Development of Agrobacterium-mediated in planta transformation protocol through coleoptile in rice

Genetic modification of rice is mainly carried out by Agrobacterium-mediated transformation of callus accompanied by tissue culture. It is time consuming, laborious and unapplicable for cultivars unable to induce callus. In this study, we have reported a novel gene transfer protocol that involves pulling out primary leaf from coleoptile and injection of Agrobacterium culture into the empty channel. Out of 25 plants survived after injection of Agrobacterium tumefaciens EHA105 culture harboring pCAMBIA1301-RD29A-AtDREB1A, 8 T0 plants revealed the expected size of around 811 bp corresponding to AtDREB1A gene and Southern blotting analysis on 18 T1 plants suggested introgression of AtDREB1A. 3 T2 lines (7-9, 12-3, 18-6) exhibited accumulation of free proline and soluble sugars, yet increase of chlorophyll content, but decrease of electrolyte leakage and methane dicarboxylic aldehyde under cold stress condition at the vegetative growth stage. Yield components investigation on T2 lines showed earlier heading date and no yield loss compared to wild type plants grown under normal condition. GUS expression analysis and integrated transgene detection in T0 and T1 plants followed by evaluation of cold stress tolerance in T2 lines suggest the advantage of this in planta transformation protocol to obtain transgenic rice.

Dynamic genome-wide association analysis and identification of candidate genes involved in anaerobic germination tolerance in rice

BACKGROUND

In Asian rice production, an increasing number of countries now choose the direct seeding mode because of rising costs, labour shortages and water shortages. The ability of rice seeds to undergo anaerobic germination (AG) plays an important role in the success of direct seeding.

RESULTS

In this study, we used 2,123,725 single nucleotide polymorphism (SNP) markers based on resequencing to conduct a dynamic genome-wide association study (GWAS) of coleoptile length (CL) and coleoptile diameter (CD) in 209 natural rice populations. A total of 26 SNP loci were detected in these two phenotypes, of which 5 overlapped with previously reported loci (S1_ 39674301, S6_ 20797781, S7_ 18722403, S8_ 9946213, S11_ 19165397), and two sites were detected repeatedly at different time points (S3_ 24689629 and S5_ 27918754). We suggest that these 7 loci (-log₁₀ (P) value > 7.3271) are the key sites that affect AG tolerance. To screen the candidate genes more effectively, we sequenced the transcriptome of the flooding-tolerant variety R151 in six key stages, including anaerobic (AN) and the oxygen conversion point (AN-A), and obtained high-quality differential expression profiles. Four reliable candidate genes were identified: Os01g0911700 (OsVP1), Os05g0560900 (OsGA2ox8), Os05g0562200 (OsDi19-1) and Os06g0548200. Then qRT-PCR and LC-MS/ MS targeting metabolite detection technology were used to further verify that the up-regulated expression of these four candidate genes was closely related to AG.

CONCLUSION

The four novel candidate genes were associated with gibberellin (GA) and abscisic acid (ABA) regulation and cell wall metabolism under oxygen-deficiency conditions and promoted coleoptile elongation while avoiding adverse effects, allowing the coleoptile to obtain oxygen, escape the low-oxygen environment and germinate rapidly. The results of this study improve our understanding of the genetic basis of AG in rice seeds, which is conducive to the selection of flooding-tolerant varieties suitable for direct seeding.

DOF, MYB and TCP transcription factors: Their possible roles on barley germination and seedling establishment

Seed germination is a multi-staged complex process during seed plant life cycle, and it is tightly regulated through a coordinated expression of diverse genes in diverse tissues. As regulatory molecules of gene expression, determination of transcription factors is crucial to understanding molecular basis and regulatory network of germination process and seedling establishment. However, limited data on the contributions of these transcription factors to the germination of crop barley (Hordeum vulgare L.) are available. Here, we investigated the expression profiles of selected transcription factors from different families (DOF, MYB and TCP) with qRT-PCR analysis in various tissues including coleoptiles, leaves and roots following the germination. Analysis of MYB and DOF gene expression profiles indicated that there were differing expressions in different aged tissues, HvMYB5 and HvDOF2 being the most outstanding one in the oldest tissue, 15-day-old root. On the other hand, investigated TCP genes were lowly expressed compared to selected MYB and DOF genes, except HvTCP3, where the highest expression was observed in 15-day-old root tissue. The obtained expression profiles illustrate the importance of potential regulatory roles of transcription factors in early developmental stages of barley germination and seedling establishment.

Ethylene regulates post-germination seedling growth in wheat through spatial and temporal modulation of ABA/GA balance

This study aimed to gain insights into the molecular mechanisms underlying the role of ethylene in regulating germination and seedling growth in wheat by combining pharmacological, molecular, and metabolomics approaches. Our study showed that ethylene does not affect radicle protrusion but controls post-germination endospermic starch degradation through transcriptional regulation of specific α-amylase and α-glucosidase genes, and this effect is mediated by alteration of endospermic bioactive gibberellin (GA) levels, and GA sensitivity via expression of the GA signaling gene, TaGAMYB. Our data implicated ethylene as a positive regulator of embryo axis and coleoptile growth through transcriptional regulation of specific TaEXPA genes. These effects were associated with modulation of GA levels and sensitivity, through expression of GA metabolism (TaGA20ox1, TaGA3ox2, and TaGA2ox6) and signaling (TaGAMYB) genes, respectively, and/or the abscisic acid (ABA) level and sensitivity, via expression of specific ABA metabolism (TaNCED2 or TaCYP707A1) and signaling (TaABI3) genes, respectively. Ethylene appeared to regulate the expression of TaEXPA3 and thereby root growth through its control of coleoptile ABA metabolism, and root ABA signaling via expression of TaABI3 and TaABI5. These results show that spatiotemporal modulation of ABA/GA balance mediates the role of ethylene in regulating post-germination storage starch degradation and seedling growth in wheat.

Phenotyping of Light Response on JA-Defective Mutant in Rice

Jasmonates are associated with stress responses. However, there are many roles for jasmonates in plant development. One such function is their participation in the regulation of growth and development of rice seedlings, especially of their coleoptile in response to light. Impairment of jasmonate biosynthesis or signaling results in obvious phenotypic effects in seedlings, which can be used for screening homozygous mutants from a heterozygous population for downstream experimental approaches. A procedure for screening mutants under light is described, which can easily be adapted to standard laboratory conditions.

Increase in coleoptile length and establishment by Lcol-A1, a genetic locus with major effect in wheat

BACKGROUND

Good establishment is important for rapid leaf area development in wheat crops. Poor establishment results in fewer, later-emerging plants, reduced leaf area and tiller number. In addition, poorly established crops suffer from increased soil moisture loss through evaporation and greater competition from weeds while fewer spikes are produced which can reduce grain yield. By protecting the emerging first leaf, the coleoptile is critical for achieving good establishment, and its length and interaction with soil physical properties determine the ability of a cultivar to emerge from depth.

RESULTS

Here we characterise a locus on chromosome 1AS, that increases coleoptile length in wheat, which we designate as Lcol-A1. We identified Lcol-A1 by bulked-segregant analysis and used a Halberd-derived population to fine map the gene to a 2 cM region, equivalent to 7 Mb on the IWGSC genome reference sequence of Chinese Spring (RefSeqv1.0). By sowing recently released cultivars and near-isogenic lines in the field at both conventional and deep sowing depths, we confirmed that Locl-A1 was associated with increased emergence from depth in the presence and absence of conventional dwarfing genes. Flanking markers IWB58229 and IWA710 were developed to assist breeders to select for long coleoptile wheats.

CONCLUSIONS

Increased coleoptile length is sought in many global wheat production areas to improve crop emergence. The identification of the gene Lcol-A1, together with tools to allow wheat breeders to track the gene, will enable improvements to be made for this important trait.

Mesocotyl Elongation is Essential for Seedling Emergence Under Deep-Seeding Condition in Rice

BACKGROUND

Direct-seeding cultivation by deep-seeding of seeds (drill seeding) is becoming popular due to the scarcity of land and labor. However, poor emergence and inadequate seedling establishment can lead to yield loss in direct-seeding cultivation by deep-sowing. In rice, mesocotyl and coleoptile are primarily responsible for seedling emergence from deeper levels of soil.

RESULTS

Quantitative trait loci (QTLs) for mesocotyl and coleoptile length at 5-cm seeding depth were detected using 98 backcross inbred lines from a cross between Kasalath and Nipponbare. Three QTLs qMel-1, qMel-3, and qMel-6 for mesocotyl length were identified on chromosomes 1, 3, and 6, respectively, in two independent replicates. At two QTLs, qMel-1 and qMel-3, the Kasalath alleles increased mesocotyl length, whereas Nipponbare allele increased at qMel-6. The Nipponbare alleles at two QTLs (qCol-3 and qCol-5) increased the coleoptile length. Further, seeds of 54 chromosome segment substitution lines (CSSLs) from the cross between Kasalath and Nipponbare sown at 5 cm soil depth showed a significant positive correlation between seedling emergence and mesocotyl elongation (r > 0.6, P < 0.0001), but not with coleoptile elongation (r = 0.05, P = 0.7). Seedling emergence of Nipponbare, Kasalath, and the 3 of the 54 CSSLs rapidly decreased with increasing sowing depth. Seedling emergence at seeding depths of 7 and 10 cm was faster in Kasalath and CSSL-5 that harbored the Kasalath alleles across the qMel-1 and qMel-3 regions than in the other two CSSLs that contained a single QTL and Nipponbare alleles. CSSL-5 showed the longest mesocotyl among the 3 CSSLs, but no difference in coleoptile length was observed among the 3 CSSLs at seeding depths of 7 and 10 cm.

CONCLUSION

Variation of mesocotyl elongation was found to be associated with seedling emergence at the seeding depth of 5 cm. To our knowledge, this is the first study performed using CSSLs to detect QTLs for mesocotyl or coleoptile elongation and to determine the effect of mesocotyl elongation on seedling emergence in rice. Our findings provides a foundation for developing rice cultivars that show higher seedling emergence after direct seeding by introgressing QTLs for mesocotyl elongation in rice breeding.

Frequency-associated transition from single-cell asynchronous motion to monotonic growth

This paper presents a Fourier analysis of the Ortega equation that examines the growth dynamics of plants, specifically the pollen tubes or non-meristematic zones of elongating coleoptiles. A frequency-induced transition from highly nonlinear (periodical) growth-like the one observed in pollen tubes-to monotonically ascending and asymptotically saturated (sigmoid-like) growth, which is anticipated within the framework of a 'two-fluid model', is shown. A dynamic phase diagram is calculated and presented in the form of a live video clip.

stem of the coleoptile

In 2009, the draft genome of the reference inbred line of maize (Zea mays L. spp. mays cv. B73) was published so that, using this specific corn variety, molecular analyses of physiological processes became possible. However, the morphology and developmental patterns of B73 maize, compared with that of the more frequently used hybrid varieties, have not yet been analyzed. Here, we describe organ development in seedlings of B73 maize and in those of six other hybrid cultivars, and document significant morphological as well as quantitative differences between these varieties of Z. mays. In a second set of experiments, we used etiolated seedlings of B73 maize to analyze the effect of blue light (BL) on the patterns of proteins in the tip vs. growing region of this sheath-like organ. By using two-dimensional difference gel electrophoresis (2D DIGE), coupled with tandem mass spectrometry, we detected, in the microsomal fraction of maize coleoptile tips, rapid changes in the abundance of protein spots of maize phototropin 1 and several metabolic enzymes. In the sub-apical (growing) region of the coleoptile, proteomic changes were less pronounced. These results suggest that the tip of the coleoptile of B73 maize may serve as a unique model system for dissecting BL responses in a light-sensitive plant organ of known function.

Analysis of Growth and Molecular Responses to Ethylene in Etiolated Rice Seedlings

Ethylene plays a key role in various submergence responses of rice plants, but the mechanism of ethylene action remains largely unclear in rice. Regarding the differences between rice and Arabidopsis in ethylene-regulated processes, rice plants may possess divergent mechanisms in ethylene signaling in addition to the conserved aspects. Forward genetic analysis is essential to fully understand the ethylene signaling mechanism in rice. Here, we describe a method for screening ethylene-response mutants and evaluating ethylene responsiveness in etiolated rice seedlings.

Rice CYO1, an ortholog of Arabidopsis thaliana cotyledon chloroplast biogenesis factor AtCYO1, is expressed in leaves and involved in photosynthetic performance

In the dicotyledonous plant Arabidopsis thaliana, the cotyledon chloroplast biogenesis factor AtCYO1 is crucial for the biogenesis of cotyledon chloroplasts. Arabidopsis mutants lacking AtCYO1 have pale cotyledons but develop normal mature leaves. In the monocotyledonous plant Oryza sativa, the gene OsCYO1 has high sequence identity to AtCYO1, but its function is unknown. We examined the role of OsCYO1 in O. sativa. We first confirmed that transformation with OsCYO1 could recover the phenotype of the Arabidopsis cyo1 mutant. Similar to AtCYO1, recombinant OsCYO1 has protein disulfide reductase (PDR) activity, which increased as a function of dieosin glutathione disulfide concentration with an apparent K_m of 3.2μM and K_cat of 0.53min^-1. The PDR activity was reduced when NADPH or NADH was used as an electron donor; however, PDR activity was observed with OsCYO1 and glutathione, suggesting that glutathione may serve as a reducing agent for OsCYO1 in vivo. In O. sativa, the OsCYO1 transcript level was higher in leaves compared with the coleoptile, which is the first leaf-like organ that forms during rice embryogenesis. Many OsCYO1 mutant lines defective in RNA interference had green leaves, however, three mutant lines had not only albino coleoptile but also albino leaves. Those having green leaves reduced photosynthetic performance in leaves. Our results demonstrate that OsCYO1 is enzymatically equivalent to AtCYO1 but that the physiological role of OsCYO1 in monocotyledonous plants may differ from that of AtCYO1 in dicotyledonous plants.

Transcriptional regulatory mechanism of alcohol dehydrogenase 1-deficient mutant of rice for cell survival under complete submergence

BACKGROUND

Rice is the only crop that germinates and elongates the coleoptile under complete submergence. It has been shown that alcohol dehydrogenase 1 (ADH1)-deficient mutant of rice with reduced alcohol dehydrogenase activity (rad) and reduced ATP level, is viable with much reduced coleoptile elongation under such condition. To understand the altered transcriptional regulatory mechanism of this mutant, we aimed to establish possible relationships between gene expression and cis-regulatory information content.

FINDINGS

We performed promoter analysis of the publicly available differentially expressed genes in ADH1 mutant. Our results revealed that a crosstalk between a number of key transcription factors (TFs) and different phytohormones altered transcriptional regulation leading to the survival of the mutant. Amongst the key TFs identified, we suggest potential involvement of MYB, bZIP, ARF and ERF as transcriptional activators and WRKY, ABI4 and MYC as transcriptional repressors of coleoptile elongation to maintain metabolite levels for the cell viability. Out of the repressors, WRKY TF is most likely playing a major role in the alteration of the physiological implications associated with the cell survival.

CONCLUSIONS

Overall, our analysis provides a possible transcriptional regulatory mechanism underlying the survival of the rad mutant under complete submergence in an energy crisis condition and develops hypotheses for further experimental validation.

A quantitative report on the impact of chloride on the kinetic coefficients of auxin-induced growth: a numerical contribution to the "acid growth hypothesis"

This work presents the application of several our own novel methods of analysing the kinetics of plant growth, which create, among others, a common platform for the comparison of experimental results. A relatively simple formula is used to parameterize the wide range of data that has been obtained for Zea mays L. in the literature, though it can also be used for different species. A biophysical/biochemical interpretation of the parameters was obtained from a theoretical model that is based on a modified Lockhart equation. The derived formula, which was extended for practical use in Zajdel et al. (Acta Physiol Plant 38:5, 2016), and which was implemented in the attached computer program (ibid.), allowed the data that was obtained from the growth-related problems to be parameterized in a simple way. As a working example that shows the robustness of our approach, we comment in detail on the qualitative assessments of the impact of chloride ions on auxin-induced growth. We note that calculated continuous curves (fits), which are rooted in the growth functional that was introduced by Pietruszka (J Theor Biol 315:119-127, 2012), were in a perfect agreement (R2 ~ 0.99998) with the raw experimental data that was published recently by Burdach et al. (Ann Bot 114:1023-1034, 2014). This fact justified the use of this strict technique, which allows for the determination of kinetic coefficients, to critically evaluate the results and suppositions (claims) therein. Moreover, we calculated the time-delay derivative of elongation growth-pH cross-correlations, and validated the "acid growth hypothesis" in figures by considering, amongst others, the magnitude of the H+-activity of elongation growth (per μm). An empirical constant (field strength), EH+ = Em/(log10 1/aH+ ∙ μm) = 0.157 ± 0.009 [V/mm] was obtained, where Em [mV] is the membrane potential in the perenchymal coleoptile cells of Zea mays L. When this relation is known, the membrane potential can not only be determined for intact growth, but also for different intervening substances exclusively from growth (or growth rate) and pH measurements, i.e. without performing electrophysiological measurements. However, the question of whether this constant is universal remains open.

Carbohydrate metabolism in germinating caryopses of Oryza sativa L. exposed to prolonged anoxia

Anoxia tolerance can be evaluated not only in terms of growth or survival of plant organs during oxygen deprivation, but also in relation to carbohydrate utilization in the context of a well-modulated fermentative metabolism. Rice (Oryza spp.) is unique among cereals, in that it has the distinctive ability to germinate under complete anaerobiosis by using the starchy reserves in its seeds to fuel the anaerobic metabolism. The aim of the present study was to evaluate the ability of germinating rice seedlings to survive a long-term oxygen deficiency [40 days after sowing (DAS)] and the effects on sugar metabolism, focusing on starch degradation as well as soluble sugars transport and storage under anoxia. No significant decline in vitality occurred until 30 DAS though no recovery was detected following longer anoxic treatments. Growth arrest was observed following anoxic treatments longer that 20 DAS, in concomitance with considerably lower ethanol production. Amylolytic activity in embryos and endosperms had similar responses to anoxia, reaching maximum content 30 days after the onset of stress, following which the levels declined for the remainder of the experiment. Under anoxia, average amylolytic activity was twofold higher in embryos than endosperms. Efficient starch degradation was observed in rice under anoxia at the onset of the treatment but it decreased over time and did not lead to a complete depletion. Our analysis of α-amylase activity did not support the hypothesis that starch degradation plays a critical role in explaining differences in vitality and coleoptile growth under prolonged oxygen deprivation.

White light-induced sugar distribution controls growth and osmotic properties in the coleoptile and the first leaf in Zea mays seedlings

The correlation of white light-induced changes in osmotic concentration in the coleoptile and the first leaf and the growth rate of these organs in maize seedlings, was examined in relation to sugar distribution and invertase activity. One hour irradiation with white light decreased the osmotic concentration in basal zones of the coleoptile and increased it in the apical zones of the first leaf. The change in the osmotic concentration was positively correlated with the growth rate of both organs. The amount of total osmotic solutes in each zone was highly correlated with that of soluble sugars. Light decreased the activity of wall-bound invertase in the coleoptile, but increased it in the first leaf. A high correlation existed between the content of soluble sugars and invertase activity in both organs. During 1 h incubation in the light, ca 2 µmol of soluble sugars per seedling was lost from the coleoptile and gained in the first leaf. Light promoted sugar exudation from the excised coleoptile, but the amount of soluble sugar exuded represented 5% of sugar loss from the coleoptile in intact seedlings. These results indicate that in maize seedlings white light controls the growth rate of the coleoptile and the first leaf through the osmotic concentration. Light may have an osmoregulatory function in the control of sugar distribution between the coleoptile and the first leaf by regulating the activity of wall-bound invertase.

Effect of low water potential of the culture medium on mesocotyl elongation of rice seedlings

At a soil water content of water potential of ca. -3.1 to -6.2 bars, mesocotyl elongation of both indica and japonica type rice was extremely stimulated. It was also stimulated in an aseptic culture medium (2.5-4.0% mannitol, water potential ca. -3.5 to -5.5 bars). The stimulation of the mesocotyl may be caused by cell multiplication.