水稻耐淹涝性状的遗传分析和SSR标记的研究

淹涝胁迫对水稻生产造成了严重影响, 发掘可应用于耐淹涝辅助选择的分子标记(MAS), 将有助于水稻耐淹涝性状的遗传改良。应用耐淹涝材料FR13A和淹涝敏感材料IR39595-503-2-1-2为亲本做正反交获得F₁和F₂代群体。对正反交的F₁群体的耐淹涝性状进行遗传分析, 发现正反交的F₁代群体在耐淹涝性状上没有显著差异, 说明耐淹涝性状是核基因控制。从两次淹涝处理中F₂代群体的分离情况来看, 来源于FR13A的耐淹特性表现出数量-质量性状遗传的特点。当淹涝胁迫压力比较轻时表现为数量性状遗传, 具有微效多基因的作用。当淹涝胁迫压力增大时, 表现为主效基因控制的质量性状。在SSR分析中, 187对SSR引物中有73对引物在两亲本间有明显的差异, 差异率为39%。用这73对差异引物, 对F2群体进行多态筛选, 结果筛选到一个与耐淹涝性状连锁的标记RM219, 验证了耐淹涝性状确实由主效基因Sub1控制, 因此, RM219在水稻耐淹涝育种中具有利用价值。     

Physiological and Molecular Basis of Susceptibility and Tolerance of Rice Plants to Complete Submergence

Rice plants are much damaged by several days of total submergence.The effect can be a serious problem for rice farmers in therainfed lowlands of Asia, and runs contrary to a widespreadbelief amongst plant biologists that rice is highly tolerantof submergence. This article assesses the characteristics ofthe underwater environment that may damage rice plants, examinesvarious physiological mechanisms of injury, and reviews recentprogress achieved using linkage mapping to locate quantitativetraits loci (QTL) for tolerance inherited from a submergence-tolerantcultivar FR13A. Progress towards identifying the gene(s) involvedthrough physical mapping of a dominant tolerance locus on chromosome9 is also summarized. Available physiological evidence pointsaway from responses to oxygen shortage as being inextricablyinvolved in submergence injury. An imbalance between productionand consumption of assimilates is seen as being especially harmful,and is exacerbated by strongly accelerated leaf extension andleaf senescence that are ethylene-mediated and largely absentfrom FR13A and related cultivars. DNA markers for a major QTLfor tolerance are shown to be potentially useful in breedingprogrammes designed to improve submergence tolerance.     

Introgression of dual abiotic stress tolerance QTLs (Saltol QTL and Sub1 gene) into Rice (Oryza sativa L.) variety Aiswarya through marker assisted backcross breeding

Salinity and submergence are two very prominent abiotic stress conditions affecting rice yield adversely in the coastal agro ecosystem. Marker Assisted Backcross Breeding (MABB) is an efficient and fast track molecular tool to incorporate a desired stress tolerant QTL/gene into an improved cultivar. The present study was carried out for the introgression of Saltol QTL responsible for salinity tolerance and Sub1 gene responsible for submergence tolerance into the high yielding rice variety Aiswarya independently through MABB. Final objective of the study is to develop dual stress tolerant (tolerance to salinity and submergence) Aiswarya rice variety by pyramiding the both target QTLs introgressed BC₂F₂ progenies having maximum background homozygosity. The donors of Saltol QTL and Sub1 gene used in the present study were FL478 and Swarna Sub1, respectively. Based on the background genome analysis of the introgressed plants, the plants with > 85–90% background similarity were selected for pyramiding of Saltol QTL and Sub1 gene into the elite background of rice variety Aiswarya. Those selected introgressed lines with Saltol QTL and Sub1 gene will be again crossed to pyramid both Saltol QTL and Sub1 gene into the rice variety Aiswarya. Such a mega rice variety pyramided with dual stress tolerant QTLs is the expected outcome of this study and can be recommended for cultivation in the flood prone saline coastal agroecosystem.     

Recent Advances of Genetic Resources,Genes and Genetic Approaches for Flooding Tolerance in Rice

Flooding is one of the most hazardous natural disasters and a major stress constraint to rice production throughout the world, which results in huge economic losses. The frequency and duration of flooding is predicted to increase in near future as a result of global climate change. Breeding of flooding tolerance in rice is a challenging task because of the complexity of the component traits, screening technique, environmental factors and genetic interactions. A great progress has been made during last two decades to find out the flooding tolerance mechanism in rice. An important breakthrough in submergence research was achieved by the identification of major quantitative trait locus (QTL) SUB1 in rice chromosomes that acts as the primary contributor for tolerance. This enabled the use of marker-assisted backcrossing (MABC) to transfer SUB1 QTL into popular varieties which showed yield advantages in flood prone areas. However, SUB1 varieties are not always tolerant to stagnant flooding and flooding during germination stage. So, gene pyramiding approach can be used by combining several important traits to develop new breeding rice lines that confer tolerances to different types of flooding. This review highlights the important germplasm/genetic resources of rice to different types of flooding stress. A brief discussion on the genes and genetic mechanism in rice exhibited to different types of flooding tolerance was discussed for the development of flood tolerant rice variety. Further research on developing multiple stresses tolerant rice can be achieved by combining SUB1 with other tolerance traits/genes for wider adaptation in the rain-fed rice ecosystems.     

水稻的耐淹性状及其Sub1基因

近4年来, 水稻(Oryza sativa L.)耐淹性状及其分子机理的研究取得了长足的进展。水稻植株的耐淹性状主要由Submergence-1 (Sub1) 基因控制。Sub1通过调节乙烯和赤霉素介导的反应, 抑制淹水期间的伸长生长和减缓碳水化合物消耗来控制耐淹性状。文章介绍了水稻应对淹涝胁迫的两种策略, 影响耐淹性状的主要生理因素, Sub1基因定位以及它控制耐淹性状的机理; 阐述了Sub1基因在我国杂交水稻生产方面的应用前景。     

Molecular and Physiological Mechanisms of Flooding Avoidance and Tolerance in Rice

Submergence is one of the major constraints in rice production. The main factor limiting rice survival during submergence is oxygen deprivation. To cope with flooding conditions, rice has developed two survival strategies: either rapid elongation of the submerged tissues to keep up with the rising water level or no elongation to save carbohydrate resources for maintenance of energy production under submerged and concomitant hypoxic conditions. The survival strategies used by rice have been studied quite extensively and the role of several phytohormones in the elongation response has been established. The mechanisms of submergence tolerance include metabolic changes, for instance, the shift to an ethanolic fermentation pathway, reduced elongation growth to save carbohydrates and energy for maintenance processes, and protective antioxidant systems. Current molecular technology can provide tools for the understanding of mechanisms developed by rice to survive submergence. In addition, cloning of genes related to submergence tolerance might open new ways to genetic improvement of this crop.     

Genes/QTLs affecting flood tolerance in rice

The adaptation of deepwater rice to flooding is attributed to two mechanisms, submergence tolerance and plant elongation. Using a QTL mapping study with replicated phenotyping under two contrasting (water qualities) submergence treatments and AFLP markers, we were able to identify several genes/QTLs that control plant elongation and submergence tolerance in a recombinant inbred rice population. Our results indicate that segregation of rice plants in their responses to different flooding stress conditions is largely due to the differential expression of a few key elongation and submergence tolerance genes. The most important gene was QIne1 mapped near sd-1 on chromosome 1. The Jalmagna (the deepwater parent) allele at this locus had a very large effect on internal elongation and contributed significantly to submergence tolerance under flooding. The second locus was a major gene, sub1(t), mapped to chromosome 9, which contributed to submergence tolerance only. The third one was a QTL, QIne4, mapped to chromosome 4. The IR74 (non-elongating parent) allele at this locus had a large effect for internal elongation. An additional locus that interacted strongly with both QIne1 and QIne4 appeared near RG403 on chromosome 5, suggesting a complex epistatic relationship among the three loci. Several QTLs with relatively small effects on plant elongation and submergence tolerance were also identified. The genetic aspects of these flooding tolerance QTLs with respect to patterns of differential expression of elongation and submergence tolerance genes under flooding are discussed. Received: 13 December 1999 / Accepted: 14 March 2000<@head-com-p1a.lf>Communicated by G. Wenzel     

Molecular Genetics of Submergence Tolerance in Rice: QTL Analysis of Key Traits

Flash flooding of young rice plants is a common problem forrice farmers in south and south-east Asia. It severely reducesgrain yield and increases the unpredictability of cropping.The inheritance and expression of traits associated with submergencestress tolerance at the seedling stage are physiologically andgenetically complex. We exploited naturally occurring differencesbetween certain rice lines in their tolerance to submergenceand used quantitative trait loci (QTL) mapping to improve understandingof the genetic and physiological basis of submergence tolerance.Three rice populations, each derived from a single cross betweentwo cultivars differing in their response to submergence, wereused to identify QTL associated with plant survival and variouslinked traits. These included total shoot elongation under water,the extent of stimulation of shoot elongation caused by submergence,a visual submergence tolerance score, and leaf senescence underdifferent field conditions, locations and years. Several majorQTL determining plant survival, plant height, stimulation ofshoot elongation, visual tolerance score and leaf senescenceeach mapped to the same locus on chromosome 9. These QTL weredetected consistently in experiments across all years and inthe genetic backgrounds of all three mapping populations. SecondaryQTL influencing tolerance were also identified and located onchromosomes 1, 2, 5, 7, 10 and 11. These QTL were specific toparticular traits, environments, or genetic backgrounds. Allidentified QTL contributed to increased submergence tolerancethrough their effects on decreased underwater shoot elongationor increased maintenance of chlorophyll levels, or on both.These findings establish the foundations of a marker-assistedscheme for introducing submergence tolerance into agriculturallydesirable cultivars of rice.     

Marker-assisted breeding of Chinese elite rice cultivar 9311 for disease resistance to rice blast and bacterial blight and tolerance to submergence

Rice (Oryza sativa L.) is the staple food crop for more than half of the world’s population. The development of hybrid rice is a practical approach to increase rice production. However, rice production was frequently affected by biotic and abiotic stresses. Rice blast and bacterial blight are two major diseases in rice growing regions. Rice plantation is also frequently affected by short-term submergence or seasonal floods in wet seasons and drought in dry seasons. The utilization of natural disease resistance (R) genes and stress tolerance genes in rice breeding is the most economic and efficient way to combat or adapt to these biotic and abiotic stresses. Rice cultivar 9311 is widely planted rice variety, either as inbred rice or the paternal line of two-line hybrid rice. Here, we report the pyramiding of rice blast R gene Pi9, bacterial blight R genes Xa21 and Xa27, and submergence tolerance gene Sub1A in 9311 genetic background through backcrossing and marker-assisted selection. The improved rice line, designated as 49311, theoretically possesses 99.2% genetic background of 9311. 49311 and its hybrid rice, GZ63S/49311, conferred disease resistance to rice blast and bacterial blight and showed tolerance to submergence for over 18 days without significant loss of viability. 49311 and its hybrids had similar agronomic traits and grain quality to 9311 and the control hybrid rice, respectively. The development of 49311 provides an improved paternal line for two-line hybrid rice production with disease resistance to rice blast and bacterial blight and tolerance to submergence.     

Mapping QTLs for submergence tolerance in rice using a population fixed for <Emphasis Type="Italic">SUB1A</Emphasis> tolerant allele

Submergence is a widespread problem of rice production, especially in low-lying areas in South and Southeast Asia. Despite the success of Sub1 mega varieties, repeated instances of prolonged and severe flooding in stress-prone areas suggests that the SUB1 gene is no longer sufficient in those regions and requires improved varieties with increased tolerance. A study was conducted to identify quantitative trait loci (QTLs) associated with submergence tolerance using 115 F₇ recombinant inbred lines (RILs) derived from the cross of Ciherang-Sub1, a popular Indonesian cultivar carrying the SUB1 gene that has relatively higher tolerance to submergence compared to the performance of most other Sub1 lines and the submergence and stagnant flooding tolerant IR10F365. As the tolerant allele at SUB1A on chromosome 9 was fixed in this mapping population, additional QTLs responsible for submergence tolerance were expected to be revealed. Genotyping with an Infinium 6K SNP chip resulted in 469 polymorphic markers that were then used for QTL mapping. Phenotyping was performed under complete submergence with two replicates. A major QTL for submergence derived from Ciherang-Sub1, named qSUB8.1, was detected on chromosome 8 with a LOD score of 10.3 and phenotypic variance of 27.5%. Additionally, a smaller QTL, also derived from Ciherang-Sub1, was detected on chromosome 2 with a LOD score of 3.5 and phenotypic variance of 12.7%. There was no digenic interaction detected between these QTLs suggesting their independent action. The QTLs detected in this study can be used in marker-assisted selection to further improve the tolerance of other Sub1 varieties.     

Genome-Wide Identification of DUF26 Domain-Containing Genes in Dongxiang Wild Rice and Analysis of Their Expression Responses under Submergence

The DUF26 domain-containing protein is an extracellular structural protein, which plays an important role in signal transduction. Dongxiang wild rice (Oryza rufipogon Griff.) is the northern-most common wild rice in China. Using domain analysis, 85 DUF26 domain-containing genes were identified in Dongxiang wild rice (DXWR) and further divided into four categories. The DUF26 domain-containing genes were unevenly distributed on chromosomes, and there were 18 pairs of tandem repeats. Gene sequence analysis showed that there were significant differences in the gene structure and motif distribution of the DUF26 domain in different categories. Motifs 3, 8, 9, 13, 14, 16, and 18 were highly conserved in all categories. It was also found that there were eight plasmodesmata localization proteins (PDLPs) with a unique motif 19. Collinearity analysis showed that DXWR had a large number of orthologous genes with wheat, maize, sorghum and zizania, of which 17 DUF26 domain-containing genes were conserved in five gramineous crops. Under the stress of anaerobic germination and seedling submergence treatment, 33 DUF26 domain-containing genes were differentially expressed in varying degrees. Further correlation analysis with the expression of known submergence tolerance genes showed that these DUF26 domain-containing genes may jointly regulate the submergence tolerance process with these known submergence tolerance genes in DXWR.     

Submergence tolerance of rice – A new glasshouse method for the experimental submergence of plants

A new method is described for evaluation of submergence tolerance of rice ( Oryza sativa L.) plants. Responses of a range of cultivars corresponded with known differences in field performance. The method 1) allows fast and effective determination of submergence tolerance, 2) allows screening of many plants in a small glasshouse area, 3) provides for recovery of superior plants for seed collection, 4) allows manipulation of many environmental variables to mimic the natural submergence environment, and 5) uses simple, inexpensive, readily available equipment. Physiological studies performed with this method gave results similar to those obtained from field studies and showed that submergence tolerance increased in older plants; it decreased with increasing depth, increasing temperature and with high or low light levels. The system is ideal for the rapid evaluation of rice germplasm under controlled conditions and physiological studies on the mechanism of rice submergence tolerance.     

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.     

Responses of the antioxidative enzymes in Malaysian rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) cultivars under submergence condition

The potential involvement of activated oxygen species by submergence stress was studied in two Malaysian rice cultivars, MR219-4 and MR219-9, and cultivar FR13A that is known to be tolerant to submergence. Seedlings of these three rice cultivars were subjected to different submergence periods (4, 8, and 12 days). Under 8 days of complete submergence, FR13A cultivar showed higher lipid peroxidation in terms of malondialdehyde level and activities of antioxidative enzymes, superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR) when compared to the MR219-4 and MR219-9 cultivars. MR219-9 showed higher SOD, APX, and GR activities after 12 days of submergence. The levels of SOD activity indicated that detoxification of O₂^·− to H₂O₂ was maintained at a stable level throughout the submergence stress until up to 8 days and increased rapidly at 12 days of submergence. The results indicated that tolerance to submergence in rice is associated until 8 days submergence for MR219-4 and FR13A cultivars. These findings suggested that tolerance to submergence stress in rice might be proven by increased the capacity of antioxidative system. In addition, CAT activity has much higher affinity for scavenges H₂O₂ than APX. Therefore, ascorbate glutathione cycle might be more efficient to scavenge H₂O₂.     

Submergence tolerance in relation to variable floodwater conditions in rice

Flash floods adversely affect rice productivity in vast areas of rainfed lowlands in South and Southeast Asia and tropical Africa. Tolerant landraces that withstand submergence for 1–2 weeks were identified; however, incorporation of tolerance into modern high-yielding varieties through conventional breeding methods has been slow because of the complexity of both the tolerance phenotype and floodwater conditions, and the ensuing discrepancies encountered upon phenotyping in different environments. Designing an effective phenotyping strategy requires a thorough understanding of the specific floodwater characteristics that most likely affect survival during flooding. We investigated the implications of floodwater temperature and light penetration, caused by artificial shading, seasonal variation, or water turbidity, for seedling survival after submergence. Three field experiments were conducted using rice genotypes contrasting in their tolerance of submergence: FR13A and Kusuma (tolerant); Gangasiuli (intermediate); Sabita, CRK-2-6 and Raghukunwar (elongating/avoiding types); and IR42 (sensitive). We tested the hypotheses that warmer floodwater decreases plant survival and that turbid water augment plant mortality by causing effects similar to those caused by shading, by reducing light penetration. Plants survive better when water is cooler, and survival decreased at about 8% per unit increase in water temperature above 26 °C. Lower intensity of light and warmer temperatures seem to reduce biomass and increase mortality under flooding. An increase in the concentrations of O₂ and CO₂ and a decrease in water pH did not improve survival in clear unshaded water. Turbid floodwater was more damaging to rice as plant mortality increased as the percentage of silt increased, and the effects of water turbidity cannot be explained by the reduction in light penetration alone. Even the most tolerant rice cultivar, FR13A, experienced higher mortality when flooded with turbid floodwater. Correlation studies revealed that cultivars with the capacity to maintain higher biomass, higher chlorophyll, and non-structural carbohydrate concentrations after submergence had higher survival. These findings help to understand the variation observed in submergence tolerance when screening is done under different environments. The study could have implications for designing proper screening strategies and assessing the damage submergence causes across different rice-growing regions.     

The beneficial effect of reduced elongation growth on submergence tolerance of rice

Adverse effects of elongation growth on tolerance to completesubmergence for up to 14 d were evaluated in rice seedlingsof cultivars which differed in submergence tolerance. Thereis a good negative correlation between per cent survival andelongation growth of genotypes during complete submergence (r= – 0.81). When elongation growth underwater is minimizedby application of a gibberellin biosynthesis inhibitor, percent survival increases by as much as 50 times for one cultivar.These effects are likely related to elongation growth since(i) addition of gibberellin had the opposite effect by reducingsurvival, and (ii) when the elongation inhibitor and gibberellinwere added together, there was no effect on elongation growthand the per cent survival did not change. A GA-deficient mutantof rice which had little elongation ability during submergenceshowed a high level of submergence tolerance when plants weresubmerged at equal initial dry weights and carbohydrate levelsrelative to a submergence-tolerant cultivar. These results areconsistent with the hypothesis that elongation growth competeswith maintenance processes for energy and hence reduces survivalduring submergence. The impact of these findings is that inenvironments where elongation ability is not required, thereis a potential to increase submergence tolerance of agriculturallyimportant cultivars by selecting for least elongation, at leastduring periods of complete submergence. Furthermore, this trade-offbetween stimulated elongation growth and submergence tolerancewill have important ecological consequences for the distributionof plant species in different flood-prone environments. Key words: Gibberellin, growth, Oryza sativa, rice, submergence