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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

Effects of genotype variation in the cultivated rice species on the biology and galling characteristics of the African rice gall midge,Orseolia oryzivora (Diptera: Cecidomyiidae)

This study assessed the effects of genotype variations in two cultivated rice species: Oryza glaberrima and Oryza sativa on the biology and galling characteristics of the African rice gall midge (AfRGM), Orseolia oryzivora Harris and Gagné. The study was conducted in the screen house at ambient temperature (27 ± 3°C), 70 ± 5% relative humidity and 12:12 h photoperiod. Shoot galling, the most visible response of rice genotypes to attack by the insect, was greatly suppressed, being only 0.7 cm long in the O. glaberrima genotypes compared to 34 cm in the O. sativa species. Larval mortality (70–88%) in the O. glaberrima genotypes was significantly higher at the first instar compared to O. sativa. Gall setting was confirmed to be an irredeemable tiller loss. Even in the susceptible O. sativa genotypes, where many larvae may colonize a tiller, only one survived to the second instar. Resistant and susceptible rice genotypes had significantly different effects on the development and reproductive anatomy of the AfRGM. The female reproductive anatomy which consists of two ovaries, each with a potential complement of 192 eggs was affected by interspecific variation in rice genotypes causing reduced potential fecundity (32); morphological distortion, 60% reduction of egg size of F1 emergent in O. glaberrima compared to emergent from the susceptible O. sativa genotypes.     

Fitness estimation through performance comparison of F1 hybrids with their parental species Oryza rufipogon and O. sativa

BACKGROUND AND AIMS: Introgression of crop genes into populations of wild relatives has important implications for germplasm conservation as well as for the persistence of novel transgenes in wild populations. Studies of hybrid fitness can be used to evaluate the potential for introgression to occur following episodes of interspecific hybridization. METHODS: This study estimated relative fitness of interspecific hybrids through performance comparison of F(1) hybrids with their parental species, a cultivated rice (Oryza sativa) Minghui-63 and perennial common wild rice (O. rufipogon) under the cultivation conditions. KEY RESULTS: Compared with their parents, the hybrids had the lowest values of seedling survival ability, pollen viability and seed production; intermediate values of seed germination, spikelet production and flag leaf areas; and the highest values of plant height, number of tillers and panicles. The hybrids performed poorly at the stage of sexual reproduction, although they had a slightly higher hybrid vigour at the vegetative growth stage and better tillering ability than their wild parent. There were no significant differences in composite fitness across the whole life-history between the hybrids and their wild parental species. CONCLUSIONS: Rice genes, including transgenes, might persist in wild rice populations through vegetative and sexual reproduction. Further studies are needed to examine whether the extent of gene flow from rice is sufficiently significant to influence genetic diversity in wild populations of O. rufipogon, a species that has become endangered in some regions of south-east Asia.     

Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara

With a small and sequenced genome, rice provides an excellent system for studying the genetics of cereal domestication. We conducted a quantitative trait locus (QTL) analysis of key domestication traits using an F2 population derived from a cross between the cultivated rice, Oryza sativa, and the annual wild species, O. nivara. We found that the QTL of large phenotypic effects were targeted by domestication selection for effective harvest and planting, including a reduction in seed shattering and seed dormancy and the synchronization of seed maturation. Selection for higher yield was probably responsible for the fixation of mutations at a cluster of QTL on chromosome 7 and a few other chromosomal locations that could have substantially improved plant architecture and panicle structure, resulting in fewer erect tillers and longer and more highly branched panicles in cultivated rice. In comparison with the wild perennial species, O. rufipogon, rice domestication from O. nivara would have involved QTL with a greater degree of chromosomal co-localization and required little genetic change associated with life history or mating system transitions. The genetic analyses of domestication traits with both wild relatives will open opportunities for the improvement of rice cultivars utilizing natural germplasm.     

Effects of seed chilling or GA3 supply on dormancy breaking and plantlet growth in Cercis siliquastrum L.

Germination and post-germination events have been compared in seeds of Cercis siliquastrum whose dormancy was removed by fulfilling the natural chilling requirement or by exogenous GA₃ application.Compared to the chilled ones, the GA₃ treated seeds showed precocious embryo growth and an earlier reserve mobilization, which started before radicle emergence.Although the hormonal application was interrupted at seed germination, the plantlets of Cercis siliquastrum that originated from GA₃-supplied seeds were taller than those from chilled ones. Moreover, they produced a greater number of leaves but a reduced root mass and had some difficulty in maintaining a good water balance.Thus, the treatment of Cercis siliquastrum seeds with exogenous GA₃ broke dormancy and induced germination, but also caused long-lasting consequences on morphogenesis of the growing plantlet.     

Physiological dormancy in seeds of two endemic species of Begonia from Yunnan Province,China: diagnosis and classification

With the purpose of assessing the status of dormancy in seeds of two Begonia species (Begonia lithophila and Begonia guishanensis), freshly matured seeds were given gibberellic acid and moist chilling and allowed to dry after ripening. The seeds were then germinated on media with or without KNO₃ at 15, 20, 25, 30 and 18/25°C. All three treatments significantly increased germination percentages. Examination by X‐ray revealed that seeds of both species have a fully developed embryo and thus have no morphological component of dormancy; seeds readily imbibed water and KNO₃ solution. Therefore, we conclude that seeds of the two Begonia species have non‐deep physiological dormancy. Although KNO₃ significantly increased germination in both species, alternating temperatures did not, suggesting that the most favorable microhabitat for germination is small‐scale disturbances under the forest canopy.     

Loblolly pine seed dormancy. I. The relationship between protein synthesis and the loss of dormancy

Embryos from the mature unstratified loblolly pine ( Pinus taeda L.) seeds used in this study were nondormant: however, they failed to germinate in situ because of constraints imposed by the surrounding tissues. During a stratification period of 35 days of moist chilling at 2°C, seed germinability increased from 19 to 76%. The total lipid content of the megagametophyte did not change during stratification, whereas the total protein content of both megagametophyte and embryo was more variable. The rate of synthesis of buffer soluble proteins in these two tissues increased and electrophoretic analysis showed that while similar proteins were synthesized during the stratification period, changes in the patterns of synthesis of some proteins did occur. In both the embryo and megagametophyte the synthesis of a set of proteins with molecular masses below 46 kDa decreased markedly after 14 days of chilling (DOC). In the megagametophyte, the synthesis of a more diverse set of proteins with molecular masses ranging from 16 to 78 kDa increased after 14 DOC. It is noteworthy that these changes in the patterns of protein synthesis coincided with the greatest relative increase in seed germinability of 35%.     

Fine linkage mapping enables dissection of closely linked quantitative trait loci for seed dormancy and heading in rice

Two quantitative trait loci (QTLs) for seed dormancy (tentatively designated Sdr1) and heading date (Hd8) have been mapped to approximately the same region on chromosome 3 by interval mapping of backcross inbred lines derived from crosses between the rice cultivars Nipponbare (japonica) and Kasalath (indica). To clarify whether Sdr1 and Hd8 could be dissected genetically, we carried out fine-scale mapping with an advanced backcross progeny. We selected a BC₄F₁ plant, in which a small chromosomal region including Sdr1 and Hd8, on the short arm of chromosome 3, remained heterozygous, whereas all the other chromosomal regions were homozygous for Nipponbare. Days-to-heading and seed germination rate in the BC₄F₂ plants showed continuous variation. Ten BC₄F₂ plants with recombination in the vicinity of Sdr1 and Hd8 were selected on the basis of the genotypes of the restriction fragment length polymorphism (RFLP) markers flanking both QTLs. Genotypes of those plants for Sdr1 and Hd8 were determined by advanced progeny testing of BC₄F₄ families. Sdr1 was mapped between the RFLP markers R10942 and C2045, and co-segregated with C1488. Hd8 was also mapped between C12534S and R10942. Six recombination events were detected between Sdr1 and Hd8. These results clearly demonstrate that Sdr1 and Hd8 were tightly linked. Nearly isogenic lines for Sdr1 and Hd8 were selected by marker-assisted selection.Communicated by D. Mackill     

A comparison of the seed dormancy characteristics of Spartina patens and Spartina alterniflora (Poaceae)

Seed dormancy characteristics of Spartina alterniflora were delineated previously by Plyler and Carrick (American Journal of Botany, vol. 80, pp. 752–756, 1993). This study was undertaken in order to determine whether or not the dormancy characteristics of S. patens are similar. As in the previous study, the site of a dormancy mechanism was determined by assessing the germinability of surgically altered dormant seeds. Likewise, the effects of three growth-regulating substances (abscisic acid, fusicoccin, and gibberellic acid), prechilling, and light were studied by assessing the germinability of appropriately treated dormant seeds. Surgical injury to the endosperm, and to a lesser extent the scutellum, produced significant germination in S. patens, whereas only injury to the scutellum produced germination in S. alterniflora. Exogenously applied abscisic acid was highly effective in maintaining dormancy in injured seeds of both species. Gibberellic acid and fusicoccin were ineffective in promoting germination in S. patens, but fusicoccin was highly effective in breaking dormancy in 5. alterniflora. Prechilling was effective in breaking dormancy in S. patens but not in S. alterniflora. In S. patens, treatments that broke dormancy were only successful when seeds were exposed to light during the germination period. It is concluded that the dissimilarities in the dormancy mechanisms may be manifestations of the different environmental adaptations these closely related species display.     

Temperature controls seed germination and dormancy in the European woodland herbaceous perennial Erythronium dens-canis (Liliaceae)

We examined the germination ecology and the temperature requirements for germination of Erythronium dens-canis, under both outdoor and laboratory conditions. E. dens-canis is a spring flowering woodland geophyte widely distributed across Europe. Germination phenology, including embryo development and radicle and cotyledon emergence, were investigated in a natural population growing in Northern Italy. Immediately after harvest, seeds of E. dens-canis were either sown on agar in the laboratory under simulated seasonal temperatures or placed in nylon mesh sachets and buried in the wild. Embryos, undifferentiated at the time of seed dispersal, grew during summer and autumn conditions in the laboratory and in the wild, culminating in radicle emergence in winter when temperatures fell to ≈ 5 °C. Emergence of cotyledons did not occur immediately after radicle emergence, but was delayed until the end of winter. Laboratory experiments showed that temperature is the main factor controlling dormancy and germination, with seeds becoming non-dormant only when given warmth, followed by cold stratification. Unlike seeds of E. dens-canis that germinate in winter, in other Erythronium species radicle emergence occurs in autumn, while in some it is delayed until seeds are transferred from winter to spring conditions. Our results suggest that there is genetic and environmental control of the expression of seed dormancy amongst Erythronium species, which is related to local climate.