Gibberellin-auxin crosstalk modulates lateral root formation

Transcription factors BZR2/MYC2 modulate brassinosteroid and jasmonic acid crosstalk during pear dormancy

Bud dormancy is an important physiological process during winter. Its release requires a certain period of chilling. In pear (Pyrus pyrifolia), the abscisic acid (ABA)-induced expression of DORMANCY-ASSOCIATED MADS-box (DAM) genes represses bud break, whereas exogenous gibberellin (GA) promotes dormancy release. However, with the exception of ABA and GA, the regulatory effects of phytohormones on dormancy remain largely uncharacterized. In this study, we confirmed brassinosteroids (BRs) and jasmonic acid (JA) contribute to pear bud dormancy release. If chilling accumulation is insufficient, both 24-epibrassinolide (EBR) and methyl jasmonic acid (MeJA) can promote pear bud break, implying that they positively regulate dormancy release. BRASSINAZOLE RESISTANT 2 (BZR2), which is a BR-responsive transcription factor, inhibited PpyDAM3 expression and accelerated pear bud break. The transient overexpression of PpyBZR2 increased endogenous GA, JA, and JA-Ile levels. In addition, the direct interaction between PpyBZR2 and MYELOCYTOMATOSIS 2 (PpyMYC2) enhanced the PpyMYC2-mediated activation of Gibberellin 20-oxidase genes PpyGA20OX1L1 and PpyGA20OX2L2 transcription, thereby increasing GA3 contents and accelerating pear bud dormancy release. Interestingly, treatment with 5 μm MeJA increased the bud break rate, while also enhancing PpyMYC2-activated PpyGA20OX expression and increasing GA3,4 contents. The 100 μm MeJA treatment decreased the PpyMYC2-mediated activation of the PpyGA20OX1L1 and PpyGA20OX2L2 promoters and suppressed the inhibitory effect of PpyBZR2 on PpyDAM3 transcription, ultimately inhibiting pear bud break. In summary, our data provide insights into the crosstalk between the BR and JA signaling pathways that regulate the BZR2/MYC2-mediated pathway in the pear dormancy release process.

Application of an Improved 2-Dimensional High-Throughput Soybean Root Phenotyping Platform to Identify Novel Genetic Variants Regulating Root Architecture Traits

Nutrient-efficient root system architecture (RSA) is becoming an important breeding objective for generating crop varieties with improved nutrient and water acquisition efficiency. Genetic variants shaping soybean RSA is key in improving nutrient and water acquisition. Here, we report on the use of an improved 2-dimensional high-throughput root phenotyping platform that minimizes background noise by imaging pouch-grown root systems submerged in water. We also developed a background image cleaning Python pipeline that computationally removes images of small pieces of debris and filter paper fibers, which can be erroneously quantified as root tips. This platform was used to phenotype root traits in 286 soybean lines genotyped with 5.4 million single-nucleotide polymorphisms. There was a substantially higher correlation in manually counted number of root tips with computationally quantified root tips (95% correlation), when the background was cleaned of nonroot materials compared to root images without the background corrected (79%). Improvements in our RSA phenotyping pipeline significantly reduced overestimation of the root traits influenced by the number of root tips. Genome-wide association studies conducted on the root phenotypic data and quantitative gene expression analysis of candidate genes resulted in the identification of 3 putative positive regulators of root system depth, total root length and surface area, and root system volume and surface area of thicker roots (DOF1-like zinc finger transcription factor, protein of unknown function, and C2H2 zinc finger protein). We also identified a putative negative regulator (gibberellin 20 oxidase 3) of the total number of lateral roots.

Gibberellins regulate lateral root development that is associated with auxin and cell wall metabolisms in cucumber

Cucumber is an economically important crop cultivated worldwide. Gibberellins (GAs) play important roles in the development of lateral roots (LRs), which are critical for plant stress tolerance and productivity. Therefore, it is of great importance for cucumber production to study the role of GAs in LR development. Here, the results showed that GAs regulated cucumber LR development in a concentration-dependent manner. Treatment with 1, 10, 50 and 100 μM GA₃ significantly increased secondary root length, tertiary root number and length. Of these, 50 μM GA₃ treatment had strong effects on increasing root dry weight and the root/shoot dry weight ratio. Pairwise comparisons identified 417 down-regulated genes enriched for GA metabolism-related processes and 447 up-regulated genes enriched for cell wall metabolism-related processes in GA₃-treated roots. A total of 3523 non-redundant DEGs were identified in our RNA-Seq data through pairwise comparisons and linear factorial modeling. Of these, most of the genes involved in auxin and cell wall metabolisms were up-regulated in GA₃-treated roots. Our findings not only shed light on LR regulation mediated by GA but also offer an important resource for functional studies of candidate genes putatively involved in the regulation of LR development in cucumber and other crops.

Identifying key regulatory genes of maize root growth and development by RNA sequencing

Root system architecture (RSA), the spatio-temporal configuration of roots, plays vital roles in maize (Zea mays L.) development and productivity. We sequenced the maize root transcriptome of four key growth and development stages: the 6th leaf stage, the 12th leaf stage, the tasseling stage and the milk-ripe stage. Differentially expressed genes (DEGs) were detected. 81 DEGs involved in plant hormone signal transduction pathway and 26 transcription factor (TF) genes were screened. These DEGs and TFs were predicted to be potential candidate genes during maize root growth and development. Several of these genes are homologous to well-known genes regulating root architecture or development in Arabidopsis or rice, such as, Zm00001d005892 (AtERF109), Zm00001d027925 (AtERF73/HRE1), Zm00001d047017 (AtMYC2, OsMYC2), Zm00001d039245 (AtWRKY6). Identification of these key genes will provide a further understanding of the molecular mechanisms responsible for maize root growth and development, it will be beneficial to increase maize production and improve stress resistance by altering RSA traits in modern breeding.

Nitrate-responsive OBP4-XTH9 regulatory module controls lateral root development in Arabidopsis thaliana

Plant root system architecture in response to nitrate availability represents a notable example to study developmental plasticity, but the underlying mechanism remains largely unknown. Xyloglucan endotransglucosylases (XTHs) play a critical role in cell wall biosynthesis. Here we assessed the gene expression of XTH1-11 belonging to group I of XTHs in lateral root (LR) primordia and found that XTH9 was highly expressed. Correspondingly, an xth9 mutant displayed less LR, while overexpressing XTH9 presented more LR, suggesting the potential function of XTH9 in controlling LR development. XTH9 gene mutation obviously alters the properties of the cell wall. Furthermore, nitrogen signals stimulated the expression of XTH9 to promote LRs. Genetic analysis revealed that the function of XTH9 was dependent on auxin-mediated ARF7/19 and downstream AFB3 in response to nitrogen signals. In addition, we identified another transcription factor, OBP4, that was also induced by nitrogen treatment, but the induction was much slower than that of XTH9. In contrast to XTH9, overexpressing OBP4 caused fewer LRs while OBP4 knockdown with OBP4-RNAi or an artificial miRNA silenced amiOBP4 line produced more LR. We further found OBP4 bound to the promoter of XTH9 to suppress XTH9 expression. In agreement with this, both OBP4-RNAi and crossed OBP4-RNAi & 35S::XTH9 lines led to more LR, but OBP4-RNAi & xth9 produced less LR, similar to xth9. Based on these findings we propose a novel mechanism by which OBP4 antagonistically controls XTH9 expression and the OBP4-XTH9 module elaborately sustains LR development in response to nitrate treatment.

Nitrate is not only a nutrient, but also a signal that controls downstream signaling genes at the whole-plant level. In plants, changes in root system architecture in response to nitrate availability represent a notable example of developmental plasticity in response to environmental stimuli. However, the molecular mechanisms underlying nitrate-associated modulation are largely unknown. Here, we identified a nitrogen-responsive signaling module that comprises both xyloglucan endotransglucosylase 9 (XTH9) and the Dof transcription factor OBP4 and controls lateral root (LR) development. We used root gravitropic bending assays to observe the gene expression of group 1 xyloglucan endotransglucosylases (XTHs) involved in LR primordia. The results showed that XTH9 expression patterns were changed and that xth9 knockout mutants displayed altered LR growth. XTH9 was expressed in the LRs and in response to nitrate treatment, and the xth9 mutants were defective in nitrate-promoted LR growth. Moreover, XTH9 overexpression increased LR length and increased tolerance to low-nitrate stress. We found that OBP4 could negatively regulate XTH9 and inhibited root growth. OBP4 and XTH9 worked downstream of ARF7/9. We conclude that OBP4 and XTH9 constitute a regulatory module which contributes to LR growth in response to different environmental nitrate concentration signals.

Comprehensive Analysis of Cucumber Gibberellin Oxidase Family Genes and Functional Characterization of CsGA20ox1 in Root Development in Arabidopsis

Cucumber (Cucumis sativus L.) is an important vegetable crop worldwide and gibberellins (GAs) play important roles in the regulation of cucumber developmental and growth processes. GA oxidases (GAoxs), which are encoded by different gene subfamilies, are particularly important in regulating bioactive GA levels by catalyzing the later steps in the biosynthetic pathway. Although GAoxs are critical enzymes in GA synthesis pathway, little is known about GAox genes in cucumber, in particular about their evolutionary relationships, expression profiles and biological function. In this study, we identified 17 GAox genes in cucumber genome and classified them into five subfamilies based on a phylogenetic tree, gene structures, and conserved motifs. Synteny analysis indicated that the tandem duplication or segmental duplication events played a minor role in the expansion of cucumber GA2ox, GA3ox and GA7ox gene families. Comparative syntenic analysis combined with phylogenetic analysis provided deep insight into the phylogenetic relationships of CsGAox genes and suggested that protein homology CsGAox are closer to AtGAox than OsGAox. In addition, candidate transcription factors BBR/BPC (BARLEY B RECOMBINANT/BASIC PENTACYSTEINE) and GRAS (GIBBERELLIC ACID-INSENSITIVE, REPRESSOR of GAI, and SCARECROW) which may directly bind promoters of CsGAox genes were predicted. Expression profiles derived from transcriptome data indicated that some CsGAox genes, especially CsGA20ox1, are highly expressed in seedling roots and were down-regulated under GA₃ treatment. Ectopic over-expression of CsGA20ox1 in Arabidopsis significantly increased primary root length and lateral root number. Taken together, comprehensive analysis of CsGAoxs would provide a basis for understanding the evolution and function of the CsGAox family.

Tall or short? Slender or thick? A plant strategy for regulating elongation growth of roots by low concentrations of gibberellin

BACKGROUND

Since the plant hormone gibberellin (GA) was discovered as a fungal toxin that caused abnormal elongation of rice shoots, the physiological function of GA has mainly been investigated in relation to the regulation of plant height. However, an indispensable role for GA in root growth has been elucidated by using severely GA-depleted plants, either with a gene mutation in GA biosynthesis or which have been treated by an inhibitor of GA biosynthesis. The molecular sequence of GA signalling has also been studied to understand GA functions in root growth.

SCOPE

This review addresses research progress on the physiological functions of GA in root growth. Concentration-dependent stimulation of elongation growth by GA is important for the regulation of plant height and root length. Thus the endogenous level of GA and/or the GA sensitivity of shoots and roots plays a role in determining the shoot-to-root ratio of the plant body. Since the shoot-to-root ratio is an important parameter for agricultural production, control of GA production and GA sensitivity may provide a strategy for improving agricultural productivity. The sequence of GA signal transduction has recently been unveiled, and some component molecules are suggested as candidate in planta regulatory sites and as points for the artificial manipulation of GA-mediated growth control.

CONCLUSIONS

This paper reviews: (1) the breakthrough dose-response experiments that show that root growth is regulated by GA in a lower concentration range than is required for shoot growth; (2) research on the regulation of GA biosynthesis pathways that are known predominantly to control shoot growth; and (3) recent research on GA signalling pathways, including GA receptors, which have been suggested to participate in GA-mediated growth regulation. This provides useful information to suggest a possible strategy for the selective control of shoot and root growth, and to explain how GA plays a role in rosette and liana plants with tall or short, and slender or thick axial organs.

Comparative analysis of root transcriptome profiles of two pairs of drought-tolerant and susceptible rice near-isogenic lines under different drought stress

BACKGROUND

Plant roots are important organs to uptake soil water and nutrients, perceiving and transducing of soil water deficit signals to shoot. The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) with a common genetic background but contrasting levels of resistance to drought stress under initial exposure to water deficit. Here, we examined two pairs of NILs in IR64 background with contrasting drought tolerance. We obtained gene expression profile in roots of rice NILs under different levels of drought stress help to identify genes and mechanisms involved in drought stress.

RESULTS

Global gene expression analysis showed that about 55% of genes differentially expressed in roots of rice in response to drought stress treatments. The number of differentially expressed genes (DEGs) increased in NILs as the level of water deficits, increased from mild to severe condition, suggesting that more genes were affected by increasing drought stress. Gene onthology (GO) test and biological pathway analysis indicated that activated genes in the drought tolerant NILs IR77298-14-1-2-B-10 and IR77298-5-6-B-18 were mostly involved in secondary metabolism, amino acid metabolism, response to stimulus, defence response, transcription and signal transduction, and down-regulated genes were involved in photosynthesis and cell wall growth. We also observed gibberellic acid (GA) and auxin crosstalk modulating lateral root formation in the tolerant NILs.

CONCLUSIONS

Transcriptome analysis on two pairs of NILs with a common genetic background (~97%) showed distinctive differences in gene expression profiles and could be effective to unravel genes involved in drought tolerance. In comparison with the moderately tolerant NIL IR77298-5-6-B-18 and other susceptible NILs, the tolerant NIL IR77298-14-1-2-B-10 showed a greater number of DEGs for cell growth, hormone biosynthesis, cellular transports, amino acid metabolism, signalling, transcription factors and carbohydrate metabolism in response to drought stress treatments. Thus, different mechanisms are achieving tolerance in the two tolerant lines.