Rice alcohol dehydrogenase 1 promotes survival and has a major impact on carbohydrate metabolism in the embryo and endosperm when seeds are germinated in partially oxygenated water

Background and Aims

Rice (Oryza sativa) has the rare ability to germinate and elongate a coleoptile under oxygen-deficient conditions, which include both hypoxia and anoxia. It has previously been shown that ALCOHOL DEHYDROGENASE 1 (ADH1) is required for cell division and cell elongation in the coleoptile of submerged rice seedlings by means of studies using a rice ADH1-deficient mutant, reduced adh activity (rad). The aim of this study was to understand how low ADH1 in rice affects carbohydrate metabolism in the embryo and endosperm, and lactate and alanine synthesis in the embryo during germination and subsequent coleoptile growth in submerged seedlings.

Methods

Wild-type and rad mutant rice seeds were germinated and grown under complete submergence. At 1, 3, 5 and 7 d after imbibition, the embryo and endosperm were separated and several of their metabolites were measured and compared.

Key results

In the rad embryo, the rate of ethanol fermentation was halved, while lactate and alanine concentrations were 2·4- and 5·7- fold higher in the mutant than in the wild type. Glucose and fructose concentrations in the embryos increased with time in the wild type, but not in the rad mutant. The rad mutant endosperm had lower amounts of the α-amylases RAMY1A and RAMY3D, resulting in less starch degradation and lower glucose concentrations.

Conclusions

These results suggest that ADH1 is essential for sugar metabolism via glycolysis to ethanol fermentation in both the embryo and endosperm. In the endosperm, energy is presumably needed for synthesis of the amylases and for sucrose synthesis in the endosperm, as well as for sugar transport to the embryo.     

Comparative analysis of anoxic coleoptile elongation in rice varieties: relationship between coleoptile length and carbohydrate levels, fermentative metabolism and anaerobic gene expression

Rice ( Oryza sativa L.) seeds can germinate under anoxia and can show coleoptile elongation. The anoxic coleoptile is usually longer than aerobic coleoptiles. Although several hypotheses have been proposed to explain the ability of rice to elongate coleoptiles under anoxia, conclusive experimental evidence explaining this physiological trait is lacking. In order to investigate whether metabolic and molecular markers correlate with anoxic coleoptile length, we screened 141 Italian and 23 Sri Lankan rice cultivars for their ability to elongate coleoptiles under anoxia. Differences in anoxic coleoptile length were used to evaluate whether a correlation exists between coleoptile length and biochemical and molecular parameters. The expression of genes coding for glycolytic and fermentative enzymes showed a very low correlation with anoxic coleoptile length. Although differences were found in carbohydrate content between the varieties tested, this parameter also does not appear to be critical in terms of coleoptile elongation. Efficient ethanol fermentation does, however, correlate well with the elongation of coleoptiles under anoxic conditions.     

Expression of α-expansin genes in young seedlings of rice (Oryza sativa L.)

 Rice is the only cereal in which germination and coleoptile elongation occur in hypoxia or anoxia. Little is known of the molecular basis directly underlying coleoptile cell extension. In this paper, we describe the expression of α-expansin genes in embryos during seed development and young seedlings grown under various oxygen concentrations. The genes Os-EXP2 and Os-EXP1 were predominantly expressed in the developing seeds, mainly in newly developed leaves, coleoptiles, and seminal roots. These expansins expressed in the developing seeds may give cells the potential to expand after seed imbibition begins. In coleoptiles, Os-EXP4 and Os-EXP2 mRNAs were greatly induced by submergence, while they were weakly detected in aerobic or anoxic conditions. Under submerged soil conditions, the signals hybridized with probes Os-EXP4 and Os-EXP2 in coleoptiles were strongest when coleoptiles elongated in the water layer. These data show that expansin gene expression is highly correlated with coleoptile elongation in response to oxygen concentrations. The Os-EXP4 gene was also expressed in leaves, mesocotyls, and coleorhizas of young seedlings. The growth of these tissues was also correlated with the presence of expansins. Therefore, the evidence derived from this study clearly demonstrates that expansins are indispensable for the growing tissues of rice seedlings. Received: 23 December 1999 / Accepted: 24 February 2000     

Preferential Induction of Alcohol Dehydrogenase in Coleoptiles of Rice Seedlings Germinated in Submergence Condition

Difference in the growth response to submergence between coleoptiles and roots of rice (Oryza sativa L.) was investigated in 9-d-old rice seedlings. The coleoptile length in the submergence condition was much greater than that in aerobic condition, whereas the root length in the submergence condition was less than that in the aerobic condition. Alcohol dehydrogenase (ADH) activity in the coleoptiles in the submergence condition was much greater than that in the aerobic condition, but ADH activity in the roots in the submergence condition increased slightly. These results suggest that the preferential ADH induction in rice seedlings may contribute to the difference in the growth response between the coleoptiles and roots under low oxygen conditions.     

Single-seeded InDel fingerprints in rice:An effective tool for indica-japonica rice classification and evolutionary studies

Asian cultivated rice(Oryza sativa L.),an important cereal crop worldwide,was domesticated from its wild ancestor 8000 years ago.During its long-term cultivation and evolution under diverse agroecological conditions, Asian cultivated rice has differentiated into indica and japonica subspecies.An effective method is required to identify rice germplasm for its indica and japonica features,which is essential in rice genetic improvements.We developed a protocol that combined DNA extraction from a single rice seed and the insertion/deletion(InDel) molecular fingerprint to determine the indica and japonica features of rice germplasm.We analyzed a set of rice germplasm,including 166 Asian rice varieties,two African rice varieties,30 accessions of wild rice species,and 42 weedy rice accessions,using the single-seeded InDel fingerprints(SSIF).The results show that the SSIF method can efficiently determine the indica and japonica features of the rice germplasm.Further analyses revealed significant indica and japonica differentiation in most Asian rice varieties and weedy rice accessions.In contrast,African rice varieties and nearly all the wild rice accessions did not exhibit such differentiation.The pattern of cultivated and wild rice samples illustrated by the SSIF supports our previous hypothesis that indica and japonica differentiation occurred after rice domestication under different agroecological conditions.In addition,the divergent pattern of rice cultivars and weedy rice accessions suggests the possibility of an endoferal origin(from crop)of the weedy rice included in the present study.     

Analysis of the Growth Response of Air-Grown Rice Coleoptiles to Submergence

The effect of submergence of air-grown rice seedlings (Oryza sativa L. var. Sasanishiki) on coleoptile growth and ultrastructure, extensibility and chemical composition of the cell walls was investigated. The lag-time between start of submergence and the onset of the enhancement of growth was less than 4 h. The growth response was associated with a drastic thinning of the cell walls and an increase in wall extensibility. At the outer epidermal wall of both air-grown and submerged coleoptiles electron-dense (osmiophilic) particles were detected. During submergence, the net accumulation of cellulose and hemicellulose was reduced, but the increase in pectic substances was unaffected. Submergence caused an 80% inhibition of the net accumulation of wall-bound phenolics (ferulic- and diferulic acid) compared with air-grown controls. The osmotic concentration of the tissue saps was not affected by submergence. Our results support the hypothesis that rapid coleoptile elongation under water is caused by an inhibition of the formation of phenolic cross-links between matrix polysaccharides via diferulate, which results in a mechanical stiffening of the cell walls in the air-grown coleoptile.     

Echinochloa crus‐galli seed physiological dormancy and germination responses to hypoxic floodwaters

• Hypoxic floodwaters can seriously damage seedlings. Seed dormancy could be an effective trait to avoid lethal underwater germination. This research aimed to discover novel adaptive dormancy responses to hypoxic floodwaters in seeds of Echinochloa crus‐galli, a noxious weed from rice fields and lowland croplands.
• Echinochloa crus‐galli dormant seeds were subjected to a series of sequential treatments. Seeds were: (i) submerged under hypoxic floodwater (simulated with hypoxic flasks) at different temperatures for 15 or 30 days, and germination tested under drained conditions while exposing seeds to dormancy‐breaking signals (alternating temperatures, nitrate (KNO₃), light); or (ii) exposed to dormancy‐breaking signals during hypoxic submergence, and germination monitored during incubation and after transfer to drained conditions.
• Echinochloa crus‐galli seed primary dormancy was attenuated under hypoxic submergence but to a lesser extent than under drained conditions. Hypoxic floodwater did not reinforced dormancy but hindered secondary dormancy induction in warm temperatures. Seeds did not germinate under hypoxic submergence even when subjected to dormancy‐breaking signals; however, these signals broke dormancy in seeds submerged under normoxic water. Seeds submerged in hypoxic water could sense light through phytochrome signals and germinated when normoxic conditions were regained.
• Hypoxic floodwaters interfere with E. crus‐galli seed seasonal dormancy changes. Dormancy‐breaking signals are overridden during hypoxic floods, drastically decreasing underwater germination. In addition, results indicate that a fraction of E. crus‐galli seeds perceive dormancy‐breaking signals under hypoxic water and germinate immediately after aerobic conditions are regained, a hazardous yet less competitive environment for establishment.

     

New insights into the genetic basis of natural chilling and cold shock tolerance in rice by genome‐wide association analysis

In order to understand cold adaptability and explore additional genetic resources for the cold tolerance improvement of rice, we investigated the genetic variation of 529 rice accessions under natural chilling and cold shock stress conditions at the seedling stage using genome‐wide association studies; a total of 132 loci were identified. Among them, 12 loci were common for both chilling and cold shock tolerance, suggesting that rice has a distinct and overlapping genetic response and adaptation to the two stresses. Haplotype analysis of a known gene OsMYB2, which is involved in cold tolerance, revealed indica–japonica differentiation and latitude tendency for the haplotypes of this gene. By checking the subpopulation and geographical distribution of accessions with tolerance or sensitivity under these two stress conditions, we found that the chilling tolerance group, which mainly consisted of japonica accessions, has a wider latitudinal distribution than the chilling sensitivity group. We conclude that the genetic basis of natural chilling stress tolerance in rice is distinct from that of cold shock stress frequently used for low‐temperature treatment in the laboratory and the cold adaptability of rice is associated with the subpopulation and latitudinal distribution.     

SUB1A‐dependent and ‐independent mechanisms are involved in the flooding tolerance of wild rice species

Crop tolerance to flooding is an important agronomic trait. Although rice (Oryza sativa) is considered a flood‐tolerant crop, only limited cultivars display tolerance to prolonged submergence, which is largely attributed to the presence of the SUB1A gene. Wild Oryza species have the potential to unveil adaptive mechanisms and shed light on the basis of submergence tolerance traits. In this study, we screened 109 Oryza genotypes belonging to different rice genome groups for flooding tolerance. Oryza nivara and Oryza rufipogon accessions, belonging to the A‐genome group, together with Oryza sativa, showed a wide range of submergence responses, and the tolerance‐related SUB1A‐1 and the intolerance‐related SUB1A‐2 alleles were found in tolerant and sensitive accessions, respectively. Flooding‐tolerant accessions of Oryza rhizomatis and Oryza eichingeri, belonging to the C‐genome group, were also identified. Interestingly, SUB1A was absent in these species, which possess a SUB1 orthologue with high similarity to O. sativa SUB1C. The expression patterns of submergence‐induced genes in these rice genotypes indicated limited induction of anaerobic genes, with classical anaerobic proteins poorly induced in O. rhizomatis under submergence. The results indicated that SUB1A‐1 is not essential to confer submergence tolerance in the wild rice genotypes belonging to the C‐genome group, which show instead a SUB1A‐independent response to submergence.     

Mobilization of Starch after Submergence of Air-Grown Rice Coleoptiles. Implications for Growth and Gravitropism

Submergence of air-grown rice seedlings (Oryza sativa L. var. Sasanishiki) induces elongation of the coleoptile. We investigated whether rapid underwater extension is associated with a loss of starch. After 1 d of submergence the starch content was reduced by 70%. This loss of reserve carbohydrate was accompanied by a 38% increase in the concentration of glucose in the cell sap of the coleoptiles. The submerged (starch-depleted) coleoptiles had a slower negative gravitropism than the air-grown controls, although the rate of elongation in the horizontal position was not impaired. We conclude that the submergence-induced mobilization of starch provides substrates and osmotica for the rapidly growing cells. In addition, our results indicate that a full complement of starch is necessary for normal gravitropism in the rice coleoptile.     

Proteomic identification of differentially expressed proteins in the anoxic rice coleoptile

Rice is the staple food for more than fifty percent of the world's population, and is therefore an important crop. However, its production is hindered by several biotic and abiotic stresses. Although rice is the only crop that can germinate even in the complete absence of oxygen (i.e. anoxia), flooding (low oxygen) is one of the major causes of reduced rice production. Rice germination under anoxia is characterized by the elongation of the coleoptile, but leaf growth is hampered. In this work, a comparative proteomic approach was used to detect and identify differentially expressed proteins in the anoxic rice coleoptile compared to the aerobic coleoptile. Thirty-one spots were successfully identified by MALDI-TOF MS analysis. The majority of the identified proteins were related to stress responses and redox metabolism. The expression levels of twenty-three proteins and their respective mRNAs were analyzed in a time course experiment.     

Integration of genomic tools to assist breeding in the <Emphasis Type="Italic">japonica</Emphasis> subspecies of rice

The cultivated rice (Oryza sativa L.) has two subspecies, indica and japonica. The japonica rice germplasm has a narrower genetic diversity compared to the indica subspecies. Rice breeders aim to develop new varieties with a higher yield potential, with enhanced resistances to biotic and abiotic stresses, and improved adaptation to environmental changes. In order to face some of these challenges, japonica rice germplasm will have to be diversified and new breeding strategies developed. Indica rice improvement could also profit from more “genepool mingling” for which japonica rice could play an important role. Interesting traits such as low-temperature tolerance, and wider climate adaptation could be introgressed into the indica subspecies. In the past decade, huge developments in rice genomics have expanded our available knowledge on this crop and it is now time to use these technologies for improving and accelerating rice breeding research. With the full sequence of the rice genome, breeders may take advantage of new genes. Also new genes may be discovered from the genepool of wild relatives, or landraces of the genus Oryza, and incorporated into elite japonica cultivars in a kind of “gene revolution” program. Expectedly, new technologies that are currently being optimized, aiming for novel gene discovery or for tracking the regions under selection, will be suggested as new breeding approaches. This paper revisits breeding strategies successfully employed in indica rice, and discusses their application in japonica rice improvement (e.g. ideotype breeding, wide hybridization and hybrid performance).     

Germination and seedling growth under anaerobic conditions in Echinochloa crus-galli (barnyard grass)*

Abstract Although rice has long been recognized to be uniquely adapted for growth in low oxygen environments of flooded rice fields, rice weeds of the Echinochloa crus-galli complex appear to be at least as well specialized for germination and growth under such unusual biological conditions. Seeds of two varieties of E. crus-galli germinate and grow for prolonged periods in a totally oxygen-free environment. E. crus-galli germinates as well as rice (Oryza sativa) under a total nitrogen atmosphere and produces as large a seedling in spite of its much smaller seed size. Like rice, the seedlings of E. crus-galli are unpigmented, the primary leaves do not emerge from the coleoptile and no root growth occurs without oxygen. Of particular interest is the ultrastructure of mitochondria from anaerobically-grown seedlings. Mitochondrial profiles from the primary leaf of seedlings grown continuously in nitrogen are very similar to those grown aerobically. The size and shape of the mitochondria are similar and the cristae are numerous and normal in appearance. This is in sharp contrast to previous studies of other species which have reported that mitochondria were vesiculate and tended to lose their normal fine-structure after similar periods without oxygen. Finally, based on ultrastructure and ¹⁴C labeling studies, anaerobically-grown seedlings are highly active metabolically, which may explain, at least for E. crus-galli var. oryzicola, its ability to germinate and emerge from flooded rice fields.     

杂草稻叶绿体籼粳分化的多重PCR分析

通过分析籼稻93-11和粳稻培矮64S的叶绿体全基因组,优化和构建了籼粳分化的叶绿体分子标记ORF100和ORF29-TrnC^GCA的多重PCR。应用这个多重PCR对200余份世界各地杂草稻和其它水稻材料进行分析。结果表明:杂草稻中有明显的叶绿体籼粳分化,表现出明显的地域性,且与传统的中国栽培稻的南籼北粳能较好的对应。推测粳型杂草稻可能是栽培稻突变或粳型水稻(作母本)与其它类型水稻材料杂交而形成的。     

Studies on the growth of rice tissue under submerged condition. I. The effect of 2,4-dichlorophenoxyacetic acid on excised segments of coleoptiles under submergence

Summary The work presented deals with the fact that rice coleoptiles elongate more rapidly and more extensively under water than in air.Coleoptile segments of rice were cultured under submerged condition as well as under floating condition. On application of 2,4-D a sharp and significant increase in growth in elongation was recorded.At higher concentrations e. g., 100 and 10 p. p. m. the growth rate was higher in floating segments of coleoptiles. But at lower concentrations, including control, the growth rate was higher in submerged ones, which apparently indicates that the optimum concentration of 2,4-D for growth of rice coleoptile is shifted with shifting of oxygen tension. Three different mutually opposing factors namely, lowered auxin destruction under submergence, concentration of auxin in the plant tissue and lowered aerobic respiration have been stated to be responsible for growth of rice tissue under water.At the end we offer our sincere thanks to Dr. P. K.Sen, Khaira Professor and Head of the Department of Agriculture, University of Calcutta for granting all facilities to complete this investigation.