Biochemical and molecular mechanisms associated with Zn deficiency tolerance and signaling in rice (Oryza sativa L.)

In this study, zinc (Zn) deficiency caused a significant reduction in growth parameters and tissue Zn concentrations in BRRI 33 (sensitive) but not in Pokkali (tolerant). The increase of proton extrusion in both genotypes under high pH suggests that it gets triggered as a common consequence of reducing pH and solubilization of Zn. Real-time PCR showed pronounced upregulation of OsZIP4, OsDMAS1, OsNAS2 and OsPCS1 in Zn-deficient roots of Pokkali, and to a lesser extent in BRRI 33 only for OsZIP4 and OsPCS1. This suggests that OsDMAS1, OsNAS2 and OsPCS1 functions as secondary consequences leading to higher chelation and uptake of Zn under Zn deficiency in Pokkali. Further, a major increase in CAT, POD, SOD, GR and key metabolites suggests that high antioxidant defense plays a critical role in Zn deficiency tolerance in Pokkali. Further, Pokkali self-grafts and plants having Pokkali rootstock combined with BRRI 33 scion showed no significant decline in plant height, root dry matter and Zn concentration along with upregulation of Zn transporters (OsZIP4 and OsIRT1) under Zn deficiency, suggesting that signal driving mechanisms for Zn deficiency tolerance mechanisms are generated in the root and Zn-inefficient BRRI 33 is not capable of producing signals or sensing them.     

Shoot tolerance mechanisms to iron toxicity in rice (Oryza sativa L.)

Iron toxicity frequently affects lowland rice and leads to oxidative stress via the Fenton reaction. Tolerance mechanisms were investigated in contrasting genotypes: the intolerant IR29 and the tolerant recombinant inbred line FL483. Seedlings were exposed to 1000 mg L^‐1 ferrous iron, and the regulation of genes involved in three hypothetical tolerance mechanisms was investigated (I) Iron uptake, partitioning and storage. The iron concentration and speciation in different plant tissues did not differ significantly between genotypes. Sub‐cellular iron partitioning genes such as vacuolar iron transporters or ferritin showed no genotypic differences. (II) Antioxidant biosynthesis. Only one gene involved in carotenoid biosynthesis showed genotypic differences, but carotenoids are unlikely to scavenge the reactive oxygen species (ROS) involved in Fe toxicity, i.e. H₂O₂ and hydroxyl radicals. (III) Enzymatic activities for ROS scavenging and antioxidants turnover. In shoots, glutathione‐S‐transferase and ascorbate oxidase genes showed genotypic differences, and consistently, the tolerant FL483 had lower dehydroascorbate reductase and higher ascorbate oxidase activity, suggesting that high rates ascorbate reduction confer sensitivity. This hypothesis was confirmed by application of exogenous reduced ascorbate or L‐galactono‐1,4‐lactone, which increased lipid peroxidation under iron toxic conditions. Our results demonstrate in planta pro‐oxidant activity of reduced ascorbate in the presence of iron.     

Heterosis breeding in rice (Oryza sativa L.)

Summary Studies conducted at the International Rice Research Institute (IRRI) during 1980 and 1981 have shown up to 73% heterosis, 59% heterobeltiosis and 34% standard heterosis for yield in rice. The latter was estimated in comparison to commercial varieties: IR36 and IR42 (yield 4–5 t/ha in wet season trials and 7–8 t/ha in dry season trials). Generally speaking, absolute yield was lower and extent of standard heterosis was higher in wet season than in dry season with some exception. Yields up to 5.9 t/ha (22% standard heterosis) in the wet season and 10.4 t/ha (34% standard heterosis) in the dry season were obtained. Most of the hybrids performed better in some season while some performed better in both seasons. Hybrids showed better lodging resistance although they were 5–10 cm taller. F₁ hybrids had significant positive correlations with the parental traits viz., yield (r = 0.446), tillering (r = 0.746), height (r = 0.810) and flowering (r = 0.843). Selection of parents among elite breeding lines on the basis of their per se yield performance, diverse origin and resistance to insects and diseases should give heterotic combination. Yield advantage of hybrids was due primarily to increase in number of spikelets per unit area even though tiller number was reduced. Grain weight was either the same or slightly higher. High yielding hybrids also showed significant heterosis and heterobeltiosis for total dry matter and harvest index. For commercial utilization of heterosis in rice, effective male sterility and fertility restoration systems are available and up to 45% natural outcrossing on male sterile lines has been observed. Consequently, F₁ rice hybrid have been successfully developed and used in China. Prospects of developing hybrid rice varieties elsewhere appear bright especially in countries that have organized seed production, certification and distribution programs and where hybrid seed can be produced at a reasonable cost.     

Mechanism associated with nonstructural carbohydrate accumulation in submergence tolerant rice (Oryza sativa L.) cultivars

Nonstructural carbohydrate (NSC) accumulation in submergence tolerant rice cultivars (cv) was studied in six Indica rice [Oryza sativa (L.)] cv under control and simulated submerged conditions. Tolerant cultivars accumulated greater contents of NSC compared to the susceptible cultivars. Starch and total NSC content showed significant positive association with survival percentage. On the other hand, elongation due to submergence was significantly a negative association with survival. The CO₂ photosynthetic rate, chlorophyll content, maximum photochemical efficiency of PS II (Fv/Fm), and activities of Rubisco were not significantly different between tolerant and susceptible cv under control condition. The ADP glucose pyrophosphorylase (AGPPase) activity was significantly higher in the tolerant cv and was a positive association with starch/NSC, whereas Fructose 1,6-diphosphatase (FDPase) activity was significantly higher in susceptible cv compared to tolerant cv and was a negative association with starch/NSC. Greater activities of AGPPase along with lower activities of FDPase might facilitate greater accumulation of NSC in tolerant rice cultivars.     

Mapping quantitative trait loci associated with root penetration ability in rice (Oryza sativa L.)

Root penetration ability is an important factor for rice drought resistance in areas with soils subject to both compaction and periodic water deficits. However, breeding for root penetration ability is inhibited by the difficulties associated with measuring root traits. Our objective was to identify restriction fragment length polymorphisms (RFLPs) associated with root penetration ability. Using wax-petrolatum layers as a proxy for compacted soil, we counted the number of vertical root axes penetrating through the layer, the total number of vertical root axes and the number of tillers per plant of 202 recombinant inbred (RI) lines over three replications. As a measure of root penetration ability, we used a root penetration index defined as the percent of the total number of vertical root axes that penetrated through a wax-petrolatum layer. The RI population exhibited a wide range in the number of penetrating roots axes (10–115 roots), the total number of roots axes (74–226 roots), tillers per plant (6–18), and in the root penetration index (0.11–0.71). Single-marker and interval quantitative trait analyses were conducted to identify RFLP loci associated with the number of penetrating roots, total root number, root penetration index, and tiller number. Four quantitative trait loci (QTLs) were associated with the number of penetrated roots, 19 with the total root number, six QTLs with the root penetration index and ten with tiller number. Individually, these QTLs accounted for a maximum of 8% of the variation in the number of penetrating roots, 19% of the variation in total root number, 13% of the variation in root penetration index and 14% of the variation in tiller number as estimated from regressions. The multimarker regression model accounting for the greatest proportion of the variation in the root penetration index was a three-marker model that accounted for 34% of the variation. Two-marker models accounted for 13% of the variation in the number of penetrated roots, 25% of the variation in total root number, and 21% of the variation in tiller number. This is the first research paper to apply RFLP quantitative trait analysis to dissect genetic loci associated with the total number of roots, root penetration ability and tiller number.Contribution from the Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University Lubbock, TX 79409, USA. Journal Number T-4-385     

Low irradiance stress tolerance in rice (Oryza sativa L.)

The effect of low irradiance on three rice cultivars (shade tolerant cvs. Swarnaprabha and CO 43 and shade susceptible cv. IR 20) was studied. The large subunit (LSU) of ribulose-1,5-bisphosphate carboxylase/oxygenase with molecular mass of 55 kDa was reduced in cv. IR 20 grown under low irradiance (LI). Native protein profile studied showed, under LI, reduction in the contents of proteins with RF values 0.03, 0.11 and 0.37. Analysis of chloroplast polypeptides revealed an induction of light-harvesting chlorphyll-protein 2 (LHCP2) under shade. The induction was more expressed in cv. CO 43 than in cv. IR 20. Under LI, in vivo labelled protein bands in the molecular range of 26 - 27 kDa were induced. These proteins were highly turned over in the LI-grown plants of cv. CO 43 than in cv. IR 20. A signal for rbcL gene sequences in EcoRI digested lanes was also found. Isozyme analysis of peroxidase showed an induction of a new band with RF 0.43 in cv. IR 20 subjected to LI. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetics of gel consistency in rice (Oryza sativa L.)

Inheritance of gel consistency in rice was studied in crossés involving highamylose, low-gelatinizalion temperature parents with hard, medium, and soft gel consistency. The results of single-grain analysis of parents, F₁, F₂, B₁F₁, B₂F₂, and their reciprocal crosses from a single-season harvest showed that the differences between hard and soft, hard and medium, and medium and soft gel consistency are under monogenic control and that modifiers affect the expression of the trait. Multiple alleles at the same locus, hereby designated asgec ^a for medium gel consistency andgec ^b for soft gel consistency, were recessive to the wild type allele for hard gel consistency andgec ^a was dominant overgec ^b. The results indicate that selection for desired gel consistency can effectively be done in early segregating generations.     

Arsenic toxicity to rice (Oryza sativa L.) in Bangladesh

Natural contamination of groundwater with arsenic (As) occurs around the world but is most widespread in the river basin deltas of South and Southeast Asia. Shallow groundwater is extensively used in the Bengal basin for irrigation of rice in the dry winter season, leading to the possibility of As accumulation in soils, toxicity to rice and increased levels of As in rice grain and straw. The impact of As contaminated irrigation water on soil-As content and rice productivity was studied over two winter-season rice crops in the command area of a single tubewell in Faridpur district, Bangladesh. After 16–17 years of use of the tubewell, a spatially variable build up of As and other chemical constituents of the water (Fe, Mn and P) was observed over the command area, with soil-As levels ranging from about 10 to 70 mg kg^?1. A simple mass balance calculation using the current water As level of 0.13 mg As L^?1 suggested that 96% of the added arsenic was retained in the soil. When BRRI dhan 29 rice was grown in two successive years across this soil-As gradient, yield declined progressively from 7–9 to 2–3 t ha^?1 with increasing soil-As concentration. The average yield loss over the 8 ha command area was estimated to be 16%. Rice-straw As content increased with increasing soil-As concentration; however, the toxicity of As to rice resulted in reduced grain-As concentrations in one of the 2 years. The likelihood of As-induced yield reductions and As accumulation in straw and grain has implications to agricultural sustainability, food quality and food security in As-affected regions throughout South and Southeast Asia.     

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.     

Plant regeneration from indica rice (Oryza sativa L.) protoplasts

Rice (Oryza sativa L.) plants of the indica cultivar IR54 were regenerated from protoplasts. Conditions were developed for isolating and purifying protoplasts from suspension cultures with protoplast yields ranging from 1·10⁶ to 15·10⁶ viable protoplasts/1 g fresh weight. Protoplast viability after purification was generally over 90%. Protoplasts were cultured in a slightly modified Kao medium in a Petri plate by placing them onto a Millipore filter positioned on top of a feeder (nurse) culture containing cells from a suspension culture of the japonica rice, Calrose 76. Plating efficiencies of protoplasts ranged from 0.5 to 3.0%; it was zero in the absence of the nurse culture. Protoplast preparations usually contained no contaminating cells, and when present, the number of cells never exceeded 0.1% of the protoplasts. After three weeks the Millipore filter with callus colonies were transferred off feeder cells and onto a Linsmaier and Skoog-type medium for an additional three weeks. Selected callus colonies that had embryo-like structures were then transferred to regeneration medium containing cytokinins, and regeneration frequencies up to 80% were obtained. Small shoots emerged and were transferred to jars for root development prior to transferring to pots of soil and growing the plants to maturity in growth chambers. Of the cytokinins evaluated, N⁶-benzylaminopurine was the most effective in promoting shoot formation; however, kinetin was also somewhat effective. Regeneration medium could be either an N₆ or Murashige and Skoog basal medium. Of 76 plants grown to maturity, 62 were fertile, and the plant heights averaged about three-fourths the height of seed-grown plants.Two other suspension cultures of IR54, one developed from the protoplast callus of the initial IR54 line, and the other developed from callus produced by mature seeds, have yielded protoplasts capable of regenerating plants when using cells of the Calrose 76 suspension as a nurse culture. In addition, protoplasts obtained from three-week-old primary callus of immature embryos of IR54 were capable of regenerating plants when using the same culture conditions.Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - pcy packed cell volume - BAP N⁶-benzylaminopurine - FDA fluorescein diacetate - FW fresh weight - IAA indole-3-acetic acid Media AA Muller and Grafe (1978) - CPW Frearson et al. (1973) - Kao^* Kao (1977) - LS Linsmaier and Skoog (1965) - MS Murashige and Skoog (1962) - N₆ Chu et al. (1975) - PCM Ludwig et al. (1985)     

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.     

Isozymic variability of traditional rice (Oryza sativa L.) in Africa

Summary Eight hundred and thirtyone traditional varieties of rice, Oryza sativa L., were collected in Africa and analysed for their isozymic variability on 15 enzymatic systems, representing 37 presumed loci. There appears to be a correlation between the type of rice growing and the two groups Indica and Japonica. The degree of genetic diversity is nearly equal in African rice and the Asian one. Alleles due to introgression or mutational events were identified. The results suggest that the evolution of O. sativa is continuous in Africa by means of inter-subspecific or inter-specific crosses.     

Phosphorylation upon cold stress in rice (Oryza sativa L.) seedlings

The response of plants to cold stress is not well understood at the biochemical level, although it has been studied extensively at the ecological level. To investigate whether protein phosphorylation may play an important role in cold stress, we exposed rice seedlings to low temperatures, prepared protein extracts from the leaves and incubated these in the presence of [γ-³²P]ATP. The proteins were then separated by two-dimensional polyacrylamide gel electrophoresis. While several proteins were found to be phosphorylated upon cold stress one protein, pp35, which has an isoelectric point of 8.0, was more phosphorylated than the others. The pp35 protein was found to be phosphorylated when rice seedlings were incubated for 6 h at 5°C before the leaf protein extract was prepared and radioactive labeling was performed. The pp35 was, however, significantly more phosphorylated in cold-tolerant rice varieties. Antibodies were raised against purified pp35 in adult rabbits. Using this pp35 antibody, which can recognize the RuBisCO large-chain subunit (LSU), and from amino acid sequencing of pp35, we were able to identify and confirm the pp35 protein as the fragment of RuBisCO LSU (EC 4.1.1.39). Phosphorylation of the RuBisCO LSU may be important in cold tolerance. Received: 7 July 1998 / Accepted: 19 December 1998     

Genetic analysis of plant regeneration in rice (Oryza sativa L.)

Summary A diallel study involving reciprocal crosses of four genotypes (IR8, 36, 54, and 64) was carried out to understand the genetic mechanism of plant regeneration from immature embryo-calli in rice. Regeneration frequency (% of calli that produced plants) varied from a high of 86% for IR54 to a low of 0% for IR36, while regenerated plants per embryo numbered from 0 to 7 when these same IR lines and the F₁ hybrids were compared. Combining ability analysis revealed that both nuclear (with both additive and dominant effects) and cytoplasmic genes are important in controlling regeneration in rice. Parental lines and F1 hybrids with high ability to regenerate were identified.