Ethylene production is associated with germination but not seed dormancy in red rice

BACKGROUND AND AIMS: The relationship between ethylene production and both seed dormancy and germination was investigated using red rice (weedy rice) as a model species. METHODS: Both fully dormant and after-ripened (non-dormant) naked caryopses were incubated with or without inhibitors of ethylene synthesis [aminoethoxyvinylglycine (AVG)] and perception [silver thiosulfate (STS)], or in the presence of the natural ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC). The kinetics of ethylene emissions were measured with a sensitive laser-photoacoustic system. KEY RESULTS: Dormant red rice caryopses did not produce ethylene. In non-dormant caryopses, ethylene evolution never preceded the first visible stage of germination (pericarp splitting), and ethylene inhibitors completely blocked ethylene production, but not pericarp splitting. Accordingly, endogenous ACC appeared to be lacking before pericarp splitting. However, early seedling growth (radicle or coleoptile attaining the length of 1 mm) followed ethylene evolution and was delayed by the inhibitors. Wounding the dormant caryopses induced them to germinate and produce ethylene, but their germination was slow and pericarp splitting could be speeded up by ethylene. CONCLUSIONS: The findings suggest that, in red rice, endogenous ethylene stimulates the growth of the nascent seedling, but does not affect seed dormancy or germination inception. Correspondingly, this phytohormone does not play a role in the dormancy breakage induced by wounding, but accelerates germination after such breakage has occurred.     

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.     

Soil burial induced dormancy in weedy rice seeds through hormone level changes: Implications in adaptive evolution and weed control

Seed dormancy plays a key role in preventing seeds of higher plants from random germination under adverse environmental conditions. Previous studies suggested that a critical temperature could regulate germination of weedy rice seeds without primary dormancy at seed dispersion. However, what will happen to the non-dormant seeds after shattering in the soil seed banks when temperature fluctuates to exceed the critical temperature remains an interesting question to be investigated. To determine whether or not soil burial can change the status of dormancy in weedy rice seeds, we examined germination ratios of weedy rice seeds after soil-burial treatments. In addition, we compared hormone levels in the untreated seeds and viable but ungerminated seeds after soil burial. Results showed that soil burial induced a proportion of 41%–72% dormant seeds in the initially non-dormant weedy rice seeds. Also, the induction of seed dormancy is associated with the change of hormone levels in the seeds treated by soil burial, suggesting that soil burial can significantly activate the control of hormone production in seeds. Together, the previously reported mechanism of critical temperature-inhibited seed germination and the newly found phenomenon of soil burial-induced seed dormancy provide a “double-security” strategy to ensure germination of weedy rice seeds under a favorable condition in agricultural ecosystems. The findings not only reveal the important role of rapid evolution of adaptive functions in weeds, such as weedy rice, in adapting to changing agricultural environments, but also facilitate the design of strategies for effective weedy rice control practices.     

No effect of transgene and strong wild parent effects on seed dormancy in crop–wild hybrids of rice: implications for transgene persistence in wild populations

Soil seed banks act as a gene pool for local plant species and, as such, can buffer local populations, especially those experiencing challenging environmental conditions. Seed dormancy has important implications to dynamics of soil seed banks. Therefore, estimating the seed dormancy of transgenic crop–wild hybrids could shed light on the persistence of transgenes in wild‐plant soil seed banks. Individuals from eight populations of wild rice Oryza rufipogon were crossed with those of three insect‐resistant transgenic rice lines. Selfed (F2–F4) and backcrossed populations (BC1, BC1F2 and BC1F3) were then made from the hybrids. Seed germination was tested under three treatments: (a) normal; (b) overwintering in soil; and (c) one‐week heat‐shocking. The effects of transgene, wild parent and hybrid generation on hybrid seed germination were examined. No significant effect of insect‐resistant transgenes (Bt and CpTI) was detected on the seed dormancy of crop–wild hybrids, while a significant wild parent effect was found. The seeds of advanced generation hybrids have higher germination percentages and lower dormancy than do those of F1 and BC1 generations. The study showed that the dormancy of hybrid seeds was determined mainly by their genetic backgrounds. All hybrid seeds have higher germination percentages and lower dormancy (and, consequently, a poorer overwintering ability), compared with wild seeds, and reduce dormancy would contribute to a fitness disadvantage, compared with wild types. Therefore, such seeds might form part of naturally occurring soil seed banks, through which crop genes would persist in wild populations.     

Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice （Oryza rufipogon L.） in relation to the domestication of cultivated rice （O. sativa L.）

It is generally accepted that Oryza rufipogon is the progenitor of Asian cultivated rice （O. sativa）. However, how the two subspecies of O. sativa （indica and japonica） were domesticated has long been debated. To investigate the genetic differentiation in O. rufipogon in relation to the domestication of O. sativa, we developed 57 subspecies-specific intron length polymorphism （SSILP） markers by comparison between 10 indica cultivars and 10 japonica cultivars and defined a standard indica rice and a standard japonica rice based on these SSILP markers. Using these SSILP markers to genotype 73 O. rufipogon accessions, we found that the indica alleles and japonica alleles of the SSILP markers were predominant in the O. rufipogon accessions, suggesting that SSILPs were highly conserved during the evolution of O. sativa. Cluster analysis based on these markers yielded a dendrogram consisting of two distinct groups： one group （Group I） comprises all the O. rufipogon accesions from tropical （South and Southeast） Asia as well as the standard indica rice; the other group （Group II） comprises all the O. rufipogon accessions from Southern China as well as the standard japonica rice. Further analysis showed that the two groups have significantly higher frequencies of indica alleles and japonica alleles, respectively. These results support the hypothesis that indica rice and japonica rice were domesticated from the O. rufipogon of tropical Asia and from that of Southern China, respectively, and suggest that the indica-japonica differentiation should have formed in O. rufipogon long before the beginning of domestication. Furthermore, with an O. glaberrima accession as an outgroup, it is suggested that the indica-japonica differentiation in O. ruffpogon might occur after its speciation from other AA-genome species.     

A large-scale field study of transgene flow from cultivated rice (Oryza sativa) to common wild rice (O. rufipogon) and barnyard grass (Echinochloa crusgalli)

The introgression of transgenes into wild relatives or weeds through pollen-mediated gene flow is a major concern in environmental risk assessment of transgenic crops. A large-scale (1.3–1.8 ha) rice gene flow study was conducted using transgenic rice containing the bar gene as a pollen donor and Oryza rufipogon as a recipient. There was a high frequency of transgene flow (11%−18%) at 0–1 m, with a steep decline with increasing distance to a detection limit of 0.01% by 250 m. To our knowledge, this is the highest frequency and longest distance of gene flow from transgenic rice to O. rufipogon reported so far. On the basis of these data, an adequate isolation distance from both conventional and transgenic rice should be taken for in situ conservation of common wild rice. Meanwhile, there is no evidence of transgene introgression into barnyard grass, even when it has coexisted with transgenic rice containing the bar gene for five successive years. Thus, the environmental risk of gene flow to this weedy species is of little concern.     

Origins and population genetics of weedy red rice in the USA

Weedy red rice (Oryza sativa spontonea) is a persistent and problematic weed of rice culture worldwide. A major hypothesis for the mechanism of production of this weed in South and Southeast Asia is hybridization between cultivated rice (Oryza sativa) and wild rice (Oryza rufipogon). However, weedy red rice can often be found outside the range of O. rufipogon leaving questions on the origin and process behind weedy rice infestations. In the USA, weedy red rice was first documented as early as 1846 and has continued to affect rice production areas. In this study, we attempt to identify the origin and population structure of weedy red rice sampled from the USA using both DNA sequence data from a neutral nuclear locus as well as microsatellite genotype data. Results suggest that two major accessions of weedy rice exist, strawhull and blackhull, and these forms may both hybridize with the cultivated rice of the USA, O. sativa japonica. Using population assignment of multilocus genotype signatures with principal component analysis and structure, an Asian origin is supported for US weedy rice. Additionally, hybridization between strawhull and blackhull varieties was inferred and may present the opportunity for the production of new weedy forms in the future.     

根据核DNA的ITS序列的RFLP分析鉴定稻属CD染色体组物种

稻属物种的染色体组类型有10种,其中具CD染色体组的物种有3种(Oryza alta Swallen,O.grandiglumis(Doell)Prod.和O.latifolia Desv.),仅分布在美洲中部和南部.这3个种在形态上和稻属其他染色体组的种比较容易区别,但它们彼此之间鉴别比较困难.近年来的研究表明,O.alta和O.grandiglumis应归并为1个种(O.grandiglumis),而O.latifolia应保持不变.本文基于代表不同分布区11个样品的核糖体转录间隔区(ITS)的77个克隆序列数据,利用DNA Striderl.2软件进行了限制性酶切位点分析,提出了一个鉴别CD染色体组物种的方法.方法的具体步骤是:(1)用通用引物扩增ITS片段;(2)用特异性的限制性内切酶Fok Ⅰ和/或Dra Ⅲ消化PCR扩增产物;(3)用1%的琼脂糖电泳并根据消化产物的多态性特征来鉴别不同物种.基于本文提出的核糖体ITS限制性片段多态性(RLFP)分析,可以快速和可靠地将稻属CD染色体组物种区别开来.     

Endogenous evolution of HCN during pre-germination periods in many seed species

Both cyanogenic ( Malus pumila Mill) and acyanogenic ( Oryza sativa L., Hordeum vulgare L., Zea mays L., Glycine max Merr., Lactuca sativa L., and Xanthium pennsylvanicum Wallr. etc.) seeds evolve HCN gas during the early periods of water imbibition. All tested seeds contained reserve cyanogens which liberated HCN upon hydrolysis with H₂SO₄ and with β-glucosidase and/or lipase. The amounts of liberated HCN were roughly comparable to those of unidentified cyanogens. It is thus conceivable that the cyanogens within seeds are available as precursors for free HCN evolved in the pre-germination period. The amounts of HCN evolved in the acyanogenic seeds were only 0.002 to 1% of that in apple, but the contents of the cyanogenic compounds in rice and cocklebur increased temporarily during the pre-germination period, then decreased and, finally, disappeared completely with the start of germination.     

转基因插入对水稻花粉活力和杂交结实的影响

以花粉活力和杂交结实率评价转基因插入对水稻品种异交潜力的影响.选用含bar、crylAb、BADH和Xa21等4种基因的5份转基因水稻品系研究转基因插入对转基因受体品种花粉离体萌发率的影响.结果表明,不同受体品种花粉离体萌发率差异显著;转基因水稻花粉离体萌发率在0.416～0.584间,与受体品种(0.004～0.574)相近;转基因品种与相应受体品种间花粉离体萌发率差异不显著.对所选配的26个人工杂交组合杂种结实调查表明,bar、crylAb基因的插入对受体品种杂交结实率影响显著,而Xa21基因的插入对受体品种杂交结实率影响较小;转基因水稻品种(花粉供体)与非转基因水稻品种的杂交结实率变幅为0.056～0.13,在受体品种(花粉供体)与非转基因水稻品种的杂交结实率范围(0.052～0.417)之内.本研究花粉离体萌发和杂交结实结果表明转基因的插入对水稻品种异交潜力的影响甚微.     

Modern elite rice varieties of the 'Green Revolution' have retained a large introgression from wild rice around the Pi33 rice blast resistance locus

During the breeding process of cultivated crops, resistance genes to pests and diseases are commonly introgressed from wild species. The size of these introgressions is predicted by theoretical models but has rarely been measured in cultivated varieties. By combining resistance tests with isogenic strains, genotyping and sequencing of different rice accessions, it was shown that, in the elite rice variety IR64, the resistance conferring allele of the rice blast resistance gene Pi33 was introgressed from the wild rice Oryza rufipogon (accession IRGC101508). Further characterization of this introgression revealed a large introgression at this locus in IR64 and the related variety IR36. The introgressed fragment represents approximately half of the short arm of rice chromosome 8. This is the first report of a large introgression in a cultivated variety of rice. Such a large introgression is likely to have been maintained during backcrossing only if a selection pressure was exerted on this genomic region. The possible traits that were selected are discussed.     

中国野生稻的现状调查

中国有三种野生稻。野生稻是栽培水稻的野生近缘种,已被列为濒危植物^[7],它们分布于中国南方８个省（区）的热带、亚热带湿热生境中。 近年来人为的干扰和生境的破坏已导致它们的居群大量绝灭,其中濒危程度最高的是普通野生稻。本文阐述了它们的生物学、生态学特性,研究了它们的群落学特征,初步报道了它们的濒危状况,探讨了致濒原因。     

Ecophysiology of seed dormancy in the Australian endemic species Acanthocarpus preissii (Dasypogonaceae)

BACKGROUND AND AIMS: Seedlings of Acanthocarpus preissii are needed for coastal sand dune restoration in Western Australia. However, seeds of this Western Australian endemic have proven to be very difficult to germinate. The aims of this study were to define a dormancy-breaking protocol, identify time of suitable conditions for dormancy-break in the field and classify the type of seed dormancy in this species. METHODS: Viability, water-uptake (imbibition) and seed and embryo characteristics were assessed for seeds collected in 2003 and in 2004 from two locations. The effects of GA(3), smoke-water, GA(3) + smoke-water and warm stratification were tested on seed dormancy-break. In a field study, soil temperature and the moisture content of soil and buried seeds were monitored for 1 year. KEY RESULTS: Viability of fresh seeds was >90 %, and they had a fully developed, curved-linear embryo. Fresh seeds imbibed water readily, with mass increasing approx. 52 % in 4 d. Non-treated fresh seeds and those exposed to 1000 ppm GA(3), 1 : 10 (v/v) smoke-water/water or 1000 ppm GA(3) + 1 : 10 (v/v) smoke-water/water germinated <8 %. Fresh seeds germinated to >80 % when warm-stratified for at least 7 weeks at 18/33 degrees C and then moved to 7/18 degrees C, whereas seeds incubated continuously at 7/18 degrees C germinated to <20 %. CONCLUSIONS: Seeds of A. preisii have non-deep physiological dormancy that is released by a period of warm stratification. Autumn (March/April) is the most likely time for warm stratification of seeds of this species in the field. This is the first report of the requirement for warm stratification for dormancy release in seeds of an Australian species.     

生长素调控种子的休眠与萌发

植物种子的休眠与萌发,是植物生长发育过程中的关键阶段,也是生命科学领域的研究热点。种子从休眠向萌发的转换是极为复杂的生物学过程,由外界环境因子、体内激素含量及信号传导和若干关键基因协同调控。大量研究表明,植物激素脱落酸(Abscisic acid, ABA)和赤霉素(Gibberellin acid, GA)是调控种子休眠水平,决定种子从休眠转向萌发的主要内源因子。ABA与GA在含量和信号传导两个层次上的精确平衡,确保了植物种子能以休眠状态在逆境中存活,并在适宜的时间启动萌发程序。生长素(Auxin)是经典植物激素之一,其对向性生长和组织分化等生物学过程的调控已有大量研究。但最近有研究证实,生长素对种子休眠有正向调控作用,这表明生长素是继ABA之后的第二个促进种子休眠的植物激素。本文在回顾生长素的发现历程、阐释生长素体内合成途径及信号传导通路的基础上,重点综述了生长素通过与ABA的协同作用调控种子休眠的分子机制,并对未来的研究热点进行了讨论和展望。     

Accumulation and leakage of abscisic acid during embryo development and seed dormancy in wheat

Seed dormancy develops latein embryogenesis after a period of potential prematuregermination and has been associated with levels ofabscisic acid (ABA) in, and sensitivity to, ABA ofembryos. In wheat (Triticum aestivum L.)embryos, there are two peaks in levels of ABA duringdevelopment: the first occurs 25 days afterpollination (DAP) and the second from 35 to 40 DAP. The first peak of ABA appears to be associated withthe development of the embryo's sensitivity to ABAsince such sensitivity was altered in seeds on earsthat were incubated in a solution of ABA from 15 and20 DAP. In the embryos of Kitakei wheat, a line thatexhibits dormancy, the second peak, at around 35 DAP,was more prolonged in comparison to Chihoku, anon-dormant line. The results support the proposedinvolvement of ABA in the formation and maintenance ofseed dormancy during middle and late embryogenesis. When developing embryos were incubated in water,embryonic ABA leaked out from the embryos, inparticular between 30 and 40 DAP. Prematuregermination observed between 30 and 40 DAP might berelated to such leakage of ABA from embryos.     

MicroRNA在种子发育、休眠与萌发过程中的作用

植物microRNA(miRNA)是一类小分子非编码RNA,对植物的生长发育发挥着重要调控作用。种子发育、休眠与萌发是植物生命进程中的重要阶段。在这一阶段内,种子受各种环境因子及内源激素调控,并且不同植物种子具有不同发育及休眠特性。随着人们对种子发育、休眠及萌发机理的探究,越来越多miRNA被鉴定,它们能够基于植物激素信号传导、抗氧化作用、关键转录因子调控等途径参与种子形态建成、物质代谢及各种胁迫响应。本文主要综述了近年来植物miRNA的形成及调控机理,以及在种子发育、休眠及萌发过程中发挥的调控作用,旨在为今后的研究方向提供参考。     

The role of light in regulating seed dormancy and germination

Seed dormancy is an adaptive trait in plants. Breaking seed dormancy determines the timing of germination and is, thereby essential for ensuring plant survival and agricultural production. Seed dormancy and the subsequent germination are controlled by both internal cues (mainly hormones) and environmental signals. In the past few years, the roles of plant hormones in regulating seed dormancy and germination have been uncovered. However, we are only beginning to understand how light signaling pathways modulate seed dormancy and interaction with endogenous hormones. In this review, we summarize current views of the molecular mechanisms by which light controls the induction, maintenance and release of seed dormancy, as well as seed germination, by regulating hormone metabolism and signaling pathways.     

Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice

Varying degrees of reduction of genetic diversity in crops relative to their wild progenitors occurred during the process of domestication. Such information, however, has not been available for the Asian cultivated rice (Oryza sativa) despite its importance as a staple food and a model organism. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationship and demographic history of O. sativa and its close relatives (Oryza rufipogon and Oryza nivara), we investigated nucleotide diversity data from 10 unlinked nuclear loci in species-wide samples of these species. The results indicated that O. rufipogon and O. nivara possessed comparable levels of nucleotide variation ((sil) = 0.0077 approximately 0.0095) compared with the relatives of other crops. In contrast, nucleotide diversity of O. sativa was as low as (sil) = 0.0024 and even lower ((sil) = 0.0021 for indica and 0.0011 for japonica), if we consider the 2 subspecies separately. Overall, only 20-10% of the diversity in the wild species was retained in 2 subspecies of the cultivated rice (indica and japonica), respectively. Because statistic tests did not reject the assumption of neutrality for all 10 loci, we further used coalescent to simulate bottlenecks under various lengths and population sizes to better understand the domestication process. Consistent with the dramatic reduction in nucleotide diversity, we detected a severe domestication bottleneck and demonstrated that the sequence diversity currently found in the rice genome could be explained by a founding population of 1,500 individuals if the initial domestication event occurred over a 3,000-year period. Phylogenetic analyses revealed close genetic relationships and ambiguous species boundary of O. rufipogon and O. nivara, providing additional evidence to treat them as 2 ecotypes of a single species. Lowest linkage disequilibrium (LD) was found in the perennial O. rufipogon where the r(2) value dropped to a negligible level within 400 bp, and the highest in the japonica rice where LD extended to the entirely sequenced region ( approximately 900 bp), implying that LD mapping by genome scans may not be feasible in wild rice due to the high density of markers needed.