'Green revolution' genes encode mutant gibberellin response modulators

Gibberellins and heterosis of plant height in wheat (Triticum aestivum L.)

Background

Heterosis in internode elongation and plant height are commonly observed in hybrid plants, and higher GAs contents were found to be correlated with the heterosis in plant height. However, the molecular basis for the increased internode elongation in hybrids is unknown.

Results

In this study, heterosis in plant height was determined in two wheat hybrids, and it was found that the increased elongation of the uppermost internode contributed mostly to the heterosis in plant height. Higher GA₄ level was also observed in a wheat hybrid. By using the uppermost internode tissues of wheat, we examined expression patterns of genes participating in both GA biosynthesis and GA response pathways between a hybrid and its parental inbreds. Our results indicated that among the 18 genes analyzed, genes encoding enzymes that promote synthesis of bioactive GAs, and genes that act as positive components in the GA response pathways were up-regulated in hybrid, whereas genes encoding enzymes that deactivate bioactive GAs, and genes that act as negative components of GA response pathways were down-regulated in hybrid. Moreover, the putative wheat GA receptor gene TaGID1, and two GA responsive genes participating in internode elongation, GIP and XET, were also up-regulated in hybrid. A model for GA and heterosis in wheat plant height was proposed.

Conclusion

Our results provided molecular evidences not only for the higher GA levels and more active GA biosynthesis in hybrid, but also for the heterosis in plant height of wheat and possibly other cereal crops.

The DELLA domain of GA INSENSITIVE mediates the interaction with the GA INSENSITIVE DWARF1A gibberellin receptor of Arabidopsis

Gibberellic acid (GA) promotes seed germination, elongation growth, and flowering time in plants. GA responses are repressed by DELLA proteins, which contain an N-terminal DELLA domain essential for GA-dependent proteasomal degradation of DELLA repressors. Mutations of or within the DELLA domain of DELLA repressors have been described for species including Arabidopsis thaliana, wheat (Triticum aestivum), maize (Zea mays), and barley (Hordeum vulgare), and we show that these mutations confer GA insensitivity when introduced into the Arabidopsis GA INSENSITIVE (GAI) DELLA repressor. We also demonstrate that Arabidopsis mutants lacking the three GA INSENSITIVE DWARF1 (GID1) GA receptor genes are GA insensitive with respect to GA-promoted growth responses, GA-promoted DELLA repressor degradation, and GA-regulated gene expression. Our genetic interaction studies indicate that GAI and its close homolog REPRESSOR OF ga1-3 are the major growth repressors in a GA receptor mutant background. We further demonstrate that the GA insensitivity of the GAI DELLA domain mutants is explained in all cases by the inability of the mutant proteins to interact with the GID1A GA receptor. Since we found that the GAI DELLA domain alone can mediate GA-dependent GID1A interactions, we propose that the DELLA domain functions as a receiver domain for activated GA receptors.

Seed germination of GA-insensitive sleepy1 mutants does not require RGL2 protein disappearance in Arabidopsis

We explore the roles of gibberellin (GA) signaling genes SLEEPY1 (SLY1) and RGA-LIKE2 (RGL2) in regulation of seed germination in Arabidopsis thaliana, a plant in which the hormone GA is required for seed germination. Seed germination failure in the GA biosynthesis mutant ga1-3 is rescued by GA and by mutations in the DELLA gene RGL2, suggesting that RGL2 represses seed germination. RGL2 protein disappears before wild-type seed germination, consistent with the model that GA stimulates germination by causing the SCF(SLY1) E3 ubiquitin ligase complex to trigger ubiquitination and destruction of RGL2. Unlike ga1-3, the GA-insensitive sly1 mutants show variable seed dormancy. Seed lots with high seed dormancy after-ripened slowly, with stronger alleles requiring more time. We expected that if RGL2 negatively controls seed germination, sly1 mutant seeds that germinate well should accumulate lower RGL2 levels than those failing to germinate. Surprisingly, RGL2 accumulated at high levels even in after-ripened sly1 mutant seeds with 100% germination, suggesting that RGL2 disappearance is not a prerequisite for seed germination in the sly1 background. Without GA, several GA-induced genes show increased accumulation in sly1 seeds compared with ga1-3. It is possible that the RGL2 repressor of seed germination is inactivated by after-ripening of sly1 mutant seeds.

Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.)

Information on single-nucleotide polymorphisms (SNPs) in hexaploid bread wheat is still scarce. The goal of this study was to detect SNPs in wheat and examine their frequency. Twenty-six bread wheat lines from different origins worldwide were used. Specific PCR-products were obtained from 21 genes and directly sequenced. SNPs were discovered from the alignment of these sequences. The overall sequence polymorphism observed in this sample appears to be low; 64 single-base polymorphisms were detected in approximately 21.5 kb (i.e., 1 SNP every 335 bp). The level of polymorphism is highly variable among the different genes studied. Fifty percent of the genes studied contained no sequence polymorphism, whereas most SNPs detected were located in only 2 genes. As expected, taking into account a synthetic line created with a wild Triticum tauschii parent increases the level of polymorphism (101 SNPs; 1 SNP every 212 bp). The detected SNPs are available at http://urgi.versailles.inra.fr/GnpSNP">http://urgi.versailles.inra.fr/GnpSNP. Data on linkage disequilibrium (LD) are still preliminary. They showed a significant level of LD in the 2 most polymorphic genes. To conclude, the genome size of hexaploid wheat and its low level of polymorphism complicate SNP discovery in this species.

Wine grape (Vitis vinifera L.) color associates with allelic variation in the domestication gene VvmybA1

During the process of crop domestication and early selection, numerous changes occur in the genetic and physiological make-up of crop plants. In grapevine (Vitis vinifera) numerous changes have occurred as a result of human selection, including the emergence of hermaphroditism and greatly increased variation in berry color. This report examines the effect of human selection on variable skin color by examining the variation present in the gene VvmybA1, a transcriptional regulator of anthocyanin biosynthesis. In over 200 accessions of V. vinifera, the insertion of the retroelement Gret1 in the promoter region of VvmybA1 was in strong association with the white-fruited phenotype. This retroelement was inserted at the same location for each individual in which it was present. Additional polymorphisms in the VvmybA1 gene were also strongly associated with red or pink fruited accessions, including variation that was generated by the excision of Gret1 from the promoter of VvmybA1. Differences in nucleotide diversity were observed between the white and pigmented alleles of VvmybA1, suggesting that the white allele arose only once or a limited number of times. Rarely, association of Gret1 with the white fruited phenotype was not observed, suggesting that the white phenotype can also be obtained through mutation in additional genes. These results provide evidence that variation in one transcriptional regulator has generated an allelic series strongly associated with fruit color variation in cultivated grapevine. These findings provide information about the evolution of grapes since domestication and have direct implications for the regulation of fruit and wine quality of this important crop plant.

Phytohormones and rice crop yield: strategies and opportunities for genetic improvement

To feed an estimated world population of 8.9 billion by 2050, strategies for increasing grain production must be developed. Several agronomically important traits for increasing yield, such as plant height, grain number, and leaf erectness, have recently been characterized in rice (Oryza sativa L.). These traits are regulated primarily by three phytohormones: gibberellins, cytokinins, and brassinosteroids. The control of biosynthesis and degradation of these key phytohormones is discussed in terms of its importance for normal plant growth. Genes involved in the biosynthesis and regulation of these phytohormones can be used to develop effective strategies to increase grain yield. Genetic manipulation of phytohormone-related gene expression is thus a practical strategy to generate high-yielding transgenic plants through the modification of levels and profile of endogenous phytohormones.

Gibberellin receptor and its role in gibberellin signaling in plants

Gibberellins (GAs) are a large family of tetracyclic, diterpenoid plant hormones that induce a wide range of plant growth responses. It has been postulated that plants have two types of GA receptors, including soluble and membrane-bound forms. Recently, it was determined that the rice GIBBERELLIN INSENSITIVE DWARF1 (GID1) gene encodes an unknown protein with similarity to the hormone-sensitive lipases that has high affinity only for biologically active GAs. Moreover, GID1 binds to SLR1, a repressor of GA signaling, in a GA-dependent manner in yeast cells. Based on these observations, it has been concluded that GID1 is a soluble receptor mediating GA signaling in rice. More recently, Arabidopsis thaliana was found to have three GID1 homologs, AtGID1a, b, and c, all of which bind GA and interact with the five Arabidopsis DELLA proteins.

Genetic characterization and functional analysis of the GID1 gibberellin receptors in Arabidopsis

We investigated the physiological function of three Arabidopsis thaliana homologs of the gibberellin (GA) receptor GIBBERELLIN-INSENSITIVE DWARF1 (GID1) by determining the developmental consequences of GID1 inactivation in insertion mutants. Although single mutants developed normally, gid1a gid1c and gid1a gid1b displayed reduced stem height and lower male fertility, respectively, indicating some functional specificity. The triple mutant displayed a dwarf phenotype more severe than that of the extreme GA-deficient mutant ga1-3. Flower formation occurred in long days but was delayed, with severe defects in floral organ development. The triple mutant did not respond to applied GA. All three GID1 homologs were expressed in most tissues throughout development but differed in expression level. GA treatment reduced transcript abundance for all three GID1 genes, suggesting feedback regulation. The DELLA protein REPRESSOR OF ga1-3 (RGA) accumulated in the triple mutant, whose phenotype could be partially rescued by loss of RGA function. Yeast two-hybrid and in vitro pull-down assays confirmed that GA enhances the interaction between GID1 and DELLA proteins. In addition, the N-terminal sequence containing the DELLA domain is necessary for GID1 binding. Furthermore, yeast three-hybrid assays showed that the GA-GID1 complex promotes the interaction between RGA and the F-box protein SLY1, a component of the SCF(SLY1) E3 ubiquitin ligase that targets the DELLA protein for degradation.

Functional classification, genomic organization, putatively cis-acting regulatory elements, and relationship to quantitative trait loci, of sorghum genes with rhizome-enriched expression

Rhizomes are organs of fundamental importance to plant competitiveness and invasiveness. We have identified genes expressed at substantially higher levels in rhizomes than other plant parts, and explored their functional categorization, genomic organization, regulatory motifs, and association with quantitative trait loci (QTLs) conferring rhizomatousness. The finding that genes with rhizome-enriched expression are distributed across a wide range of functional categories suggests some degree of specialization of individual members of many gene families in rhizomatous plants. A disproportionate share of genes with rhizome-enriched expression was implicated in secondary and hormone metabolism, and abiotic stimuli and development. A high frequency of unknown-function genes reflects our still limited knowledge of this plant organ. A putative oligosaccharyl transferase showed the highest degree of rhizome-specific expression, with several transcriptional or regulatory protein complex factors also showing high (but lesser) degrees of specificity. Inferred by the upstream sequences of their putative rice (Oryza sativa) homologs, sorghum (Sorghum bicolor) genes that were relatively highly expressed in rhizome tip tissues were enriched for cis-element motifs, including the pyrimidine box, TATCCA box, and CAREs box, implicating the gibberellins in regulation of many rhizome-specific genes. From cDNA clones showing rhizome-enriched expression, expressed sequence tags forming 455 contigs were plotted on the rice genome and aligned to QTL likelihood intervals for ratooning and rhizomatous traits in rice and sorghum. Highly expressed rhizome genes were somewhat enriched in QTL likelihood intervals for rhizomatousness or ratooning, with specific candidates including some of the most rhizome-specific genes. Some rhizomatousness and ratooning QTLs were shown to be potentially related to one another as a result of ancient duplication, suggesting long-term functional conservation of the underlying genes. Insight into genes and pathways that influence rhizome growth set the stage for genetic and/or exogenous manipulation of rhizomatousness, and for further dissection of the molecular evolution of rhizomatousness.

Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis

Severe Arabidopsis (Arabidopsis thaliana) gibberellin (GA)-deficient mutant ga1-3 fails to germinate and is impaired in floral organ development. In contrast, the ga1-3 gai-t6 rga-t2 rgl1-1 rgl2-1 mutant confers GA-independent seed germination and floral development. This fact suggests that GA-regulated transcriptomes for seed germination and floral development are DELLA dependent. However, it is currently not known if all GA-regulated genes are GA regulated in a DELLA-dependent fashion and if a similar set of DELLA-regulated genes is mobilized to repress both seed germination and floral development. Here, we compared the global gene expression patterns in the imbibed seeds and unopened flower buds of the ga1-3 mutant with that of the wild type and of the ga1-3 gai-t6 rga-t2 rgl1-1 rgl2-1 mutant. We found that about one-half of total GA-regulated genes are apparently regulated in a DELLA-dependent fashion, suggesting that there might be a DELLA-independent or -partially-dependent component of GA-dependent gene regulation. A cross-comparison based on gene identity revealed that the GA-regulated DELLA-dependent transcriptomes in the imbibed seeds and flower buds are distinct from each other. Detailed ontology analysis showed that, on one hand, DELLAs differentially regulate the expression of different individual members of a gene family to run similar biochemical pathways in seeds and flower. Meanwhile, DELLAs control many functionally different genes to run specific pathways in seeds or flower buds to mark the two different developmental processes. Our data shown here not only confirm many previous reports but also single out some novel aspects of DELLA functions that are instructive to our future research.

Common mechanisms regulating expression of rice aleurone genes that contribute to the primary response for gibberellin

During germination of cereal seeds, aleurone cells respond to gibberellins (GA) by synthesizing and secreting hydrolytic enzymes that mobilize the reserved nutrients. It has been shown that products of early GA response genes, like a transcription factor GAMyb, act as key molecules leading to this regulation. Pivotal roles of GAMyb on expression of hydrolase genes have been well documented, whereas regulation of GAMyb expression itself remains obscure. In order to understand virtual mechanisms of the GA-mediated expression of genes, it is important to know how GA control expression of early GA response genes. Using an aleurone transient expression system of rice (Oryza sativa L.), we examined GA responsive domains of early GA response genes in the aleurone, such as GAMyb and OsDof3. The upstream promoter could not confer GA response. Extensive analyses revealed the presence of enhancer-like activities in a large first intron. In Arabidopsis, intron enhancers have been identified in MADS-box homeotic genes, AGAMOUS (AG) and FLOWERING LOCUS C (FLC), in which large introns should not only confer proper gene expressions, but also associate with gene silencing by covalent modifications of both DNA and histone. These evidences prompt us to assign that chromatin-based control might be important for initial GA action. Based on this assumption, we have identified DNA methylation of the GAMyb locus in germinated rice seeds.

Homoeologous gene silencing in hexaploid wheat

The vast majority of angiosperms are (or were once) polyploid, and as hexaploid bread wheat has undergone two ploidy events separated by approximately 0.5 million years, it represents an elegant model to study gene silencing over time in polyploids. Using an SSCP platform, we have analysed patterns of transcriptional silencing (frequency, genome identity and organ specificity) within 236 single-copy genes, each mapping to one locus on one of the three homoeologous chromosomes within groups 1, 2, 3 and 7 of wheat. In about 27% of unigenes expressed in leaf, and about 26% of those in root, one (rarely two) members of a gene set (homoeoalleles) were not present in the cDNA template. Organ-specific regulation is commonplace, with many homoeoalleles transcribed in leaf but not root (and vice versa). There was little indication of extensive bias towards selective silencing of a particular genome copy. Expression of some of the silenced homoeoalleles was restored in certain aneuploid lines and varieties, and these displayed a significant degree of genetic variation for the silencing of a given homoeoallele. We propose that a substantial proportion of this phenomenon is effected by an epigenetic mechanism, and suggest that this form of genetic variation may be a significant player in the determination of phenotypic diversity in breeding populations.

How to be early flowering: an evolutionary perspective

In wild and cultivated annual plant species, flowering time is an important life-history trait that coordinates the life cycle with local environmental conditions. Extensive studies on the genetic basis of flowering time in the model species Arabidopsis thaliana have revealed a complex genetic network that can detect environmental and internal signals. Based on this knowledge and on known pleiotropic effects associated with flowering time genes, we suggest that a natural shift towards an early-flowering life cycle might involve only particular functional regions in a limited number of genes. Our predictions are supported by genetic theories of adaptation and by recent data about genes associated with natural variation. We analyse the extent to which these predictions can also apply to crop species.

The Quest to Understand the Basis and Mechanisms that Control Expression of Introduced Transgenes in Crop Plants

We discuss mechanisms and factors that influence levels and stability of expressed heterologous proteins in crop plants. We have seen substantial progress in this field over the past two decades in model experimental organisms such as Arabidopsis and tobacco. There is no question such studies have resulted in furthering our understanding of key processes in the plant cell and the elaboration of sophisticated models to explain underlying mechanisms that might influence the fate, levels and stability of expression of recombinant heterologous proteins in plants. However, very often, such information is not applicable outside these laboratory experimental models. In order to generate a knowledge basis that can be used to achieve high levels and stability of heterologous proteins in relevant crop plants it is imperative to perform such studies on the target crops. With this in mind, we discuss key elements of the process at the DNA, RNA and protein levels. We believe it is essential to discuss recombinant protein production in crops in a holistic manner in order to develop a comprehensive knowledge base that will in turn serve plant biotechnology applications well.

Transgenic modification of gai or rgl1 causes dwarfing and alters gibberellins, root growth, and metabolite profiles in Populus

In Arabidopsis and other plants, gibberellin (GA)-regulated responses are mediated by proteins including GAI, RGA and RGL1-3 that contain a functional DELLA domain. Through transgenic modification, we found that DELLA-less versions of GAI (gai) and RGL1 (rgl1) in a Populus tree have profound, dominant effects on phenotype, producing pleiotropic changes in morphology and metabolic profiles. Shoots were dwarfed, likely via constitutive repression of GA-induced elongation, whereas root growth was promoted two- to threefold in vitro. Applied GA(3 )inhibited adventitious root production in wild-type poplar, but gai/rgl1 poplars were unaffected by the inhibition. The concentrations of bioactive GA(1) and GA(4) in leaves of gai- and rgl1-expressing plants increased 12- to 64-fold, while the C(19) precursors of GA(1) (GA(53), GA(44) and GA(19)) decreased three- to ninefold, consistent with feedback regulation of GA 20-oxidase in the transgenic plants. The transgenic modifications elicited significant metabolic changes. In roots, metabolic profiling suggested increased respiration as a possible mechanism of the increased root growth. In leaves, we found metabolite changes suggesting reduced carbon flux through the lignin biosynthetic pathway and a shift towards allocation of secondary storage and defense metabolites, including various phenols, phenolic glucosides, and phenolic acid conjugates.

Morphological alteration caused by brassinosteroid insensitivity increases the biomass and grain production of rice

The rice (Oryza sativa) dwarf mutant d61 phenotype is caused by loss of function of a rice BRASSINOSTEROID INSENSITIVE1 ortholog, OsBRI1. We have identified nine d61 alleles, the weakest of which, d61-7, confers agronomically important traits such as semidwarf stature and erect leaves. Because erect-leaf habit is considered to increase light capture for photosynthesis, we compared the biomass and grain production of wild-type and d61-7 rice. The biomass of wild type was 38% higher than that of d61-7 at harvest under conventional planting density because of the dwarfism of d61-7. However, the biomass of d61-7 was 35% higher than that of wild type at high planting density. The grain yield of wild type reached a maximum at middensity, but the yield of d61-7 continued to increase with planting density. These results indicate that d61-7 produces biomass more effectively than wild type, and consequently more effectively assimilates the biomass in reproductive organ development at high planting density. However, the small grain size of d61-7 counters any increase in grain yield, leading to the same grain yield as that of wild type even at high density. We therefore produced transgenic rice with partial suppression of endogenous OsBRI1 expression to obtain the erect-leaf phenotype without grain changes. The estimated grain yield of these transformants was about 30% higher than that of wild type at high density. These results demonstrate the feasibility of generating erect-leaf plants by modifying the expression of the brassinosteroid receptor gene in transgenic rice plants.

Genealogy of the "Green Revolution" gene in rice

During the "Green Revolution" of rice, high-yielding varieties (HYVs) were developed using a semi-dwarf gene (sd1 or OsGA20ox2). The presence or absence of the two mutant alleles (DGWG type in Dee-geo-woo-gen and JKK type in Jikkoku) were surveyed by PCR using 256 accessions of eight wild and two cultivate rice species. The DGWG allele was detected in a landrace (Oryza sativa) and two accessions of wild rice (O. rufipogon), all of which are from China, showing their limited distribution. Genealogical studies of the OsGA20ox2 gene showed that the 62 sequences of O. sativa and O. rufipogon included 20 distinct haplotypes, indicating that the species complex contained OsGA20ox2 genes from two different lineages. The silent site nucleotide diversities (pi and theta(w)) were extremely low in Japonica rice, suggesting a genetic bottleneck. The haplotype network showed that the DGWG and JKK alleles were derived in different lineages. The DGWG carrier (W1944) had unique polymorphisms in the surrounding region of the locus, suggesting that the DGWG allele has been preserved in the wild progenitor, rather than that the DGWG allele has been introgressed from HYVs to W1944. Although a semi-dwarfing plant is a weak competitor under saturated fields, the crossing experiment revealed that the DGWG variant might have been preserved as a hidden variation in the genetic background of wild rice, without expressing a short-stature.

Genes controlling plant architecture

Plant architecture, referring here to the aerial part of a higher plant, is mainly determined by factors affecting shoot branching, plant height and inflorescence morphology. Significant progress has been made in isolating and characterizing genes that are directly involved in the formation of plant architecture, especially those controlling the initiation and outgrowth of axillary buds, elongation of stems and architecture of inflorescences. Most of these genes are conserved between dicotyledonous and monocotyledonous plants, indicating that these plants share similar regulatory pathways to establish their shape. The conservation of these genes makes them of great agronomical importance for improving crop yields.

Function and transcript analysis of gibberellin-biosynthetic enzymes in wheat

The enzymes gibberellin (GA) 20-oxidase and 3-oxidase are major sites of regulation in GA biosynthesis. We have characterised one member of each of the gene families encoding these enzymes that are highly expressed in elongating stems and in developing and germinating grains of wheat and are therefore likely to have prominent developmental roles in these tissues. We mapped the three homoeologues of the GA 20-oxidase gene TaGA20ox1 to chromosomes 5BL, 5DL and 4AL. TaGA20ox1 is expressed mainly in the nodes and ears of the elongating stem, and also in developing and germinating embryos. Expression in the nodes, ears and germinating embryos is predominantly from the A and D genomes. Each homoeologous cDNA encodes a functional enzyme that catalyses the multi-step conversions of GA12-GA9, and GA53-GA20. Time course and enzyme kinetic studies indicate that the initial oxidation steps from GA12 and GA53 to the free alcohol forms of GA15 and GA44, respectively, occur rapidly but that subsequent steps occur more slowly. The intermediate GA19 has an especially low affinity for the enzyme, consistent with its accumulation in wheat tissues. The three homoeologous cDNAs for the 3-oxidase gene TaGA3ox2 encode functional enzymes, one of which was shown to possess low levels of 2beta-hydroxylase, 2,3-desaturase, 2,3-epoxidase and even 13-hydroxylase activities in addition to 3beta-hydroxylase activity. In contrast to TaGA20ox1, TaGA3ox2 is expressed in internodes, as well as nodes and the ear of the elongating stem. It is also highly expressed in developing and germinated embryos.

EUI1, encoding a putative cytochrome P450 monooxygenase, regulates internode elongation by modulating gibberellin responses in rice

Elongation of rice internodes is one of the most important agronomic traits, which determines the plant height and underlies the grain yield. It has been shown that the elongation of internodes is under genetic control, and various factors are implicated in the process. Here, we report a detailed characterization of an elongated uppermost internode1 (eui1) mutant, which has been used in hybrid rice breeding. In the eui1-2 mutant, the cell lengths in the uppermost internodes are significantly longer than that of wild type and thus give rise to the elongated uppermost internode. It was found that the level of active gibberellin was elevated in the mutant, whereas its growth in response to gibberellin is similar to that of the wild type, suggesting that the higher level accumulation of gibberellin in the eui1 mutant causes the abnormal elongation of the uppermost internode. Consistently, the expression levels of several genes which encode gibberellin biosynthesis enzymes were altered. We cloned the EUI1 gene, which encodes a putative cytochrome P450 monooxygenase, by map-based cloning and found that EUI1 was weakly expressed in most tissues, but preferentially in young panicles. To confirm its function, transgenic experiments with different constructs of EUI1 were conducted. Overexpression of EUI1 gave rise to the gibberellin-deficient-like phenotypes, which could be partially reversed by supplementation with gibberellin. Furthermore, apart from the alteration of expression levels of the gibberellin biosynthesis genes, accumulation of SLR1 protein was found in the overexpressing transgenic plants, indicating that the expression level of EUI1 is implicated in both gibberellin-mediated SLR1 destruction and a feedback regulation in gibberellin biosynthesis. Therefore, we proposed that EUI1 plays a negative role in gibberellin-mediated regulation of cell elongation in the uppermost internode of rice.

Ectopic expression of pumpkin gibberellin oxidases alters gibberellin biosynthesis and development of transgenic Arabidopsis plants

Immature pumpkin (Cucurbita maxima) seeds contain gibberellin (GA) oxidases with unique catalytic properties resulting in GAs of unknown function for plant growth and development. Overexpression of pumpkin GA 7-oxidase (CmGA7ox) in Arabidopsis (Arabidopsis thaliana) resulted in seedlings with elongated roots, taller plants that flower earlier with only a little increase in bioactive GA4 levels compared to control plants. In the same way, overexpression of the pumpkin GA 3-oxidase1 (CmGA3ox1) resulted in a GA overdose phenotype with increased levels of endogenous GA4. This indicates that, in Arabidopsis, 7-oxidation and 3-oxidation are rate-limiting steps in GA plant hormone biosynthesis that control plant development. With an opposite effect, overexpression of pumpkin seed-specific GA 20-oxidase1 (CmGA20ox1) in Arabidopsis resulted in dwarfed plants that flower late with reduced levels of GA4 and increased levels of physiological inactive GA17 and GA25 and unexpected GA34 levels. Severe dwarfed plants were obtained by overexpression of the pumpkin GA 2-oxidase1 (CmGA2ox1) in Arabidopsis. This dramatic change in phenotype was accompanied by a considerable decrease in the levels of bioactive GA4 and an increase in the corresponding inactivation product GA34 in comparison to control plants. In this study, we demonstrate the potential of four pumpkin GA oxidase-encoding genes to modulate the GA plant hormone pool and alter plant stature and development.

ELONGATED UPPERMOST INTERNODE encodes a cytochrome P450 monooxygenase that epoxidizes gibberellins in a novel deactivation reaction in rice

The recessive tall rice (Oryza sativa) mutant elongated uppermost internode (eui) is morphologically normal until its final internode elongates drastically at the heading stage. The stage-specific developmental effect of the eui mutation has been used in the breeding of hybrid rice to improve the performance of heading in male sterile cultivars. We found that the eui mutant accumulated exceptionally large amounts of biologically active gibberellins (GAs) in the uppermost internode. Map-based cloning revealed that the Eui gene encodes a previously uncharacterized cytochrome P450 monooxygenase, CYP714D1. Using heterologous expression in yeast, we found that EUI catalyzed 16alpha,17-epoxidation of non-13-hydroxylated GAs. Consistent with the tall and dwarfed phenotypes of the eui mutant and Eui-overexpressing transgenic plants, respectively, 16alpha,17-epoxidation reduced the biological activity of GA(4) in rice, demonstrating that EUI functions as a GA-deactivating enzyme. Expression of Eui appeared tightly regulated during plant development, in agreement with the stage-specific eui phenotypes. These results indicate the existence of an unrecognized pathway for GA deactivation by EUI during the growth of wild-type internodes. The identification of Eui as a GA catabolism gene provides additional evidence that the GA metabolism pathway is a useful target for increasing the agronomic value of crops.

Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene

To investigate the genetic basis of maize adaptation to temperate climate, collections of 375 inbred lines and 275 landraces, representative of American and European diversity, were evaluated for flowering time under short- and long-day conditions. The inbred line collection was genotyped for 55 genomewide simple sequence repeat (SSR) markers. Comparison of inbred line population structure with that of landraces, as determined with 24 SSR loci, underlined strong effects of both historical and modern selection on population structure and a clear relationship with geographical origins. The late tropical groups and the early "Northern Flint" group from the northern United States and northern Europe exhibited different flowering times. Both collections were genotyped for a 6-bp insertion/deletion in the Dwarf8 (D8idp) gene, previously reported to be potentially involved in flowering time variation in a 102 American inbred panel. Among-group D8idp differentiation was much higher than that for any SSR marker, suggesting diversifying selection. Correcting for population structure, D8idp was associated with flowering time under long-day conditions, the deletion allele showing an average earlier flowering of 29 degree days for inbreds and 145 degree days for landraces. Additionally, the deletion allele occurred at a high frequency (>80%) in Northern Flint while being almost absent (<5%) in tropical materials. Altogether, these results indicate that Dwarf8 could be involved in maize climatic adaptation through diversifying selection for flowering time.

Integration of Plant Responses to Environmentally Activated Phytohormonal Signals

Plants live in fixed locations and survive adversity by integrating growth responses to diverse environmental signals. Here, we show that the nuclear-localized growth-repressing DELLA proteins of Arabidopsis integrate responses to independent hormonal and environmental signals of adverse conditions. The growth restraint conferred by DELLA proteins is beneficial and promotes survival. We propose that DELLAs permit flexible and appropriate modulation of plant growth in response to changes in natural environments.

Letting the gene out of the bottle: the population genetics of genetically modified crops

Genetically modified (GM) plants are rapidly becoming a common feature of modern agriculture. This transition to engineered crops has been driven by a variety of potential benefits, both economic and ecological. The increase in the use of GM crops has, however, been accompanied by growing concerns regarding their potential impact on the environment. Here, we focus on the escape of transgenes from cultivation via crop x wild hybridization. We begin by reviewing the literature on natural hybridization, with particular reference to gene flow between crop plants and their wild relatives. We further show that natural selection, and not the overall rate of gene flow, is the most important factor governing the spread of favorable alleles. Hence, much of this review focuses on the likely effects of transgenes once they escape. Finally, we consider strategies for transgene containment.

Physical restriction of pods causes seed size reduction of a brassinosteroid-deficient faba bean (Vicia faba)

BACKGROUND AND AIMS

A brassinosteroid-deficient mutant faba bean (Vicia faba 'Rinrei') shows dwarfism in many organs including pods and seeds. 'Rinrei' has normal-sized seeds together with dwarf seeds, suggesting that dwarfism in the seed may be indirectly caused by brassinosteroid deficiency. The mechanism of seed size reduction in this mutant was investigated.

METHODS

The associations between seed orientation in the pod, seed numbers per pod and pod lengths with seed sizes were analysed in 'Rinrei' and the wild-type plant.

KEY RESULTS

'Rinrei' seeds are tightly arranged in pods containing two or three seeds. Seed size decreased as the number of seeds per pod increased or as the length of the pod decreased. Where no physical restriction occurred between seeds in a pod, the wild-type faba bean seeds had a nearly constant size regardless of seed number per pod or pod length. 'Rinrei' seeds in pods containing single seeds were the same size as wild-type seeds. Brassinolide treatment increased the seed size and the length of pods containing three seeds in 'Rinrei'.

CONCLUSION

Seed size of 'Rinrei' is mainly regulated through a reduction of pod length due to brassinosteroid deficiency; physical restriction within pods causes a reduction in seed size. These results suggest a possible mechanism for increasing faba bean yields to optimal levels.

Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice

New cultivars with very erect leaves, which increase light capture for photosynthesis and nitrogen storage for grain filling, may have increased grain yields. Here we show that the erect leaf phenotype of a rice brassinosteroid-deficient mutant, osdwarf4-1, is associated with enhanced grain yields under conditions of dense planting, even without extra fertilizer. Molecular and biochemical studies reveal that two different cytochrome P450s, CYP90B2/OsDWARF4 and CYP724B1/D11, function redundantly in C-22 hydroxylation, the rate-limiting step of brassinosteroid biosynthesis. Therefore, despite the central role of brassinosteroids in plant growth and development, mutation of OsDWARF4 alone causes only limited defects in brassinosteroid biosynthesis and plant morphology. These results suggest that regulated genetic modulation of brassinosteroid biosynthesis can improve crops without the negative environmental effects of fertilizers.

Loss of function of four DELLA genes leads to light- and gibberellin-independent seed germination in Arabidopsis

The Arabidopsis severe gibberellin-deficient mutant ga1-3 does not germinate even when the optimal light and temperature conditions are provided. This fact suggests that (1) gibberellin (GA) is absolutely necessary for the germination of an intact seed and (2) the ga1-3 mutant can be used as a good system to identify factors that repress seed germination. In this report, using ga1-3 mutation as the genetic background, we confirm that RGL2, one member of the DELLA family, encodes the predominant repressor of seed germination in Arabidopsis and show that the other DELLA genes GAI,RGA and RGL1 enhance the function of RGL2. More importantly, we show that ga1-3 seeds lacking RGA, RGL1 and RGL2 or GAI, RGL1 and RGL2, confer GA-independent germination in the light but not in the darkness whilst ga1-3 seeds lacking GAI, RGA and RGL2 germinate both in the light and darkness. This suggests that the destabilization or inactivation of RGA and GAI is not only triggered by GA but also possibly by light. In addition, ga1-3 seeds lacking in all the aforementioned four DELLA genes have elongated epidermal cells and confer light-, cold- and GA-independent seed germination. Therefore, DELLA proteins likely act as integrators of environmental and endogenous cues to regulate seed germination.

Overexpression of a GRAS protein lacking the DELLA domain confers altered gibberellin responses in rice

The rice SLR1 (SLENDER RICE 1) gene encodes a DELLA protein that belongs to a subfamily of the GRAS protein superfamily and that functions as a repressor of gibberellin (GA) signaling. Based on the constitutive GA response phenotype of slr1 mutants, SLR1 has been thought to be the sole DELLA-type protein suppressing GA signals in rice. However, in rice genome databases we identified two sequences homologous to SLR1: SLR1-like1 and -2 (SLRL1 and -2). SLRL1 and SLRL2 contain regions with high similarity to the C-terminal conserved domains in SLR1, but lack the N-terminal conserved region of the DELLA proteins. The expression of SLRL1 was positively regulated by GA at the mRNA level and occurred preferentially in reproductive organs, whereas SLRL2 was moderately expressed in mature leaf organs and was not affected by GA. Transformation of SLRL1 into the slr1 mutant rescued the slender phenotype of this mutant. Moreover, overexpression of SLRL1 in normal rice plants induced a dwarf phenotype with an increased level of OsGA20ox2 gene expression and diminished the GA-induced shoot elongation, suggesting that SLRL1 acts as a repressor of GA signaling. Consistent with the fact that SLRL1 does not have a DELLA domain, which is essential for degradation of DELLA proteins, a level of SLRL1 protein was not degraded by application of gibberellic acid. However, the repressive activity of SLRL1 against GA signaling was much weaker than a truncated SLR1 lacking the DELLA domain. Based on these characteristics of SLRL1, the functional roles of SLRL1 in GA signaling in rice are discussed.

Wheat cytogenetics in the genomics era and its relevance to breeding

Hexaploid wheat is a species that has been subjected to most extensive cytogenetic studies. This has contributed to understanding the mechanism of the evolution of polyploids involving diploidization through genetic restriction of chromosome pairing to only homologous chromosomes. The availability of a variety of aneuploids and the ph mutants (Ph1 and Ph2) in bread wheat also allowed chromosome manipulations leading to the development of alien addition/substitution lines and the introgression of alien chromosome segments into the wheat genome. More recently in the genomics era, molecular tools have been used extensively not only for the construction of molecular maps, but also for identification/isolation of genes/QTLs (including epistatic QTLs, eQTLs and PQLs) for several agronomic traits. It has also been possible to identify gene-rich regions and recombination hot spots in the wheat genome, which are now being subjected to sequencing at the genome level, through development of BAC libraries. In the EST database also, among all plants wheat ESTs are the highest in number, and are only next to those for human, mouse, Ciona intestinalis (a chordate), rat and zebrafish genomes. These ESTs and sequences of several genomic regions have been subjected to a variety of applications including development of perfect markers and establishment of microcollinearity. The technique of in situ hybridization (including FISH, GISH and McFISH) and the development of deletion stocks also facilitated the preparation of physical maps. Molecular markers are also used for marker-assisted selection in wheat breeding programs in several countries. Construction of a wheat DNA chip, which will also become available soon, may further facilitate wheat genomics research. These enormous resources, knowledge base and the fast development of additional molecular tools and high throughput approaches for genotyping will prove extremely useful in future wheat research and will lead to development of improved wheat cultivars.

Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions

The naturally occurring waxy and low-amylose variants of foxtail millet and other cereals, like rice and barley, originated in East and Southeast Asia under human selection for sticky foods. Mutations in the GBSS1 gene for granule-bound starch synthase 1 are known to be associated with these traits. We have analyzed the gene in foxtail millet, and found that, in this species, these traits were originated by multiple independent insertions of transposable elements and by subsequent secondary insertions into these elements or deletion of parts of the elements. The structural analysis of transposable elements inserted in the GBSS1 gene revealed that the non-waxy was converted to the low-amylose phenotype once, while shifts from non-waxy to waxy occurred three times, from low amylose to waxy once and from waxy to low amylose once. The present results, and the geographical distribution of different waxy molecular types, strongly suggest that these types originated independently and were dispersed into their current distribution areas. The patterns of GBSS1 variation revealed here suggest that foxtail millet may serve as a key to solving the mystery of the origin of waxy-type cereals in Asia. The GBSS1 gene in foxtail millet provides a new example of the evolution of a gene involved in the processes of domestication and its post-domestication fate under the influence of human selection.

Identification of the conserved serine/threonine residues important for gibberellin-sensitivity of Arabidopsis RGL2 protein

The DELLA proteins GAI, RGA, RGL1 and RGL2 in Arabidopsis are plant growth repressors, repressing diverse developmental processes. Studies have shown that gibberellin (GA) attenuates the repressive function of DELLA proteins by triggering their degradation via the proteasome pathway. However, it is not known if GA-induced protein degradation is the only pathway for regulating the bioactivity of DELLA proteins. We show here that tobacco BY2 cells represent a suitable system for studying GA signaling. RGL2 exists in a phosphorylated form in BY2 cells. RGL2 undergoes GA-induced degradation, and this process is blocked by proteasome inhibitors and serine/threonine phosphatase inhibitors; however, serine/threonine kinase inhibitors had no detectable effect, suggesting that dephosphorylation of serine/threonine is probably a prerequisite for degradation of RGL2 via the proteasome pathway. Site-directed substitution of all 17 conserved serine and threonine residues showed that six mutants (RGL2(S441D, RGL2(S542D), RGL2(T271E), RGL2(T319E), RGL2(T411E) and RGL2(T535E)) mimicking the status of constitutive phosphorylation are resistant to GA-induced degradation. This suggests that these sites are potential phosphorylation sites. A functional assay based on the expression of GA 20-oxidase revealed that RGL2(T271E) is probably a null mutant, RGL2(S441D), RGL2(S542D), RGL2(T319E) and RGL2(T411E) only retained about 4-17% of the activity of the wild type RGL2, whereas RGL2(T535E) retained about 66% of the activity of the wild type RGL2. However, expression of GA 20-oxidase in BY2 cells expressing these mutant proteins is still responsive to GA, suggesting that the stabilization of RGL2 protein is not the only pathway for regulating its bioactivity.

The plant architecture of rice (Oryza sativa)

Plant architecture, a collection of the important agronomic traits that determine grain production in rice, is mainly affected by factors including tillering, plant height and panicle morphology. Recently, significant progress has been made in isolating and collecting of mutants that are defective in rice plant architecture. Although our understanding of the molecular mechanisms that control rice tillering, panicle development and plant height are still limited, new findings have begun to emerge. This review, therefore, summarizes the recent progress in exploring the mechanisms that control rice plant architecture.

How can we use genomics to improve cereals with rice as a reference genome?

Rice serves as a model crop for cereal genomics. The availability of complete genome sequences, together with various genomic resources available for both rice and Arabidopsis, have revolutionized our understanding of the genetic make-up of crop plants. Both macrocolinearity revealed by comparative mapping and microcolinearity revealed by sequence comparisons among the grasses indicate that sequencing and functional analysis of the rice genome will have a significant impact on other cereals in terms of both genomic studies and crop improvement. The availability of mutants, introgression libraries, and advanced transformation techniques make functional genomics in rice and other cereals more manageable than ever before. A wide array of genetic markers, including anchor markers for comparative mapping, SSRs and SNPs are widely used in genetic mapping, germplasm evaluation and marker assisted selection. An integrated database that combines genome information for rice and other cereals is key to the effective utilization of all genomics resources for cereal improvement. To maximize the potential of genomics for plant breeding, experiments must be further miniaturized and costs must be reduced. Many techniques, including targeted gene disruption or allele substitution, insertional mutagenesis, RNA interference and homologous recombination, need to be refined before they can be widely used in functional genomic analysis and plant breeding.

Interaction of auxin and ERECTA in elaborating Arabidopsis inflorescence architecture revealed by the activation tagging of a new member of the YUCCA family putative flavin monooxygenases

The aboveground body of higher plants has a modular structure of repeating units, or phytomers. As such, the position, size, and shape of the individual phytomer dictate the plant architecture. The Arabidopsis (Arabidopsis thaliana) ERECTA (ER) gene regulates the inflorescence architecture by affecting elongation of the internode and pedicels, as well as the shape of lateral organs. A large-scale activation-tagging genetic screen was conducted in Arabidopsis to identify novel genes and pathways that interact with the ER locus. A dominant mutant, super1-D, was isolated as a nearly complete suppressor of a partial loss-of-function allele er-103. We found that SUPER1 encodes YUCCA5, a novel member of the YUCCA family of flavin monooxygenases. The activation tagging of YUCCA5 conferred increased levels of free indole acetic acid, increased auxin response, and mild phenotypic characteristics of auxin overproducers, such as elongated hypocotyls, epinastic cotyledons, and narrow leaves. Both genetic and cellular analyses indicate that auxin and the ER pathway regulate cell division and cell expansion in a largely independent but overlapping manner during elaboration of inflorescence architecture.

Transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots

It is not known how representative the Arabidopsis thaliana complement of transcription factors (TFs) is of other plants. The availability of rice (Oryza sativa) genome sequences makes possible a comparative analysis of TFs between monocots and eudicots, the two major monophyletic groups of angiosperms. Here, we identified 1611 TF genes that belong to 37 gene families in rice, comparable to the 1510 in Arabidopsis. Several gene subfamilies, but no families, were found to be lineage-specific. Phylogenetic analyses indicated that nearly half of the TF genes form clear orthologous pairs or groups, which were derived from 383 ancestral genes in the common ancestor of rice and Arabidopsis. Investigating gene duplication mechanisms revealed twelve pairs of large intragenomic duplicated blocks, which account for more than 40% of the rice genome. About 60% of the duplicated TF genes have been retained on duplicated segments. Functional conservation and diversification of TFs across monocot and eudicot lineages are discussed.

Molecular mapping of gibberellin-responsive dwarfing genes in bread wheat

Opportunities exist for replacing reduced height (Rht) genes Rht-B1b and Rht-D1b with alternative dwarfing genes for bread wheat improvement. In this study, the chromosomal locations of several height-reducing genes were determined by screening populations of recombinant inbred lines or doubled haploid lines varying for plant height with microsatellite markers. Linked markers were found for Rht5 (on chromosome 3BS), Rht12 (5AL) and Rht13 (7BS), which accounted for most of the phenotypic variance in height in the respective populations. Large height differences between genotypes (up to 43 cm) indicated linkage to major height-reducing genes. Rht4 was associated with molecular markers on chromosome 2BL, accounting for up to 30% of the variance in height. Confirming previous studies, Rht8 was linked to markers on chromosome 2DS, whereas a population varying for Rht9 revealed a region with a small but significant height effect on chromosome 5AL. The height-reducing effect of these dwarfing genes was repeatable across a range of environments. The molecular markers developed in this study will be useful for marker-assisted selection of alternative height-reducing genes, and to better understand the effects of different Rht genes on wheat growth and agronomic performance.

Cytokinin oxidase regulates rice grain production

Most agriculturally important traits are regulated by genes known as quantitative trait loci (QTLs) derived from natural allelic variations. We here show that a QTL that increases grain productivity in rice, Gn1a, is a gene for cytokinin oxidase/dehydrogenase (OsCKX2), an enzyme that degrades the phytohormone cytokinin. Reduced expression of OsCKX2 causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield. QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailormade crop improvement.

Genetic transformation: a powerful tool for dissection of adaptive traits in trees

Plant transformation and regeneration systems have become indispensable parts of gene discovery and functional characterization over the last two decades. Adoption of transformation methods in studies of plant adaptation to natural environments has been slow. This is a result of poor genomic knowledge and inefficient transformation systems for species dominating terrestrial ecosystems, and logistical difficulties in conducting field tests of genetically engineered organisms. In trees, where long generation cycles, high background polymorphism, large sizes and outcrossing systems of mating make production of near-isogenic lines and large experiments difficult, transformation is an attractive alternative for establishing direct linkages between genes and adaptively significant phenotypes. Here, we outline the capabilities, challenges, and prospects for transformation to become a significant tool for studying the ecophysiological adaptation of trees to the environment. Focusing on poplars (genus Populus) as model system, we describe how transformation-based approaches can provide insights into the genes that control adaptive traits. The availability of the poplar genome sequence, along with its large expressed sequences tag (EST) databanks, facile transformation and rapid growth, enable reverse genetic approaches to be used to test virtually any hypothesis of gene function.

Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.)

The timing of transition from vegetative growth to flowering is important in nature as well as in agriculture. One of several pathways influencing this transition in plants is the gibberellin (GA) pathway. In maize (Zea mays L.), the Dwarf8 (D8) gene has been identified as an orthologue of the gibberellic acid-insensitive (GAI) gene, a negative regulator of GA response in Arabidopsis. Nine intragenic polymorphisms in D8 have been linked with variation in flowering time of maize. We tested the general applicability of these polymorphisms as functional markers in an independent set of inbred lines. Single nucleotide primer extension (SNuPe) and gel-based indel markers were developed, and a set of 71 elite European inbred lines were phenotyped for flowering time and plant height across four environments. To control for population structure, we genotyped the plant material with 55 simple sequence repeat markers evenly distributed across the genome. When population structure was ignored, six of the nine D8 polymorphisms were significantly associated with flowering time and none with plant height. However, when population structure was taken into consideration, an association with flowering time was only detected in a single environment, whereas an association across environments was identified between a 2-bp indel in the promoter region and plant height. As the number of lines with different haplotypes within subpopulations was a limiting factor in the analysis, D8 alleles would need to be compared in isogenic backgrounds for a reliable estimation of allelic effects.

The recessive potyvirus resistance gene pot-1 is the tomato orthologue of the pepper pvr2-eIF4E gene

The translation initiation factor 4E (eIF4E) has been implicated in naturally occurring resistance to Potato virus Y (PVY) determined by the pvr2 locus in pepper (Capsicum annuum). Here, the molecular basis of the recessive resistance to PVY and Tobacco etch virus (TEV) controlled by the pot-1 locus in tomato (Lycopersicon esculentum; now Solanum lycopersicum) was investigated. On the basis of genetic mapping data that indicated that pot-1 and pvr2 are located in syntenic regions of the tomato and pepper genomes, the possible involvement of eIF4E in pot-1-mediated resistance was assessed. Genetic mapping of members of the eIF4E multigenic family in tomato introgression lines revealed that an eIF4E locus indeed maps in the same genomic region as pot-1. By comparing eIF4E coding sequences between resistant and susceptible Lycopersicon genotypes, a small number of polymorphisms that co-segregate with the pot-1 locus were identified, suggesting that this gene could be involved in resistance to potyviruses. Functional complementation experiments using Potato virus X-mediated transient expression of eIF4E from a susceptible genotype in a resistant pepper genotype confirmed that a small number of amino acid substitutions in the eIF4E protein indeed account for resistance/susceptibility to both the PVY and TEV, and consequently that pot-1 and pvr2 are orthologues. Taken together, these results support the role of this eIF4E gene as a key component of recessive resistance to potyviruses, and validate the comparative genomic approach for the molecular characterization of recessive resistance genes.

The leaf morphologies of the subtropical rheophyte Solenogyne mikadoi and its temperate relative S. bellioides (Asteraceae) are affected differently by plant hormones and their biosynthesis inhibitors

Solenogyne mikadoi is a subtropical rheophyte endemic to the Ryukyu Archipelago that develops rosette leaves 2-3 cm in diameter. In contrast, the other three species of this genus all occur in temperate grasslands of Australia and develop rosette leaves about 10 cm in diameter. To examine the involvement of the plant hormones gibberellin and brassinosteroid in the adaptive dwarfism of S. mikadoi, we compared the effects of GA(3) and brassinolide, and their biosynthesis inhibitors on the morphology of the first leaves of S. mikadoi and its temperate relative S. bellioides. In S. mikadoi, one-directional (lengthwise) leaf elongation was strongly facilitated by the application of GA(3) and suppressed by a gibberellin-biosynthetic inhibitor, uniconazole-P, while leaf width (transverse) expansion was insensitive to and was never facilitated by any of the compounds used. Conversely, in S. bellioides, brassinolide facilitated both the elongation and expansion of leaves, while a brassinosteroid-specific biosynthesis inhibitor, brassinazole220, suppressed both. One-directional leaf elongation caused by the reduced sensitivity to brassinolide in S. mikadoi and brassinolide-dependent two-dimensional leaf expansion in S. bellioides both appear to be adaptations to their respective habitats: S. mikadoi has narrow leaves resistant to flowing water, whereas S. bellioides has broad leaves capable of harnessing sufficient light and water in temperate grasslands.

Phloem long-distance trafficking of GIBBERELLIC ACID-INSENSITIVE RNA regulates leaf development

The phloem translocation stream contains a population of RNA molecules, suggesting plants use RNA to integrate developmental processes, at the whole-plant level. In the present study, we analyzed the role of long-distance trafficking in the delivery of transcripts from two members of the GRAS family, namely CmGAIP and GAI. These two homologs were chosen because of their involvement as transcriptional regulators in GA signaling. A combination of pumpkin, tomato and Arabidopsis was employed to examine the processes involved in long-distance delivery, to sink tissues, of RNA for engineered dominant gain-of-function pumpkin (Cmgaip) and Arabidopsis (DeltaDELLA-gai) genes. Our studies demonstrate that gai RNA entry into functional sieve elements occurs via a selective process. Both engineered mutant gai transcripts were able to exit the scion phloem and traffic cell to cell into the shoot apex. Delivery of Cmgaip and DeltaDELLA-gai RNA mediated highly reproducible changes in leaf phenotype in transgenic tomato lines grown under greenhouse conditions. Phenotypic analysis indicated that tomato leaflet morphology was influenced quite late in development. In addition, tissue sink strength did not appear to dictate gai RNA delivery, suggesting complexity in the process underlying macromolecular trafficking. These results establish that the molecular properties of the Cmgaip and DeltaDELLA-gai transcripts are compatible with the tomato cell-to-cell and long-distance macromolecular trafficking systems. An important conclusion, based on our work, is that control over GAI RNA delivery, via the phloem, may be regulated by sequence motifs conserved between plant families. We propose that RNA delivery via the phloem allows for flexibility in fine tuning of developmental programs to ensure newly developing leaves are optimized for performance under the prevailing environmental conditions.

A novel dwarfing mutation in a green revolution gene from Brassica rapa

Mutations in the biosynthesis or signaling pathways of gibberellin (GA) can cause dwarfing phenotypes in plants, and the use of such mutations in plant breeding was a major factor in the success of the Green Revolution. DELLA proteins are GA signaling repressors whose functions are conserved in different plant species. Recent studies show that GA promotes stem growth by causing degradation of DELLA proteins via the ubiquitin-proteasome pathway. The most widely utilized dwarfing alleles in wheat (Triticum aestivum; e.g. Rht-B1b and Rht-D1b) encode GA-resistant forms of a DELLA protein that function as dominant and constitutively active repressors of stem growth. All of the previously identified dominant DELLA repressors from several plant species contain N-terminal mutations. Here we report on a novel dwarf mutant from Brassica rapa (Brrga1-d) that is caused by substitution of a conserved amino acid in the C-terminal domain of a DELLA protein. Brrga1-d, like N-terminal DELLA mutants, retains its repressor function and accumulates to high levels, even in the presence of GA. However, unlike wild-type and N-terminal DELLA mutants, Brrga1-d does not interact with a protein component required for degradation, suggesting that the mutated amino acid causes dwarfism by preventing an interaction needed for its degradation. This novel mutation confers nondeleterious dwarf phenotypes when transferred to Arabidopsis (Arabidopsis thaliana) and oilseed rape (Brassica napus), indicating its potential usefulness in other crop species.

Modulation of F1 hybrid stature without altering parent plants through trans-activated expression of a mutated rice GAI homologue

Hybrid breeding, by taking advantage of heterosis, brings about many superior properties to the F1 progeny. However, some properties, such as increased plant height, are not desirable for agronomic purposes. To specifically counter the height increase associated with hybrid progeny, we employed an Arabidopsis model and tested a trans-activation system for specifically expressing a mutated GAI gene only in the F1 hybrid plants to reduce plant stature. A transcriptional activator, the Gal4 DNA-binding domain fused to the acidic activation domain of herpes simplex virus VP16 protein, driven by a maize ubiquitin promoter, was introduced in one parental line. A rice GAI homologue with an N-terminal deletion of the DELLA domain, driven by a promoter that is responsive to the transcriptional activator, was transferred into another parental line. After genetic crossing, trans-activation of the GAI mutant gene resulted in a dwarf phenotype. Over 50 pair-wise crosses between the parental lines were performed, and analyses suggested that the percentage of F1 progeny exhibiting dwarfism ranged from about 25% to 100%. Furthermore, the dwarfism trait introduced in F1 progeny did not seem to affect total seed yield. Our result suggests the feasibility of manipulating F1 hybrid progeny traits without affecting parent plants or the agronomic property of the progeny.

A high-density genetic map of hexaploid wheat (Triticum aestivum L.) from the cross Chinese Spring x SQ1 and its use to compare QTLs for grain yield across a range of environments

A population of 96 doubled haploid lines (DHLs) was prepared from F1 plants of the hexaploid wheat cross Chinese Spring x SQ1 (a high abscisic acid-expressing breeding line) and was mapped with 567 RFLP, AFLP, SSR, morphological and biochemical markers covering all 21 chromosomes, with a total map length of 3,522 cM. Although the map lengths for each genome were very similar, the D genome had only half the markers of the other two genomes. The map was used to identify quantitative trait loci (QTLs) for yield and yield components from a combination of 24 site x treatment x year combinations, including nutrient stress, drought stress and salt stress treatments. Although yield QTLs were widely distributed around the genome, 17 clusters of yield QTLs from five or more trials were identified: two on group 1 chromosomes, one each on group 2 and group 3, five on group 4, four on group 5, one on group 6 and three on group 7. The strongest yield QTL effects were on chromosomes 7AL and 7BL, due mainly to variation in grain numbers per ear. Three of the yield QTL clusters were largely site-specific, while four clusters were largely associated with one or other of the stress treatments. Three of the yield QTL clusters were coincident with the dwarfing gene Rht-B1 on 4BS and with the vernalisation genes Vrn-A1 on 5AL and Vrn-D1 on 5DL. Yields of each DHL were calculated for trial mean yields of 6 g plant(-1) and 2 g plant(-1) (equivalent to about 8 t ha(-1) and 2.5 t ha(-1), respectively), representing optimum and moderately stressed conditions. Analyses of these yield estimates using interval mapping confirmed the group-7 effects on yield and, at 2 g plant(-1), identified two additional major yield QTLs on chromosomes 1D and 5A. Many of the yield QTL clusters corresponded with QTLs already reported in wheat and, on the basis of comparative genetics, also in rice. The implications of these results for improving wheat yield stability are discussed.

Gibberellin metabolism and signaling

Gibberellins (GAs) are a family of plant hormones controlling many aspects of plant growth and development including stem elongation, germination, and the transition from vegetative growth to flowering. Cloning of the genes encoding GA biosynthetic and inactivating enzymes has led to numerous insights into the developmental regulation of GA hormone accumulation that is subject to both positive and negative feedback regulation. Genetic and biochemical analysis of GA-signaling genes has revealed that posttranslational regulation of DELLA protein accumulation is a key control point in GA response. The highly conserved DELLA proteins are a family of negative regulators of GA signaling that appear subject to GA-stimulated degradation through the ubiquitin-26S proteasome pathway. This review discusses the regulation of GA hormone accumulation and signaling in the context of its role in plant growth and development.