique, two salt-inducible and one salt-repressed cDNA fragments were isolated from rice. The three cDNA fragments were characterized respectively as partial sequence of rice S-adenosylmethionine decarboxylase (SAMDC) gene, a new member of translation elongation factor 1A gene (namedREF1 A), and a novel gene whose function is unknown (namedSRG1). The full-length cDNA of SAMDC gene (namedSAMDC1) was further isolated by RT-PCR approach and the deduced polypeptide was found to be homologous to SAMDC proteins of other plants, yeast and buman. Northern hybridization revealed that expression of SAMDCl and REFlA was induced, while SRGl was dramatically repressed, by salinity stress. Southern blot analysis demonstrated that SAMDCl and SRGl were present as a single copy gene in rice genome, whereas riceREF1 A gene was organized as a gene family. TheREF1 A,SAMDC1, andSRG1 genes were located on chromosome 3,4, and 6 respectively by RFLP mapping approach using ZYQ8/JX17 DH population and RFLP linkage maps. Project supported by the National “863” High-Technology Program.     

Molecular cloning and nucleotide sequence cDNA encoding nucleoside diphosphate kinase of rice (Oryza sativa L.)

We isolated a rice cDNA encoding nucleoside diphosphate kinase (NDK, EC 2.7.4.6). The deduced amino acid sequence of the rice NDK shows highest homology to spinach NDK-I. The rice NDK gene exhibits a strong codon bias (73.8% GC) in the third position of the codon. DNA blot analysis indicated that at least single NDK gene is present in rice genome.     

Efficient transformation of Korean rice cultivars (Oryza sativa L) mediated byAgrobacterium tumefaciens

The purpose of this study was to improve transformation efficiency for three Korean rice cultivars, Ilpum, Dasan, and Namyang. Using two different media with or without light, efficiencies of callus induction, regeneration, and transformation of the Korean cultivars were compared to Japanese cultivar, Nipponbare, as a control. Immature cv. Nipponbare seeds produced 35.5% and 16.1% regeneration efficiency on CIM and N6D media, respectively. Among the Korean cultivars, only cv. Ilpum induced on CIM in the dark was actively regenerated with efficiency of 8.2%. With LBA4404 (pTOK233), no difference for the efficiency of transformation was found between mature and immature seeds of cv. Ilpum. This result reveals that mature seeds can be substituted for this study with no difference. The anther-derived calli of cv. Namyang inoculated with either LBA4404 (pTOK233) or EHA101 (pSMABuba) showed regeneration efficiencies of 14.5% and 20.9%, respectively, even though efficiency of transformation did not differ with these two vectors. We suggest that the anther-derived calli are better-materials for transformation experiment due to their genotype-independent regeneration. In the assay of GUS, all of the calli that survived on the second selection medium were strongly stained. PCR-Southern blot analyses confirmed that T-DNA was stably transformed into all tissues selected. Cvs. Nipponbare and Namyang transformed by LBA4404 (pTOK233) showed positive color in the NPTII ELISA.     

Ammonium nutrition increases photosynthesis rate under water stress at early development stage of rice (Oryza sativa L.)

An hydroponic experiment with a simulated water stress induced by PEG (6000) was conducted in a greenhouse to study the effects of nitrate (NO₃ ⁻), ammonium (NH₄ ⁺) and the mixture of NO₃ ⁻ and NH₄ ⁺, on water stress tolerance of rice seedlings. Rice (Shanyou 63) was grown under non- or simulated water stress condition (10% (w/v) PEG, MW6000) with the 3 different N forms during 4 weeks. Under non-stressed condition no difference was observed among the N treatments. Under simulated water stress, seedlings grown on N-NO₃ ⁻ were stunted. Addition of PEG did not affect rice seedling growth in the treatment of only NH₄ ⁺ supply but slightly inhibited the rice seedling growth in the treatment of mixed supply of NO₃ ⁻ and NH₄ ⁺. Simulated water stress, when only N-NH₄ ⁺ was present, did not affect leaf area and photosynthesis rate, however, both parameters decreased significantly in the NO₃ ⁻ containing solutions. Under water stress, Rubisco content in newly expanded leaves significantly increased in the sole NH₄ ⁺ supplied plants as compared to that in plants of the other two N treatments. Under water stress, the ratio of carboxylation efficiency to Rubisco content was, respectively, decreased by 13 and 23% in NH₄ ⁺ and NO₃ ⁻ treatments, respectively. It is concluded that, water stress influenced the Rubisco activity than stomatal limitation, and this effects could be regulated by N forms. Responsible Editor: Herbert Johannes Kronzucker. Shiwei Guo and Gui Chen contributed equally to this paper.     

Alternative ecotilling protocol for rapid, cost-effective single-nucleotide polymorphism discovery and genotyping in rice (Oryza sativa L.)

Ecotilling is a high-throughput method of discovery and analysis of single-nucleotide polymorphism (SNP) variations in natural populations, but it requires a substantial investment in sophisticated equipment, costly reagents, and specialized software programs and implementation of several time-consuming steps that limit its use in laboratories with modest financial resources. Moreover, labeling efficiency of PCR primers with fluorescent dyes during Ecotilling can be reduced by unwanted exonuclease activity of single strand-specific nucleases. A new alternative protocol involving a simplified gel system, unlabeled primers, DNA staining after single strand-specific nuclease digestion, and standard gel data analysis was optimized to address these constraints. Using this alternative protocol, we successfully identified four new SNPs verified by sequencing in a collection of 57 diverse rice accessions along with 2 previously reported SNPs in a 922-bp DNA region from thealk gene. An SNP cluster containing a deletion within a 472-bp fragment of thewaxy gene was also characterized. In addition, 4 previously reported SNPs in thealk andwaxy genes were faithfully genotyped among the 57 accessions based on comparisons with sequencing results. Associations between the genotyped SNPs and amylose class and starch gelatinization temperature were as anticipated. These results, along with detailed time and cost comparisons between the 2 methods, suggest that alternative Ecotilling is a simple and reproducible method for SNP discovery and genotyping in rice that leads to substantial savings in equipment, reagents, software, and time compared with the standard Ecotilling procedure. Approved for publication by the Director of the Louisiana Agricultural Experiment Station as paper No. 06-14-0237.     

Spectral response of rice (Oryza sativa L.) leaves to Fe2+ stress

In the management of lake eutrophication, the regulation effect of Fe is considered, in addition to the controlling nitrogen- and phosphorus input. Based on the “Fe hypothesis”, this paper tentatively ap-plied plant spectral response to the remote sensing early-warning mechanism of lake eutrophication. A laboratory water culture experiment with rice (Oryza sativa L.) was conducted to study Fe uptake by plants and the chlorophyll concentration and visible-near infrared spectrum of vegetable leaves as well as their interrelations under Fe²⁺ stress. Three spectral indices, i.e., A₁ (integral value of the changes of spectral reflectivity in the range 460―670 nm under Fe²⁺ stress), A₂ (integral value of the changes of spectral reflectivity in the range of 760―1000 nm under Fe²⁺ stress) and S (blue-shift range of red edge curve under Fe²⁺ stress), were used to establish quantitative models about the relationships between the rice leaf spectrum and Fe²⁺ stress. With the increase of Fe²⁺ in a culture solution, the Fe content in rice plants increased, while the chlorophyll concentration in vegetative leaves decreased. The spectral reflectivity of vegetable leaves increased in the visible light band but decreased in the near infrared band, and the blue-shift range of the red edge curve increased. The indices _A1, A₂ and S all had sig-nificant correlations with the Fe content in rice leaves, the correlation coefficient being respectively 0.951 (P < 0.01), −0.988 (P < 0.01) and 0.851 (P < 0.01), and simulated (multiple correlation coefficients R² > 0.96) and predict the Fe level in rice leaves.     

QTLs for nitrate induced elongation and initiation of lateral roots in rice (Oryza sativa L.)

To investigate the genetic background of nitrate-induced elongation and initiation of lateral roots in rice (Oryza sativa L.), a doubled haploid (DH) population, derived from a cross between IR64 and Azucena, which showed different responses to local supplied NO₃ ^– in lateral root elongation and initiation, was used in an agar culture experiment with three separated layers. The second agar layer was supplied with 3 mM NO₃ ^– or without NO₃ ^– as two treatments. Average lateral root length, lateral root number and surface area of lateral roots in the second agar layers with and without nitrate, respectively, were measured. The ratio of the parameters from the two treatments were calculated as derived parameters. Seven putative Quantitative trait loci (QTLs) for the 6 lateral root traits in nitrate-deficient and nitrate-supplied layers were detected. These QTLs individually explained about 9% to 15% of the total phenotypic variations in the traits. Identical QTLs for root traits from other reports with QTLs detected in this case were found, which suggests that the genetic factors responsive to local supplied NO₃ ^– is involved in root growth and development     

Simple dehydration treatment promotes plantlet regeneration of rice (Oryza sativa L.) callus

Summary To increase plantlet regeneration frequency, rice callus was dehydrated in a Petri dish with a single layer of filter paper prior to transfer to the regeneration medium. With a 24 h dehydration treatment, the regeneration frequency was increased to 47 %, while the regeneration frequency of the untreated control was less than 5 %. This relatively simple method provides an alternative method for improving the regeneration frequency of rice callus.     

Structural changes in the plastid DNA of rice (Oryza sativa L.) during tissue culture

To investigate the rearrangement of the plastid genome during tissue culture, DNA from rice callus lines, which had been derived individually from single protoplasts isolated from seed or pollen callus (protoclones), was analyzed by Southern hybridization with rice chloroplast DNA (ctDNA) clones as probes. Among 44 long-term cultured protoclones, maintained for 4, 8 or 11 years, 28 contained plastid DNA (ptDNA) from which portions had been deleted. The ptDNA of all protoclones that had been maintained for 11 years had a deletion that covered a large region of the plastid genome. The deletions could be classified into 15 types from their respective sizes and positions. By contrast, no deletions were found in the ptDNA of 38 protoclones that had been maintained for only 1 month. These results indicate that long-term culture causes deletions in the plastid genome. Detailed hybridization experiments revealed that plastid genomes with deletions in several protoclones were organized as head-to-head or tail-to-tail structures. Furthermore, ptDNAs retained during long-term culture all had a common terminus at one end, where extensive rearrangement is known to have occurred during the speciation of rice and tobacco. Morphological analysis revealed the accumulation of starch granules in plastids and amyloplasts in protoclones in which the plastid genome had undergone deletion. Our observations indicated that novel structural changes in the plastid genome and morphological changes in the plastid had occurred in rice cells during long-term tissue culture. Moreover, the morphological changes in plastids were associated with deletions in the plastid genome.     

RFLP mapping of QTLs for yield and related characters in rice (Oryza sativa L.)

Quantitative triat loci (QTLs) for yield and related traits in rice were mapped based on RFLP maps from two indica/indica F₂ populations, Tesanai 2/CB and Waiyin 2/CB. In Tesanai 2/CB, 14 intervals carrying QTLs for eight traits were detected, including 3 for grain weight per plant (GWT), 2 for number of panicles per plant (NP), 2 for number of grains per panicle (NG), 1 for total number of spikelets per panicle (TNS), 1 for spikelet fertility (SF), 3 for 1000-grain weight (TGWT), 1 for spikelet density (SD), and 1 for number of first branches per main panicle. The 3 QTLs for GWT were located on chromosomes 1, 2, and 4, with 1 in each chromosome. The additive effect of the single locus ranged from 2.0 g to 9.1 g. A major gene (np4) for NP was detected on chromosome 4 within the interval of RG143–RG214, about 4cM for RG143, and this locus explained 26.1% of the observed phenotypic variance for NP. The paternal allele of this locus was responsible for reduced panicles per plant (3 panicles per plant). In another population, Waiyin 2/CB, 12 intervals containing QTLs for six of the above-mentioned traits were detected, including 3 for GWT, 2 for each of NP, TNS, TGWT and SD, 1 for SF. Three QTLs for GWT were located on chromosome 1, 4, and 5, respectively. The additive effect of the single locus for GWT ranged from 6.7 g to 8.8 g, while the dominance effect was 1.7–11.5 g. QTL mapping in two populations with a common male parent is compared and discussed.     

RFLP analysis of rice (Oryza sativa L.) introgression lines

Summary Fifty-two introgression lines (BC₂F₈) from crosses between two Oryza sativa parents and five accessions of O. officinalis were analyzed for the introgression of O. officinalis chromosome segments. DNA from the parents and introgression lines was analyzed with 177 RFLP markers located at approximately 10-cM intervals over the rice chromosomes. Most probe/enzyme combinations detected RFLPs between the parents. Of the 174 informative markers, 28 identified putative O. officinalis introgressed chromosome segments in 1 or more of the introgression lines. Introgressed segments were found on 11 of the 12 rice chromosomes. In most cases of introgression, O. sativa RFLP alleles were replaced by O. officinalis alleles. Introgressed segments were very small in size and similar in plants derived from early and later generations. Some nonconventional recombination mechanism may be involved in the transfer of such small chromosomal segments from O. officinalis chromosomes to those of O. sativa. Some of the introgressed segments show association with genes for brown planthopper (BPH) resistance in some introgressed lines, but not in others. Thus, none of the RFLP markers could be unambiguously associated with BPH resistance.     

Cloning and characterization of a novel splicing isoform of the iron-superoxide dismutase gene in rice (Oryza sativa L.)

Superoxide dismutases (SODs) are ubiquitous metalloenzymes in aerobic organisms that play a crucial role in protecting organisms against ROS. Here, we report the molecular cloning and functional characterization of a novel alternatively spliced variant of the iron-superoxide dismutase gene, OsFe-SODb, from a rice panicle cDNA library. The alternative splicing event occurred in the fourth exon of the OsFe-SOD gene, and led to the translation of two isoforms of different sizes. The 5′ flanking region of the OsFe-SOD was cloned and many cis-acting regulatory elements were found that are involved in light responsiveness, including a G-box and an I-box. RT-PCR analysis showed that the two alternative forms of OsFe-SOD were expressed in both the vegetative and reproductive tissues of Cpslo17. Moreover, accumulation of both isoforms was upregulated by light induction. In addition, the alternative splicing of OsFe-SOD mRNA was sensitive to low temperature. High yield production of the two recombinant OsFe-SOD isoforms was achieved in Escherichia coli. SOD assays showed that C-terminal truncation in OsFe-SODb did not result in a loss of SOD enzyme activity.     

Production of doubled haploid rice plants (Oryza sativa L.) by anther culture

The results of anther culture of F₂ pollen issued from 23 single crosses are presented. A relation between the morphology of the panicle and the microspore stage was established. After cold-pretreatment (8 days at 4°C), the anthers were cultured on the callus-induction medium N6 supplemented with 1 mg l^–1 naphthaleneacetic acid. The calli were transferred to MS plant regeneration medium supplemented with 3 mg l^–1 kinetin + 0.5 mg l^–1 naphthaleneacetic acid. The induction frequency varied from 0.22% to 29% and the regeneration frequency from 0% to 144.4%, dependent upon the crosses used. On average, 27% of the plants obtained were albinos and 59% of the green plants underwent spontaneous chromosome doubling. Thirtynine doubled haploid lines were evaluated and multiplied in the field. Lines with an excellent behaviour in upland culture conditions were selected from two crosses.     

Overexpression of the rFCA RNA Recognition Motif Affects Morphologies Modifications in Rice (Oryza sativa L.)

RNA recognition motifs as important regulators of gene expression are highly conserved in animals and plants. The FCA floral promotion gene in Arabidopsis encodes a protein, containing two RNA recognition motifs (RRM) and a WW protein interaction domain. Here we isolated FCA cDNA from rice. FCA in rice (rFCA) was homologous to FCA-gamma of Arabidopsis and contained conserved domains. To investigate the function of RRM domain, fragment RRM1 and RRM2 of rFCA were introduced into rice subspecies Oryza sativa L. subsp. Indica var. 9311 and another rice subspecies Oryza sativa L. subsp. Japonica var. zhonghua11 transformation. Two transgenic lines exhibited similar phenotypes, flowering time delay, seed size and cell volume of transgenic plants was increased. These results showed that constitutive expression of RRMs could regulate cellular size. The patterns of overexpression of two RRM domains and their similar morphologies indicate they may play a same role.     

A comparison of methods for callus culture and plant regeneration of RD25 rice (Oryza sativa L.) in two laboratories

While methodology is transferable from one laboratory to another, an exact transfer does not usually occur and even a nearly exact transfer of methods does not always result in repeatable data. Researchers should not expect that an effort to duplicate a published procedure will necessarily lead to identical results.In attempting to transfer rice tissue culture methods between laboratories in Fort Collins, Colorado, USA and Bangkok, Thailand, we discovered that a combination of the methods of each laboratory produced the best results in term of callus productions and plant regeneration. In the experiments reported here, the type of culture vessel used and the geographical location were also important variables.Supported by the USAID/Cooperative Agreement No DAN-4137-A-00-4053-00.     

Diallel analysis of heading date in rice (Oryza sativa L.)

Summary The genetics of heading date was investigated in an 8×8 diallel set of crosses involving diverse rice cultivars. Wr, Vr graph analysis revealed the presence of a complementary type of non-allelic interaction which apparently affected the position and slope of the regression line such as if there were overdominance. Omission of two interacting parents resulted in a 6×6 subset of diallel crosses from which, as observed in the Wr, Vr graph, the non-allelic interaction had disappeared and the regression line exhibited partial dominance. Estimates of the genetic components of variation were in close conformity with the results obtained from the Wr, Vr graph: the average degree of dominance, as measured by (H₁/D)^1/2, was in overdominance range in the interacting 8×8 set of diallel crosses whereas it was reduced to partial dominance in the non-interacting 6×6 set of crosses. Further analysis by a standardized deviations graph indicated that earliness was controlled, on the average, by an excess of dominant alleles.     

Antioxidative defenses and water deficit-induced oxidative damage in rice (Oryza sativa L.) growing on non-flooded paddy soils with ground mulching

Rice (Oryza sativa L.) cultivation under non-flooded conditions using polyethylene film as ground mulching materials, namely plastic film-mulching cultivation system (PFMCS), is an alternative to the conventional rice cultivation system in regions where rainfall and fresh water resources are limited. Two-year field trials (1998–1999) were performed in this study to investigate the growth-stage-dependent changes in activities of antioxidative enzymes and lipid peroxidation in leaves of rice subjected to mulching with plastic film or kraft paper and zero mulching under non-flooded conditions compared with continuously flooded treatment. Significantly higher activities of peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX) but lower concentration of malondialdehyde (MDA) were observed in mulching treatments than in zero mulching treatment at all growth stages in the drier growing season (1999). The concentration of MDA was significantly higher especially at late growth stages in zero mulching treatment than in the other treatments. In contrast, essentially no significant difference existed in the activities of the major antioxidant enzymes (except POD) or in the concentration of MDA between any two treatments in the wetter growing season (1998). This change tendency of antioxidant enzyme activity and MDA level over two contrasting growing seasons was in line with both soil and leaf moisture status, and rice yields of different treatments. These results strongly suggest that plastic film-mulching treatment or paper mulching treatment significantly alleviated oxidative damages induced by water-deficit stress in rice. The efficacy of ground-mulching-induced enhancement of antioxidative defense to drought stress is discussed with respect to water deficit status in both soils and rice plants.     

Hybrid rice (Oryza sativa L.): identification and parentage determination by RAPD fingerprinting

Summary DNA from three families of rice plants selected in Northern China (each comprising the male sterile, the restorer, the hybrid F1 and the maintainer lines) has been extracted and amplified by PCR with different random DNA primers (RAPD analysis). Then, DNA has been analysed by agarose gel electrophoresis and DNA bands scored as present or absent. The generated matrices are reproducible and amenable for identification of each single plant line. Thus, RAPD fingerprinting of the inbred parental lines and of the resulting hybrid is proposed as a convenient tool for the identification, protection and parentage determination of plant hybrids. Furthermore, by offering a molecular tool to verify the degree of dissimilarity between the parental lines, the RAPD analysis may also be used to search for new parental combinations.