Genetic Regulation of Development in Sorghum bicolor (VIII. Shoot Growth, Tillering, Flowering, Gibberellin Biosynthesis, and Phytochrome Levels Are Differentially Affected by Dosage of the ma3R Allele

Evolutionary divergence of phytochrome protein function in Zea mays PIF3 signaling

Two maize phytochrome-interacting factor (PIF) basic helix-loop-helix (bHLH) family members, ZmPIF3.1 and ZmPIF3.2, were identified, cloned and expressed in vitro to investigate light-signaling interactions. A phylogenetic analysis of sequences of the maize bHLH transcription factor gene family revealed the extent of the PIF family, and a total of seven predicted PIF-encoding genes were identified from genes encoding bHLH family VIIa/b proteins in the maize genome. To investigate the role of maize PIFs in phytochrome signaling, full-length cDNAs for phytochromes PhyA2, PhyB1, PhyB2 and PhyC1 from maize were cloned and expressed in vitro as chromophorylated holophytochromes. We showed that ZmPIF3.1 and ZmPIF3.2 interact specifically with the Pfr form of maize holophytochrome B1 (ZmphyB1), showing no detectable affinity for the Pr form. Maize holophytochrome B2 (ZmphyB2) showed no detectable binding affinity for PIFs in either Pr or Pfr forms, but phyB Pfr from Arabidopsis interacted with ZmPIF3.1 similarly to ZmphyB1 Pfr. We conclude that subfunctionalization at the protein-protein interaction level has altered the role of phyB2 relative to that of phyB1 in maize. Since the phyB2 mutant shows photomorphogenic defects, we conclude that maize phyB2 is an active photoreceptor, without the binding of PIF3 seen in other phyB family proteins.

Three FLOWERING LOCUS T-like genes function as potential florigens and mediate photoperiod response in sorghum

Sorghum is a typical short-day (SD) plant and its use in grain or biomass production in temperate regions depends on its flowering time control, but the underlying molecular mechanism of floral transition in sorghum is poorly understood. Here we characterized sorghum FLOWERING LOCUS T (SbFT) genes to establish a molecular road map for mechanistic understanding. Out of 19 PEBP genes, SbFT1, SbFT8 and SbFT10 were identified as potential candidates for encoding florigens using multiple approaches. Phylogenetic analysis revealed that SbFT1 clusters with the rice Hd3a subclade, while SbFT8 and SbFT10 cluster with the maize ZCN8 subclade. These three genes are expressed in the leaf at the floral transition initiation stage, expressed early in grain sorghum genotypes but late in sweet and forage sorghum genotypes, induced by SD treatment in photoperiod-sensitive genotypes, cooperatively repressed by the classical sorghum maturity loci, interact with sorghum 14-3-3 proteins and activate flowering in transgenic Arabidopsis plants, suggesting florigenic potential in sorghum. SD induction of these three genes in sensitive genotypes is fully reversed by 1 wk of long-day treatment, and yet, some aspects of the SD treatment may still make a small contribution to flowering in long days, indicating a complex photoperiod response mediated by SbFT genes.

Molecular evolution of the Sorghum Maturity Gene Ma3

Time to maturity is a critical trait in sorghum (Sorghum bicolor) breeding, as it determines whether a variety can be grown in a particular cropping system or ecosystem. Understanding the nucleotide variation and the mechanisms of molecular evolution of the maturity genes would be helpful for breeding programs. In this study, we analyzed the nucleotide diversity of Ma3, an important maturity gene in sorghum, using 252 cultivated and wild sorghum materials from all over the world. The nucleotide variation and diversity were analyzed based both on race- and usage-based groups. We also sequenced 12 genes around the Ma3 gene in 185 of these materials to search for a selective sweep and found that purifying selection was the strongest force on Ma3, as low nucleotide diversity and low-frequency amino acid variants were observed. However, a very special mutation, described as ma3R, seemed to be under positive selection, as indicated by dramatically reduced nucleotide variation not only at the loci but also in the surrounding regions among individuals carrying the mutations. In addition, in an association study using the Ma3 nucleotide variations, we detected 3 significant SNPs for the heading date at a high-latitude environment (Beijing) and 17 at a low-latitude environment (Hainan). The results of this study increases our understanding of the evolutionary mechanisms of the maturity genes in sorghum and will be useful in sorghum breeding.

Plant growth enhancement and associated physiological responses are coregulated by ethylene and gibberellin in response to harpin protein Hpa1

The harpin protein Hpa1 produced by the bacterial blight pathogen of rice induces several growth-promoting responses in plants, activating the ethylene signaling pathway, increasing photosynthesis rates and EXPANSIN (EXP) gene expression levels, and thereby enhancing the vegetative growth. This study was attempted to analyze any mechanistic connections among the above and the role of gibberellin in these responses. Hpa1-induced growth enhancement was evaluated in Arabidopsis, tomato, and rice. And growth-promoting responses were determined mainly as an increase of chlorophyll a/b ratio, which indicates a potential elevation of photosynthesis rates, and enhancements of photosynthesis and EXP expression in the three plant species. In Arabidopsis, Hpa1-induced growth-promoting responses were partially compromised by a defect in ethylene perception or gibberellin biosynthesis. In tomato and rice, compromises of Hpa1-induced growth-promoting responses were caused by a pharmacological treatment with an ethylene perception inhibitor or a gibberellin biosynthesis inhibitor. In the three plant species, moreover, Hpa1-induced growth-promoting responses were significantly impaired, but not totally eliminated, by abolishing ethylene perception or gibberellin synthesis. However, simultaneous nullifications in both ethylene perception and gibberellin biosynthesis almost canceled the full effects of Hpa1 on plant growth, photosynthesis, and EXP2 expression. Theses results suggest that ethylene and gibberellin coregulate Hpa1-induced plant growth enhancement and associated physiological and molecular responses.

Heterosis, stress, and the environment: a possible road map towards the general improvement of crop yield

Contemporary plant breeding is under pressure to improve crop productivity at a rate surpassing past achievements. Different research groups dealing with this issue reached similar conclusions that the solution lies in improved biomass production by way of enhanced light capture and use efficiency, modified photosystem biochemistry, and improved partitioning of assimilates to the economic part of the plant. There seems to be a consensus of sorts. This 'opinion paper' calls attention to the phenomenon of heterosis, as expressed in maize, sorghum, and other crops where, depending on the case and the trait, larger biomass and greater yield have been achieved without a change in growth duration, photosystem biochemistry, or harvest index. This discussion maintains that there is no consensus about the genetics or the genomics of heterosis in regulating yield under diverse environments. Therefore, in a search for the basis of heterosis in yield and adaptation, the discussion bypasses the genetics and searches for answers in the phenomics of heterosis. The heterotic phenotype in itself provides challenging and important hints towards improving the yield of open-pollinated crops in general. These hints are linked to the homeostasis of photosynthesis with respect to temperature, the photobiology of the plant as mediated by phytochrome, the architectural foundations of the formation of a large sink, and the associated hormones and signals in controlling sink differentiation and source-sink communication. This discussion does not lay out plans and protocols but provides clues to explore within and beyond the current thinking about breeding for high yield.

Association studies identify natural variation at PHYC linked to flowering time and morphological variation in pearl millet

The identification of genes selected during and after plant domestication is an important research topic to enhance knowledge on adaptative evolution. Adaptation to different climates was a key factor in the spread of domesticated crops. We conducted a study to identify genes responsible for these adaptations in pearl millet and developed an association framework to identify genetic variations associated with the phenotype in this species. A set of 90 inbred lines genotyped using microsatellite loci and AFLP markers was used. The population structure was assessed using two different Bayesian approaches that allow inbreeding or not. Association studies were performed using a linear mixed model considering both the population structure and familial relationships between inbred lines. We assessed the ability of the method to limit the number of false positive associations on the basis of the two different Bayesian methods, the number of populations considered and different morphological traits while also assessing the power of the methodology to detect given additive effects. Finally, we applied this methodology to a set of eight pearl millet genes homologous to cereal flowering pathway genes. We found significant associations between several polymorphisms of the pearl millet PHYC gene and flowering time, spike length, and stem diameter in the inbred line panel. To validate this association, we performed a second association analysis in a different set of pearl millet individuals from Niger. We confirmed a significant association between genetic variation in this gene and these characters.

Stable expression of AtGA2ox1 in a low-input turfgrass (Paspalum notatum Flugge) reduces bioactive gibberellin levels and improves turf quality under field conditions

Bahiagrass (Paspalum notatum Flugge) is a prime candidate for molecular improvement of turf quality. Its persistence and low input characteristics made it the dominant utility turfgrass along highways in the south-eastern USA. However, the comparatively poor turf quality due to reduced turf density and prolific production of unsightly inflorescences currently limits the widespread use of bahiagrass as residential turf. Alteration of endogenous gibberellin (GA) levels by application of growth regulators or transgenic strategies has modified plant architecture in several crops. GA catabolizing AtGA2ox1 was subcloned under the control of the constitutive maize ubiquitin promoter and Nos 3'UTR. A minimal AtGA2ox1 expression cassette lacking vector backbone sequences was stably introduced into apomictic bahiagrass by biolistic gene transfer as confirmed by Southern blot analysis. Expression of AtGA2ox1 in bahiagrass as indicated by reverse transcription-polymerase chain reaction and Northern blot analysis resulted in a significant reduction of endogenous bioactive GA(1) levels compared to wild type. Interestingly, transgenic plants displayed an increased number of vegetative tillers which correlated with the level of AtGA2ox1 expression and enhanced turf density under field conditions. This indicates that GAs contribute to signalling the outgrowth of axillary buds in this perennial grass. Transgenic plants also showed decreased stem length and delayed flowering under controlled environment and field conditions. Consequently, turf quality following weekly mowing was improved in transgenic bahiagrass. Transgene expression and phenotype were transmitted to seed progeny. Argentine bahiagrass produces seeds asexually by apomixis, which reduces the risk of unintended transgene dispersal by pollen and results in uniform progeny.

Subfunctionalization of PhyB1 and PhyB2 in the control of seedling and mature plant traits in maize

Phytochromes are the primary red/far-red photoreceptors of higher plants, mediating numerous developmental processes throughout the life cycle, from germination to flowering. In seed plants, phytochromes are encoded by a small gene family with each member performing both distinct and redundant roles in mediating physiological responses to light cues. Studies in both eudicot and monocot species have defined a central role for phytochrome B in mediating responses to light in the control of several agronomically important traits, including plant height, transitions to flowering and axillary branch meristem development. Here we characterize Mutator-induced alleles of PhyB1 and a naturally occurring deletion allele of PhyB2 in Zea mays (maize). Using single and double mutants, we show that the highly similar PhyB1 and PhyB2 genes encode proteins with both overlapping and non-redundant functions that control seedling and mature plant traits. PHYB1 and PHYB2 regulate elongation of sheath and stem tissues of mature plants and contribute to the light-mediated regulation of PhyA and Cab gene transcripts. However, PHYB1 and not PHYB2 contributes significantly to the inhibition of mesocotyl elongation under red light, whereas PHYB2 and to a lesser extent PHYB1 mediate the photoperiod-dependent floral transition. This sub functionalization of PHYB activities in maize has probably occurred since the tetraploidization of maize, and may contribute to flowering time variation in modern-day varieties.

Regulation of transcript levels of a potato gibberellin 20-oxidase gene by light and phytochrome B

Up to three gibberellin (GA) 20-oxidase genes have now been cloned from several species including Arabidopsis, bean (Phaseolus vulgaris), and potato (Solanum tuberosum). In each case the GA 20-oxidase genes exhibit different patterns of tissue expression. We have performed extensive northern analysis on one of the potato GA 20-oxidase genes (StGA20ox1), which is the only one that shows significant transcript levels in leaves. We show that levels of StGA20ox1 transcript are elevated in transgenic antisense plants that have reduced levels of phytochrome B (PHYB) compared with wild-type plants, implicating PHYB in the control of GA biosynthesis. We show that StGA20ox1 transcript levels vary in leaves of different age throughout the plant and cycle throughout the day, furthermore they are up-regulated by light and down-regulated in the dark. The degree of the response to the light-on signal is similar in potato plants deficient in phytochrome A or PHYB and wild-type plants. The induction of StGA20ox1 by blue light raises the possibility that a blue light receptor may be involved in the control of this gene by light.

Phytochrome B affects the levels of a graft-transmissible signal involved in tuberization

Grafting experiments between phytochrome B antisense and wild-type potato (Solanum tuberosum L. subsp. andigena [line 7540]) plants provide evidence that phytochrome B is involved in the production of a graft-transmissible inhibitor of tuberization, the level of which is reduced in the antisense plants, allowing them to tuberize in noninducing photoperiods.

Photoperiod control of gibberellin levels and flowering in sorghum

Regulation of rhythmic peaks in levels of endogenous gibberellins (GAs) by photoperiod was studied in the short-day monocot sorghum (Sorghum bicolor [L.] Moench). Comparisons were made between three maturity (Ma) genotypes: 58M (Ma1Ma1, Ma2Ma2, phyB-1phyB-1, and Ma4Ma4 [a phytochrome B null mutant]); 90M (Ma1Ma1, Ma2Ma2, phyB-2phyB-2, and Ma4Ma4); and 100M (Ma1Ma1, Ma2Ma2, PHYBPHYB, and Ma4Ma4). Plants were grown for 14 d under 10-, 14-, 16-, 18-, and 20-h photoperiods, and GA levels were assayed by gas chromatography-mass spectrometry every 3 h for 24 h. Under inductive 10-h photoperiods, the peak of GA20 and GA1 levels in 90M and 100M was shifted from midday, observed earlier with 12-h photoperiods, to an early morning peak, and flowering was hastened. In addition, the early morning peaks in levels of GA20 and GA1 in 58M under conditions allowing early flowering (10-, 12-, and 14-h photoperiods) were shifted to midday by noninductive (18- and 20-h) photoperiods, and flowering was delayed. These results are consistent with the possibility that the diurnal rhythm of GA levels plays a role in floral initiation and may be one way by which the absence of phytochrome B causes early flowering in 58M under most photoperiods.

Comparative genetics of flowering time

Analysis of genes controlling flowering time (heading date) contributes to our understanding of fundamental principles of plant development and is of practical importance because of the effects of flowering time on plant adaptation and crop yield. This review discusses the extent to which plants may share common genetic mechanisms for the control of flowering time and the implications of such conservation for gene isolation from the major cereal crops. Gene isolation may exploit the small genome of rice in map-based approaches, utilizing the conservation of gene order that is revealed when common DNA markers are mapped in different species. Alternatively, mechanisms may be conserved within plants as a whole, in which case genes cloned from the model dicot Arabidopsis thaliana provide an alternative route.

Comparative genetics of flowering time

Analysis of genes controlling flowering time (heading date) contributes to our understanding of fundamental principles of plant development and is of practical importance because of the effects of flowering time on plant adaptation and crop yield. This review discusses the extent to which plants may share common genetic mechanisms for the control of flowering time and the implications of such conservation for gene isolation from the major cereal crops. Gene isolation may exploit the small genome of rice in map-based approaches, utilizing the conservation of gene order that is revealed when common DNA markers are mapped in different species. Alternatively, mechanisms may be conserved within plants as a whole, in which case genes cloned from the model dicot Arabidopsis thaliana provide an alternative route.

The Brassica rapa elongated internode (EIN) gene encodes phytochrome B

The elongated internode (ein) mutation of Brassica rapa leads to a deficiency in immunochemically detectable phytochrome B. Molecular analysis of the PHYB gene from ein indicates a deletion in the flanking DNA 5' of the ATG start codon, which could interfere either with PHYB transcription or processing of the PHYB transcript. Restriction fragment length polymorphisms and inverse PCR fragments generated from the PHYB gene of wild-type and ein seedlings demonstrate the deletion to be 500 bp in length. Seedlings of heterozygote, EIN/ein, contain about 50% of the level of immunochemically detectable phytochrome B of equivalent wild-type EIN/EIN seedlings. Etiolated seedlings of EIN/ein show a responsiveness to red light almost intermediate between that of ein/ein and EIN/EIN homozygotes. Furthermore, whereas the ein/ein homozygote is poorly responsive to low red/far-red ratio light, the presence of one functional allele of EIN in the heterozygote confers an elongation response intermediate between that of the homozygotes EIN/EIN and ein/ein in these light conditions. The partial dominance of ein indicates a close relationship between phytochrome B level and phenotype.

Phytochrome B affects responsiveness to gibberellins in Arabidopsis

Plant responses to red and far-red light are mediated by a family of photoreceptors called phytochromes. Arabidopsis thaliana seedlings lacking one of the phytochromes, phyB, have elongated hypocotyls and other tissues, suggesting that they may have an alteration in hormone physiology. We have studied the possibility that phyB mutations affect seedling gibberellin (GA) perception and metabolism by testing the responsiveness of wild-type and phyB seedlings to exogenous GAs. The phyB mutant elongates more than the wild type in response to the same exogenous concentrations of GA3 or GA4, showing that the mutation causes an increase in responsiveness to GAs. Among GAs that we were able to detect, we found no significant difference in endogenous levels between wild-type and phyB mutant seedlings. However, GA4 levels were below our limit of detectability, and the concentration of that active GA could have varied between wild-type and phyB mutant seedlings. These results suggest that, although GAs are required for hypocotyl cell elongation, phyB does not act primarily by changing total seedling GA levels but rather by decreasing seedling responsiveness to GAs.

LIGHT CONTROL OF SEEDLING DEVELOPMENT

Light control of plant development is most dramatically illustrated by seedling development. Seedling development patterns under light (photomorphogenesis) are distinct from those in darkness (skotomorphogenesis or etiolation) with respect to gene expression, cellular and subcellular differentiation, and organ morphology. A complex network of molecular interactions couples the regulatory photoreceptors to developmental decisions. Rapid progress in defining the roles of individual photoreceptors and the downstream regulators mediating light control of seedling development has been achieved in recent years, predominantly because of molecular genetic studies in Arabidopsis thaliana and other species. This review summarizes those important recent advances and highlights the working models underlying the light control of cellular development. We focus mainly on seedling morphogenesis in Arabidopsis but include complementary findings from other species.

Far-red light stimulates internode elongation, cell division, cell elongation, and gibberellin levels in bean

The contributions of cell division and cell elongation and the potential role of gibberellins in the far-red light stimulation of bean internode elongation were investigated. When bean plants, Phaseolus vulgaris cv. Kentucky Wonder, were grown in white light supplemented with far-red light a significant increase, up to threefold, in internode elongation was observed. Microscopic examination revealed that cell lengths were also increased but by a lower magnitude than internode length. Cell-labeling studies with [3H]thymidine showed that nuclei labeling was increased in internodes receiving supplemental far-red light. Thus far-red light induced increased internode elongation is a result of both increased cell elongation and increased cell division. Gibberellins A1, A20, A19, A44, and A4 and kaurenoic acid were identified in extracts of internode tissue by gas chromatography – mass spectroscopy using [2H2]-labeled internal standards for quantification. It thus appears that the early C-13 hydroxylation pathway is operative in the elongating internode. Endogenous GA1 and GA20 were approximately twofold higher in the first internodes of plants receiving supplemental far-red light. A comparison of the metabolism of exogenously supplied [2H2]GA19 suggested that GA turnover was greater in tissues exposed to supplemental far-red light. These results indicate that both cell division and elongation contribute to the enhanced elongation response of bean internodes to far-red light and that these processes are correlated with an increase in GA levels and (or) metabolism. Keywords: Phaseolus, gibberellins, phytochrome, far-red light.

Expression of functional oat phytochrome A in transgenic rice

To investigate the biological functions of phytochromes in monocots, we generated, by electric discharge particle bombardment, transgenic rice (Oryza sativa cv Gulfmont) that constitutively expresses the oat phytochrome A apoprotein. The introduced 124-kD polypeptide bound chromophore and assembled into a red- and far-red-light-photoreversible chromoprotein with absorbance spectra indistinguishable from those of phytochrome purified from etiolated oats. Transgenic lines expressed up to 3 and 4 times more spectrophotometrically detectable phytochrome than wild-type plants in etiolated and green seedlings, respectively. Upon photo-conversion to the far-red-absorbing form of phytochrome, oat phytochrome A was degraded in etiolated seedlings with kinetics similar to those of endogenous rice phytochromes (half-life approximately 20 min). Although plants overexpressing phytochrome A were phenotypically indistinguishable from wild-type plants when grown under high-fluence white light, they were more sensitive as etiolated seedlings to light pulses that established very low phytochrome equilibria. This indicates that the introduced oat phytochrome A was biologically active. Thus, rice ectopically expressing PHY genes may offer a useful model to help understand the physiological functions of the various phytochrome isoforms in monocotyledonous plants.

A Temporarily Red Light-Insensitive Mutant of Tomato Lacks a Light-Stable, B-Like Phytochrome

We have selected four recessive mutants in tomato (Lycopersicon esculentum Mill.) that, under continuous red light (R), have long hypocotyls and small cotyledons compared to wild type (WT), a phenotype typical of phytochrome B (phyB) mutants of other species. These mutants, which are allelic, are only insensitive to R during the first 2 days upon transition from darkness to R, and therefore we propose the gene symbol tri (temporarily red light insensitive). White light-grown mutant plants have a more elongated growth habit than that of the WT. An immunochemically and spectrophotometrically detectable phyB-like polypeptide detectable in the WT is absent or below detection limits in the tri1 mutant. In contrast to the absence of an elongation growth response to far-red light (FR) given at the end of the daily photoperiod (EODFR) in all phyB-deficient mutants so far characterized, the tri1 mutant responds to EODFR treatment. The tri1 mutant also shows a strong response to supplementary daytime far-red light. We propose that the phyB-like phytochrome deficient in the tri mutants plays a major role during de-etiolation and that other light-stable phytochromes can regulate the EODFR and shade-avoidance responses in tomato.

Genetic Regulation of Development in Sorghum bicolor (X. Greatly Attenuated Photoperiod Sensitivity in a Phytochrome-Deficient Sorghum Possessing a Biological Clock but Lacking a Red Light-High Irradiance Response)

The role of a light-stable, 123-kD phytochrome in the biological clock, in photoperiodic flowering and shoot growth in extended photoperiods, and in the red light-high irradiance response was studied in Sorghum bicolor using a phytochrome-deficient mutant, 58M (ma3R ma3R), and a near-isogenic wild-type cultivar, 100M (Ma3 Ma3). Since chlorophyll a/b-binding protein mRNA and ribulose bisphosphate carboxylase small subunit mRNA cycled in a circadian fashion in both 58M and 100M grown in constant light, the 123-kD phytochrome absent from 58M does not appear necessary for expression or entrainment of a functional biological clock. Although 58M previously appeared photoperiod insensitive in 12-h photoperiods, extending the photoperiod up to 24 h delayed floral initiation for up to 2 weeks but did not much affect shoot elongation. Thus, although 58M flowers early in intermediate photoperiods, a residual photoperiod sensitivity remains that presumably is not due to the missing 123-kD phytochrome. Since rapid shoot elongation persists in 58M under extended photoperiods despite delayed floral initiation, long photoperiods uncouple those processes. The observed absence of a red light-high irradiance response in 58M, in contrast to the presence of the response in 100M, strengthens the suggestion that the 123-kD phytochrome missing from 58M is a phyB.

Genetic Regulation of Development in Sorghum bicolor (IX. The ma3R Allele Disrupts Diurnal Control of Gibberellin Biosynthesis)

The diurnal regulation of gibberellin (GA) concentrations in Sorghum bicolor was studied in a mutant lacking a light-stable 123-kD phytochrome (ma3Rma3R), wild-type (ma3ma3,Ma3Ma3), and heterozygous (ma3ma3R) cultivars. GAs were determined in shoots of 14-d-old plants by gas chromatography-selected ion-monitoring-mass spectrometry. GA12 levels fluctuated rhythmically in Ma3Ma3, ma3ma3, and,ma3Rma3R; Peak levels occured 3 to 9 h after lights-on. In some experiments, GA53 levels followed a similar pattern. There was no rhythmicity in levels of GA19 and GA8 in any genotype. In ma3ma3 and Ma3Ma3, GA20 levels increased at lights-on, peaked in the afternoon, and decreased to minimum levels in darkness. In ma3Rma3R, peak GA20 levels occured at lights-on, 9 h earlier than in the wild-type genotypes. The pattern for GA1 levels closely followed GA20 levels in all cultivars. One copy of ma3 restored near wild-type regulation of GA20 levels. GA rhythms persisted in 25-d-old ma3ma3 plants. Since absence of the 123-kD phytochrome disrupted diurnal regulation of the GA19 -> GA20 step, the ma3Rma3R genotype may be viewed as being phase shifted in the rhythmic levels of GA20 and GA1 rather than as simply overproducing them.