Evaluation of a plant regeneration test of embryogenic cell suspension cultures of rice (Oryza sativa L. cv Taipei 309)

Summary In this paper we discuss the changes in the number of plants developed per embryogenic mass, the percentage of embryogenic masses that developed plants, the percentage of plant regeneration, and the index of vigor of regenerated plants for embryogenic masses that were induced from daily samples of a cell suspension culture of rice (Oryza sativa L. cv. Taipei 309). The results indicate that embryogenic masses that matured first and were induced from freshly subecultured cell suspension culture had the highest values for the four parameters. An index of vigor of the regenerated plants was defined.     

Totipotency of coleoptile tissue in indica rice (Oryza sativa L. cv. ch 1039)

Embryogenic and non-embryogenic calluses were induced from 3,4,5 and 7d old coleoptile segments of indica rice (Oryza sativa L. cv. CH 1039). Compact, globular, yellow and creamy embryogenic and white friable non-embryogenic callus arose from the cut end and entire length of the coleoptile segments. Murashige and Skoog's (MS) medium supplemented with 2.5mg/1 2,4-D was used as callus induction medium. Plant regeneration from coleoptile segments occurred with the transfer of embryogenic callus to MS basal medium supplemented with 2.0mg/1 BAP and 0.5mg/1 NAA in combination. Average number of regenerated plants from one coleoptile ranged from9.1 to 14.0.Four day old coleoptiles showed the highest frequency of plant regeneration.Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - BAP 6-benzylaminopurine - MS Murashige and Skoog (1962) - NAA 1-naphthalene acetic acid     

Genetic analysis of salinity tolerance in rice (Oryza sativa L.)

Summary The genetics of salinity tolerance in rice was investigated by a nine-parent complete diallel including reciprocals. Test materials involved susceptible (IR28, IR29, and MI-48), moderately tolerant (IR4595-4-1-13, IR9884-54-3-1E-P1, and IR10206-29-2-1), and tolerant (Nona Bokra, Pokkali, and SR26B) parents. Twoweek-old seedlings were grown in a salinized (EC = 12 dS/m) culture solution for 19 days under controlled conditions in the IRRI phytotron. Typical characteristics of salinity tolerance in rice were found to be Na⁺ exclusion and an increased absorption of K⁺ to maintain a good Na-K balance in the shoot. Genetic component analysis (GCA) revealed that a low Na-K ratio is governed by both additive and dominance gene effects. The trait exhibited overdominance, and two groups of genes were detected. Environmental effects were large, and the heritability of the trait was low. Our findings suggest that when breeding for salt tolerance, selection must be done in a later generation and under controlled conditions in order to minimize environmental effects. Modified bulk and single-seed descent would be the suitable breeding methods. Combining ability analysis revealed that both GCA and specific combining ability (SCA) effects were important in the genetics of salt tolerance. Moderately tolerant parents — e.g., IR4595-4-1-13 and IR9884-54-3-1E-P1 — were the best general combiners. Most of the best combinations had susceptible parents crossed either to moderate or tolerant parents. The presence of reciprocal effects among crosses necessitates the use of susceptible parents as males in hybridization programs. Large heterotic effects suggest the potential of hybrid rice for salt-affected lands.     

Potassium nutrition of rice (Oryza sativa L.) varieties under NaCl salinity

A salt-tolerant (Pokkali) and a salt-sensitive (IR28) variety of rice (Oryza sativa L.) were grown in a phytotron to investigate the effect of K (0, 25, 50 and 75 mg K kg^–1 soil) application on their salt tolerance. Potassium application significantly increased potential photosynthetic activity (Rfd value), percentage of filled spikelets, yield and K concentration in straw. At the same time, it also significantly reduced Na and Mg concentrations and consequently improved the K/Na, K/Mg and K/Ca ratios. IR28 responded better to K application than Pokkali. Split application of K failed to exert any beneficial effect over basal application.     

A DESD-box helicase functions in salinity stress tolerance by improving photosynthesis and antioxidant machinery in rice (Oryza sativa L. cv. PB1)

The exact mechanism of helicase-mediated salinity tolerance is not yet understood. We have isolated a DESD-box containing cDNA from Pisum sativum (Pea) and named it as PDH45. It is a unique member of DEAD-box helicase family; containing DESD instead of DEAD/H. PDH45 overexpression driven by constitutive cauliflower mosaic virus-35S promoter in rice transgenic [Oryza sativa L. cv. Pusa Basmati 1 (PB1)] plants confers salinity tolerance by improving the photosynthesis and antioxidant machinery. The Na⁺ ion concentration and oxidative stress parameters in leaves of the NaCl (0, 100 or 200 mM) treated PDH45 overexpressing T₁ transgenic lines were lower as compared to wild type (WT) rice plants under similar conditions. The 200 mM NaCl significantly reduced the leaf area, plant dry mass, net photosynthetic rate (P_N), stomatal conductance (gs), intercellular CO₂ (Ci), chlorophyll (Chl) content in WT plants as compared to the transgenics. The T₁ transgenics exhibited higher glutathione (GSH) and ascorbate (AsA) contents under salinity stress. The activities of antioxidant enzymes viz. superoxide dismutase (SOD), ascorbate peroxidase (APX), guaiacol peroxidase (GPX) and glutathione reductase (GR) were significantly higher in transgenics; suggesting the existence of an efficient antioxidant defence system to cope with salinity induced-oxidative damage. Yeast two-hybrid assay indicated that the PDH45 protein interacts with Cu/Zn SOD, adenosine-5′-phosphosulfate-kinase, cysteine proteinase and eIF(4G), thus confirming the involvement of ROS scavenging machinery in the transgenic plants to provide salt tolerance. Furthermore, the T₂ transgenics were also able to grow, flower, and set viable seeds under continuous salinity stress of 200 mM NaCl. This study provides insights into the mechanism of PDH45 mediated salinity stress tolerance by controlling the generation of stress induced reactive oxygen species (ROS) and also by protecting the photosynthetic machinery through a strengthened antioxidant system.     

Optimization of ammonium acquisition and metabolism by potassium in rice (Oryza sativa L. cv. IR-72)

We present the first characterization of K⁺ optimization of N uptake and metabolism in an NH₄⁺‐tolerant species, tropical lowland rice (cv. IR‐72). ¹³N radiotracing showed that increased K⁺ supply reduces futile NH₄⁺ cycling at the plasma membrane, diminishing the excessive rates of both unidirectional influx and efflux. Pharmacological testing showed that low‐affinity NH₄⁺ influx may be mediated by both K⁺ and non‐selective cation channels. Suppression of NH₄⁺ influx by K⁺ occurred within minutes of increasing K⁺ supply. Increased K⁺ reduced free [NH₄⁺] in roots and shoots by 50–75%. Plant biomass was maximized on 10 mm NH₄⁺ and 5 mm K⁺, with growth 160% higher than 10 mm NO₃^‐‐grown plants, and 220% higher than plants grown at 10 mm NH₄⁺ and 0.1 mm K⁺. Unlike in NH₄⁺‐sensitive barley, growth optimization was not attributed to a reduced energy cost of futile NH₄⁺ cycling at the plasma membrane. Activities of the key enzymes glutamine synthetase and phosphoenolpyruvate carboxylase (PEPC) were strongly stimulated by elevated K⁺, mirroring plant growth and protein content. Improved plant performance through optimization of K⁺ and NH₄⁺ is likely to be of substantial agronomic significance in the world's foremost crop species.     

Plant regeneration from haploid cell suspension-derived protoplasts of Mediterranean rice (Oryza sativa L. cv. Miara)

More than 750 plants were regenerated from protoplasts isolated from microspore callus-derived cell suspensions of the Mediterranean japonica rice Miara, using a nurse-feeder technique and N6-based culture medium. The mean plating efficiency and the mean regeneration ability of the protocalluses were 0.5% and 49% respectively. Flow cytometric evaluation of the DNA contents of 7 month old-cell and protoplast suspensions showed that they were still haploid. Contrastingly, the DNA contents of leaf cell nuclei of the regenerated protoclones ranged from 1C to 5C including 60% 2C plants. This was consistent with the morphological type and the fertility of the mature plants. These results and the absence of chimeric plants suggest that polyploidization occurred during the early phase of protoplast culture.Abbreviations BAP 6-benzylamino purine - 2,4-D 2,4-dichlorophenoxyacetic acid - FDA fluorescein diacetate - GA3 gibberellic acid - NAA -naphthaleneacetic acid - PAS periodic acid Schiff - PCM protoplast culture medium - PCV packed cell volume     

Studies on some genetic parameters of rice (Oryza sativa L.)

Summary In order to utilize the available useful variation in breeding rice to improve yield and quality of grain, the performance of a wide range of rice germ plasm comprising 30 varieties was evaluated in northern India, a major rice growing belt. Plant performance revealed high genetic divergence and phenotypic variability in the crop, with the maximum range of variation being for grain number per panicle and the minimum for grain dimensions. There were also significant differences among varietal means for ten phenotypic traits. Genotypic and phenotypic variance contributed profoundly to the variance of the phenotypic traits studied, but, since genetic variability in the traits related to yield was considerable, there is scope for further improvement in yielding ability. Grain number per panicle, number of effective tillers per plant and culm length exhibit high heritability, and genotypic coefficient of variation and therefore a high genetic advance. Thus, selection for these traits would be effective in crop improvement. Moreover, grain number per panicle shows a significant positive correlation with yield, and this trait could profitably form a reliable index for the yielding capacity of this crop.     

Genome-wide association mapping of salinity tolerance in rice (Oryza sativa)

Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium high-throughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na⁺/K⁺ ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5–18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na⁺/K⁺ ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.     

The chemical composition of suberin in apoplastic barriers affects radial hydraulic conductivity differently in the roots of rice (Oryza sativa L. cv. IR64) and corn (Zea mays L. cv. Helix)

Apoplastic transport barriers in the roots of rice (Oryza sativa L. cv. IR64) and corn (Zea mays L. cv. Helix) were isolated enzymatically. Following chemical degradation (monomerization, derivatization), the amounts of aliphatic and aromatic suberin monomers were analysed quantitatively by gas chromatography and mass spectrometry. In corn, suberin was determined for isolated endodermal (ECW) and rhizo-hypodermal (RHCW) cell walls. In rice, the strong lignification of the central cylinder (CC), did not allow the isolation of endodermal cell walls. Similarly, exodermal walls could not be separated from the rhizodermal and sclerenchyma cell layers. Suberin analyses of ECW and RHCW of rice, thus, refer to either the entire CC or to the entire outer part of the root (OPR), the latter lacking the inner cortical cell layer. In both species, aromatic suberin was mainly composed of coumaric and ferulic acids. Aliphatic suberin monomers released from rice and corn belonged to five substance classes: primary fatty acids, primary alcohols, diacids, omega-hydroxy fatty acids, and 2-hydroxy fatty acids, with omega-hydroxy fatty acids being the most prominent substance class. Qualitative composition of aliphatic suberin of rice was different from that of corn; (i) it was much less diverse, and (ii) besides monomers with chain lengths of C(16), a second maximum of C(28) was evident. In corn, C(24) monomers represented the most prominent class of chain lengths. When suberin quantities were related to surface areas of the respective tissues of interest (hypodermis and/or exodermis and endodermis), exodermal cell walls of rice contained, on average, six-times more aliphatic suberin than those of corn. In endodermal cell walls, amounts were 34 times greater in rice than in corn. Significantly higher amounts of suberin detected in the apoplastic barriers of rice corresponded with a substantially lower root hydraulic conductivity (Lp(r)) compared with corn, when water flow was driven by hydrostatic pressure gradients across the apoplast. As the OPR of rice is highly porous and permeable to water, it is argued that this holds true only for the endodermis. The results imply that some caution is required when discussing the role of suberin in terms of an efficient transport barrier for water. The simple view that only the quantity of suberin present is important, may not hold. A more detailed consideration of both the chemical nature of suberins and of the microstructure of deposits is required, i.e. how suberins impregnate wall pores.     

Cloning and expression of a lipase gene from rice (Oryza sativa cv. Dongjin)

Lipases are useful enzymes that are primarily responsible for the hydrolysis of acylglycerides during lipid processing. We have cloned a lipase gene from a rice seed coat cDNA library (Oryza sativa cv. Dongjin). The cDNA was 1,445 bp in length and encoded 361 amino acid residues (GenBank accession No. AY580163). The deduced amino acid sequence had 82 and 56% identity to Oryza sativa (cv. Chuchung) and Arabidopsis thaliana lipase genes, respectively, and there was a GxSxG consensus motif near the catalytic triad at the active serine site. The deduced sequence had little homology to mammalian and microbial lipases. When the Oryza sativa lipase gene was expressed in Escherichia coli with the pET expression system, activity was found mainly in the pellet fraction. The purified product had lipolytic activity towards tributyrin and was about 40 kDa in size.     

Candidate genes for drought tolerance and improved productivity in rice (Oryza sativa L.)

Candidate genes are sequenced genes of known biological action involved in the development or physiology of a trait. Twenty-one putative candidate genes were designed after an exhaustive search in the public databases along with an elaborate literature survey for candidate gene products and/or regulatory sequences associated with enhanced drought resistance. The downloaded sequences were then used to design primers considering the flanking sequences as well. Polymerase chain reaction (PCR) performed on 10 diverse cultivars that involvedJaponica, Indica and local accessions, revealed 12 polymorphic candidate genes. Seven polymorphic candidate genes were then utilized to genotype 148 individuals of CT9993 × IR62266 doubled haploid (DH) mapping population. The segregation data were tested for deviation from the expected Mendelian ratio (1:1) using a Chi-square test (<1%). Based on this, four candidate genes were assessed to be significant and the remaining three, as non-significant. All the significant candidate genes were biased towards CT9993, the female parent in the DH mapping population. Single-marker analysis strongly associated (<1%) them to different traits under both well-watered and low-moisture stress conditions. Two candidate genes,EXP15 andEXP13, were found to be associated with root number and silicon content in the stem respectively, under both well-watered and low-moisture stress conditions     

Prediction of evapotranspiration and grain yield of rice (Oryza sativa L. cv Thriveni) in a humid tropical climate

Summary In a humid tropical climate at Pattambi (10° 48 N, 76° 12 E), the evapotranspiration (ET) rates of rice (Oryza sativa L. cv. Thriveni) were 2.8–5.7 mm/day during the first crop season (May–September) and 6.2–9.1 mm/day during the second crop season (September–January). The crop was grown at the Station in the irrigated lowlands on sandy soils with average yields of 3025 and 2925 kg/ha in the first and second cropping seasons, respectively. The seasonal ET, water requirements, water use efficiency and field water use efficiency of the crop were 400 mm, 1150 mm, 7.56 and 2.63 kg/ha per mm in the first crop season and 650 mm, 1500 mm, 4.50 and 1.95 kg/ha per millimetre in the second crop season. Using the reference crop ET computed by Blaney-Criddle, Radiation, and Penman methods and measured evaporation from class A pan, Colorado and GGI 3000 pans, the crop coefficients were worked out. Correlations between weather parameters and the biomass of rice were obtained. The grain yield (Y, in kg/ha) of the crop was predicted using the equationY=1.71Y ₀–56S+85F–2430 (N=8,r=0.920), whereY ₀ is the sample of biomass of the rice at flowering in kg/ha,S andF are the duration of sunshine hours and maximum air temperatures (°C) between the 46th day of transplanting and maturity.     

A calcium- and phospholipid-dependent protein kinase from rice (Oryza sativa) leaves

Protein kinases in plants have not been examined in detail, but protein phosphorylation has been shown to be essential for regulating plant growth via the signal transduction system. A Ca²⁺- and phospholipid-dependent protein kinase, possibly involved in the intracellular signal transduction system from rice leaves, was partially purified by sequential chromatography on DE52, Phenyl Superose and Superose 12. This protein kinase phosphorylated the substrate, histone III-S, in the presence of Ca²⁺ and phosphatidylserine. The apparent molecular mass of the Ca²⁺- and phosphatidylserine-dependent protein kinase (Ca²⁺/PS PK), determined by phosphorylation in SDS-polyacrylamide gel containing histone III-S, was 50 kDa. The protein kinase differed from Ca²⁺-dependent protein kinase (CDPK) in rice leaves in that Ca²⁺/PS PK showed phospholipid dependency and the molecular mass of Ca²⁺/PS PK exceeded that of CDPK. Investigations were carried out on changes in Ca²⁺/PS PK and CDPK activity in the cytosolic and membrane fractions during germination. The maximum activity of Ca²⁺/PS PK in the cytosolic fraction was observed before imbibition and that of CDPK in the membrane fraction was noted at 6 days following imbibition. Protein kinases are likely to regulate plant growth through protein phosphorylation.     

Genetics of amylose content in rice (Oryza sativa L)

Inheritance of amylose content was studied in crosses involving very low-, intermediate-, and high-amylose parents. The single-grain analysis of parents, F₁, F₂, B₁F₁, and B₂F₁ seed from a single-season harvest, showed that the parental mean difference of 14–17 % in IR37307-8/BPI 121-407 or IR37307-8/IR24632-34 and about 20% in the cross IR37307-8/IR8 were controlled by a single gene with major effect, along with some minor genes and/or modifiers. The appearance of segregants inbetween the two parents was attributed to gene dosage effects in the endosperm. The results indicate that selection for amylose level can effectively be done in early segregating generations. Selection for intermediary segregants would be ineffective because the dosage effects would dissipate in further generations.     

Water-use efficiency in rice (Oryza sativa L.) in relation to resistance to salinity

Abstract The effects of sodium chloride on water-use efficiency of a number of varieties of rice have been investigated. Sensitivity to salinity in rice arises in large part from excessive rates of sodium ion transport to the shoot consequent upon high rates of transpirational water loss. Varietal differences in water-use efficiency were found: these were greater when measured for whole shoots over a period of one week, than when made as instantaneous measurements on individual leaves. Salinity had rather little effect on water use efficiency but overall resistance of seedlings to salt was, in general, greater the greater the water-use efficiency. The reasons for the differences between varieties are discussed in terms of differences in growth pattern: among the seven varieties investigated, water-use efficiency and salt-resistance were lower in dwarfed as opposed to non-dwarfed varieties.