SAUR39, a small auxin-up RNA gene, acts as a negative regulator of auxin synthesis and transport in rice

Comparative Analysis of the Transcriptomes of Persisting and Abscised Fruitlets: Insights into Plant Hormone and Carbohydrate Metabolism Regulated Self-Thinning of Pecan Fruitlets during the Early Stage

Pecan is one of the most popular nut species in the world. The fruit drop rate of the pecan ‘Pawnee’ is more than 57%, with four fruit drop stages, which is very serious. In this study, we conducted transcriptomic profiling of persisting and abscised fruitlets in early fruit development by RNA-seq. A total of 11,976 differentially expressed genes (DEGs) were identified, 3012 upregulated and 8964 downregulated, in a comparison of abscised vs. persisting fruitlets at 35 days after anthesis (DAA). Our transcriptomic data suggest that gene subsets encoding elements involving the biosynthesis, metabolism, perception, signal transduction, and crosstalk of the plant hormones abscisic acid (ABA), auxin, cytokinin, ethylene, and gibberellin (GA) and plant growth regulators jasmonates, salicylic acid, and brassinosteroids were differentially expressed. In addition, the majority of transcriptionally activated genes involved in hormone signaling (except for ethylene and salicylic acid signaling) were downregulated in abscised fruitlets. The differential expression of transcripts coding for enzymes involved in sucrose, glucose, trehalose, starch, galactose, and galactinol metabolism shows that sucrose, galactinol, and glucose synthesis and starch content were reduced as starch biosynthesis was blocked, and retrogradation and degradation intensified. These results suggest that the abscised pecan fruitlets stopped growing and developing for some time before dropping, further indicating that their sugar supply was reduced or stopped. The transcriptome characterization described in this paper contributes to unravelling the molecular mechanisms and pathways involved in the physiological abscission of pecan fruits.

Comparative transcriptome analysis of root types in salt tolerant and sensitive rice varieties in response to salinity stress

Salinity tolerance in rice is a very important trait, especially in areas that are affected by soil salinity, such as tsunami-devastated areas and coastal regions in rice-producing countries. The roots are the key organs that first detect and respond to salinity stress; thus, it is important to have an understanding of how roots contribute to salinity tolerance in agricultural crops. After salinity treatment of the salt tolerant (Mulai) and sensitive (IR29) rice varieties, it appeared that among the three types of roots, the L-type lateral roots (LLR) were the most sensitive to salinity stress in Mulai and the most tolerant in IR29. The nodal roots (NR) and the S-type lateral roots (SLR) were all negatively affected by salinity treatment in both rice varieties. In order to elucidate the molecular mechanism of the difference in stress response among rice root types, the RNA-seq transcriptome profiles of NR, LLR, and SLR were analyzed in Mulai and IR29. Between the two rice varieties, more transporters were found to participate in the regulation of salt tolerance in Mulai roots, such as those involved in ion and sugar transport. In IR29, many of the genes detected were associated with transcription regulation, including stress-inducible genes such as NAC, WRKY and MYB. Among the different root types, gene expression in LLR and SLR were significantly regulated in both rice varieties. Taken together, the genes identified in this study may be utilized in the varietal improvement of rice with very specific root traits that can enhance tolerance to salinity stress.

Meta-QTLs, ortho-MQTLs and candidate genes for the traits contributing to salinity stress tolerance in common wheat (Triticum aestivum L.)

A meta-analysis of QTLs associated with the traits contributing to salinity tolerance was undertaken in wheat to detect consensus and robust meta-QTLs (MQTLs) using 844 known QTLs retrieved from 26 earlier studies. A consensus map with a total length of 4621.56 cM including 7710 markers was constructed using 21 individual linkage maps and three previously published integrated genetic maps. Out of 844 QTLs, 571 QTLs were projected on the consensus map which gave origin to 100 MQTLs. Interestingly, 49 MQTLs were co-located with marker-trait associations reported in wheat genome-wide association studies for the traits contributing to salinity stress tolerance. Five potential MQTLs associated with the major salinity-responsive traits were also identified to be utilized in the breeding programme. In the resulted MQTLs, the average confidence interval (CI, 3.58 cM) was reduced up to 4.16 folds compared to the mean CI of the initial QTLs. Furthermore, as many as 617 gene models including 81 most likely candidate genes (CGs) were identified in the high confidence MQTL regions. These most likely CGs encoded proteins mainly belonging to the following families: B-box-type zinc finger, cytochrome P450 protein, pentatricopeptide repeat, phospholipid/glycerol acyltransferase, F-box protein, small auxin-up RNA, UDP-glucosyltransferase, glutathione S-transferase protein, etc. In addition, ortho-MQTL analysis based on synteny among wheat, rice and barley was also performed which permitted the identification of six ortho-MQTLs among these three cereals. This meta-analysis defines a genome-wide landscape on the most stable and consistent loci associated with reliable molecular markers and candidate genes for salinity tolerance in wheat.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01112-0.

Global Transcriptomic Analysis Reveals Differentially Expressed Genes Involved in Embryogenic Callus Induction in Drumstick (Moringa oleifera Lam.)

The plant embryogenic callus (EC) is an irregular embryogenic cell mass with strong regenerative ability that can be used for propagation and genetic transformation. However, difficulties with EC induction have hindered the breeding of drumstick, a tree with diverse potential commercial uses. In this study, three drumstick EC cDNA libraries were sequenced using an Illumina NovaSeq 6000 system. A total of 7191 differentially expressed genes (DEGs) for embryogenic callus development were identified, of which 2325 were mapped to the KEGG database, with the categories of plant hormone signal transduction and Plant-pathogen interaction being well-represented. The results obtained suggest that auxin and cytokinin metabolism and several embryogenesis-labeled genes are involved in embryogenic callus induction. Additionally, 589 transcription factors from 20 different families were differentially expressed during EC formation. The differential expression of 16 unigenes related to auxin signaling pathways was validated experimentally by quantitative real time PCR (qRT-PCR) using samples representing three sequential developmental stages of drumstick EC, supporting their apparent involvement in drumstick EC formation. Our study provides valuable information about the molecular mechanism of EC formation and has revealed new genes involved in this process.

Unravelling the Molecular Regulation Mechanisms of Slow Ripening Trait in Prunus persica

Fruit development is a complex process that involves the interplay of cell division, expansion, and differentiation. As a model to study fruit development, nectarines incapable of ripening were described as slow ripening. Slow ripening fruits remained firm and exhibited no rise in CO₂ or ethylene production rates for one month or more at 20 °C. Different studies suggest that this trait is controlled by a single gene (NAC072). Transcriptome analysis between normal and slow ripening fruits showed a total of 157, 269, 976, and 5.224 differentially expressed genes in each fruit developmental stage analyzed (T1, T2, T3, and T7, respectively), and no expression of NAC072 was found in the slow ripening individuals. Using this transcriptomic information, we identified a correlation of NAC072 with auxin-related genes and two genes associated with terpene biosynthesis. On the other hand, significant differences were observed in hormonal biosynthetic pathways during fruit development between the normal and slow ripening individuals (gibberellin, ethylene, jasmonic acid and abscisic acid). These results suggest that the absence of NAC072 by the direct or indirect expression control of auxins or terpene-related genes prevents normal peach fruit development.

Reproductive Stage Drought Tolerance in Wheat: Importance of Stomatal Conductance and Plant Growth Regulators

Drought stress requires plants to adjust their water balance to maintain tissue water levels. Isohydric plants (‘water-savers’) typically achieve this through stomatal closure, while anisohydric plants (‘water-wasters’) use osmotic adjustment and maintain stomatal conductance. Isohydry or anisohydry allows plant species to adapt to different environments. In this paper we show that both mechanisms occur in bread wheat (Triticum aestivum L.). Wheat lines with reproductive drought-tolerance delay stomatal closure and are temporarily anisohydric, before closing stomata and become isohydric at higher threshold levels of drought stress. Drought-sensitive wheat is isohydric from the start of the drought treatment. The capacity of the drought-tolerant line to maintain stomatal conductance correlates with repression of ABA synthesis in spikes and flag leaves. Gene expression profiling revealed major differences in the drought response in spikes and flag leaves of both wheat lines. While the isohydric drought-sensitive line enters a passive growth mode (arrest of photosynthesis, protein translation), the tolerant line mounts a stronger stress defence response (ROS protection, LEA proteins, cuticle synthesis). The drought response of the tolerant line is characterised by a strong response in the spike, displaying enrichment of genes involved in auxin, cytokinin and ethylene metabolism/signalling. While isohydry may offer advantages for longer term drought stress, anisohydry may be more beneficial when drought stress occurs during the critical stages of wheat spike development, ultimately improving grain yield.

Auxin Interactions with Other Hormones in Plant Development

Auxin is a crucial growth regulator that governs plant development and responses to environmental perturbations. It functions at the heart of many developmental processes, from embryogenesis to organ senescence, and is key to plant interactions with the environment, including responses to biotic and abiotic stimuli. As remarkable as auxin is, it does not act alone, but rather solicits the help of, or is solicited by, other endogenous signals, including the plant hormones abscisic acid, brassinosteroids, cytokinins, ethylene, gibberellic acid, jasmonates, salicylic acid, and strigolactones. The interactions between auxin and other hormones occur at multiple levels: hormones regulate one another's synthesis, transport, and/or response; hormone-specific transcriptional regulators for different pathways physically interact and/or converge on common target genes; etc. However, our understanding of this crosstalk is still fragmentary, with only a few pieces of the gigantic puzzle firmly established. In this review, we provide a glimpse into the complexity of hormone interactions that involve auxin, underscoring how patchy our current understanding is.

Evaluation of drought resistance and transcriptome analysis for the identification of drought-responsive genes in Iris germanica

Iris germanica, a species with very high ornamental value, exhibits the strongest drought resistance among the species in the genus Iris, but the molecular mechanism underlying its drought resistance has not been evaluated. To investigate the gene expression profile changes exhibited by high-drought-resistant I. germanica under drought stress, 10 cultivars with excellent characteristics were included in pot experiments under drought stress conditions, and the changes in the chlorophyll (Chl) content, plasma membrane relative permeability (RP), and superoxide dismutase (SOD), malondialdehyde (MDA), free proline (Pro), and soluble protein (SP) levels in leaves were compared among these cultivars. Based on their drought-resistance performance, the 10 cultivars were ordered as follows: 'Little Dream' > 'Music Box' > 'X'Brassie' > 'Blood Stone' > 'Cherry Garden' > 'Memory of Harvest' > 'Immortality' > 'White and Gold' > 'Tantara' > 'Clarence'. Using the high-drought-resistant cultivar 'Little Dream' as the experimental material, cDNA libraries from leaves and rhizomes treated for 0, 6, 12, 24, and 48 h with 20% polyethylene glycol (PEG)-6000 to simulate a drought environment were sequenced using the Illumina sequencing platform. We obtained 1, 976, 033 transcripts and 743, 982 unigenes (mean length of 716 bp) through a hierarchical clustering analysis of the resulting transcriptome data. The unigenes were compared against the Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and gene ontology (GO) databases for functional annotation, and the gene expression levels in leaves and rhizomes were compared between the 20% PEG-6000 stress treated (6, 12, 24, and 48 h) and control (0 h) groups using DESeq2. 7849 and 24,127 differentially expressed genes (DEGs) were obtained from leaves and rhizomes, respectively. GO and KEGG enrichment analyses of the DEGs revealed significantly enriched KEGG pathways, including ribosome, photosynthesis, hormone signal transduction, starch and sucrose metabolism, synthesis of secondary metabolites, and related genes, such as heat shock proteins (HSPs), transcription factors (TFs), and active oxygen scavengers. In conclusion, we conducted the first transcriptome sequencing analysis of the I. germanica cultivar 'Little Dream' under drought stress and generated a large amount of genetic information. This study lays the foundation for further exploration of the molecular mechanisms underlying the responses of I. germanica to drought stress and provides valuable genetic resources for the breeding of drought-resistant plants.

Genome-Wide Association Study of the Genetic Basis of Effective Tiller Number in Rice

BACKGROUND

Effective tiller number (ETN) has a pivotal role in determination of rice (Oryza sativa L.) grain yield. ETN is a complex quantitative trait regulated by both genetic and environmental factors. Despite multiple tillering-related genes have been cloned previously, few of them have been utilized in practical breeding programs.

RESULTS

In this study, we conducted a genome-wide association study (GWAS) for ETN using a panel of 490 rice accessions derived from the 3 K rice genomes project. Thirty eight ETN-associated QTLs were identified, interestingly, four of which colocalized with the OsAAP1, DWL2, NAL1, and OsWRKY74 gene previously reported to be involved in rice tillering regulation. Haplotype (Hap) analysis revealed that Hap5 of OsAAP1, Hap3 and 6 of DWL2, Hap2 of NAL1, and Hap3 and 4 of OsWRKY74 are favorable alleles for ETN. Pyramiding favorable alleles of all these four genes had more enhancement in ETN than accessions harboring the favorable allele of only one gene. Moreover, we identified 25 novel candidate genes which might also affect ETN, and the positive association between expression levels of the OsPILS6b gene and ETN was validated by RT-qPCR. Furthermore, transcriptome analysis on data released on public database revealed that most ETN-associated genes showed a relatively high expression from 21 days after transplanting (DAT) to 49 DAT and decreased since then. This unique expression pattern of ETN-associated genes may contribute to the transition from vegetative to reproductive growth of tillers.

CONCLUSIONS

Our results revealed that GWAS is a feasible way to mine ETN-associated genes. The candidate genes and favorable alleles identified in this study have the potential application value in rice molecular breeding for high ETN and grain yield.

Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in Hevea brasiliensis

BACKGROUND

Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE are still not well understood.

RESULTS

In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36,937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE.

CONCLUSIONS

This study provides important information to elucidate the molecular regulation during rubber tree late SE.

A genome-wide association study reveals that the glucosyltransferase OsIAGLU regulates root growth in rice

Good root growth in the early post-germination stages is an important trait for direct seeding in rice, but its genetic control is poorly understood. In this study, we examined the genetic architecture of variation in primary root length using a diverse panel of 178 accessions. Four QTLs for root length (qRL3, qRL6, qRL7, and qRL11) were identified using genome-wide association studies. One candidate gene was validated for the major QTL qRL11, namely the glucosyltransferase OsIAGLU. Disruption of this gene in Osiaglu mutants reduced the primary root length and the numbers of lateral and crown roots. The natural allelic variations of OsIAGLU contributing to root growth were identified. Functional analysis revealed that OsIAGLU regulates root growth mainly via modulating multiple hormones in the roots, including levels of auxin, jasmonic acid, abscisic acid, and cytokinin. OsIAGLU also influences the expression of multiple hormone-related genes associated with root growth. The regulation of root growth through multiple hormone pathways by OsIAGLU makes it a potential target for future rice breeding for crop improvement.

The Rice Small Auxin-Up RNA Gene OsSAUR33 Regulates Seed Vigor via Sugar Pathway during Early Seed Germination

Seed vigor affects seed germination and seedling emergence, and therefore is an important agronomic trait in rice. Small auxin-up RNAs (SAURs) function in a range of developmental processes, but their role in seed vigor remains unclear. Here, we observed that disruption of OsSAUR33 resulted in reduced germination rates and low seed uniformity in early germination. Expression of OsSAUR33 was higher in mature grains and early germinating seeds. RNA-seq analysis revealed that OsSAUR33 modulated seed vigor by affecting the mobilization of stored reserves during germination. Disruption of OsSAUR33 increased the soluble sugar content in dry mature grains and seeds during early germination. OsSAUR33 interacted with the sucrose non-fermenting-1-related protein kinase OsSnRK1A, a regulator of the sugar signaling pathway, which influences the expression of sugar signaling-related genes during germination. Disruption of OsSAUR33 increased sugar-sensitive phenotypes in early germination, suggesting OsSAUR33 likely affects seed vigor through the sugar pathway. One elite haplotype of OsSAUR33 associated with higher seed vigor was identified mainly in indica accessions. This study provides insight into the effects of OsSAUR33 on seed vigor in rice.

Transcriptome Analysis Reveals the Symbiotic Mechanism of Ustilago esculenta-Induced Gall Formation of Zizania latifolia

Zizania latifolia is a perennial aquatic vegetable, whose symbiosis with the fungus Ustilago esculenta (member of Basidiomycota, class Ustilaginaceae) results in the establishment of swollen gall formations. Here, we analyzed symbiotic relations of Z. latifolia and U. esculenta, using a triadimefon (TDF) treatment and transcriptome sequencing (RNA-seq). Specifically, accurately identify the whole growth cycle of Z. latifolia. Microstructure observations showed that the presence of U. esculenta could be clearly observed after gall formation but was absent after the TDF treatment. A total of 17,541 differentially expressed genes (DEGs) were identified, based on the transcriptome. According to gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway results, plant hormone signal transduction, and cell wall-loosening factors were all significantly enriched due to U. esculenta infecting Z. latifolia; relative expression levels of hormone-related genes were identified, of which downregulation of indole 3-acetic acid (IAA)-related DEGs was most pronounced in JB_D versus JB_B. The ultra-high performance liquid chromatography analysis revealed that IAA, zeatin+trans zeatin riboside, and gibberellin 3 were increased under U. esculenta infection. Based on our results, we proposed a hormone-cell wall loosening model to study the symbiotic mechanism of gall formation after U. esculenta infects Z. latifolia. Our study thus provides a new perspective for studying the physiological and molecular mechanisms of U. esculenta infection of Z. latifolia causing swollen gall formations as well as a theoretical basis for enhancing future yields of cultivated Z. latifolia.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. 2021.

Systematic identification and characterization of circular RNAs involved in flag leaf senescence of rice

Circular RNAs (circRNAs) identification, expression profiles, and construction of circRNA-parental gene relationships and circRNA-miRNA-mRNA ceRNA networks indicate that circRNAs are involved in flag leaf senescence of rice. Circular RNAs (circRNAs) are a class of 3'-5' head-to-tail covalently closed non-coding RNAs which have been proved to play important roles in various biological processes. However, no systematic identification of circRNAs associated with leaf senescence in rice has been studied. In this study, a genome-wide high-throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. Here, a total of 6612 circRNAs were identified, among which, 113 circRNAs were differentially expressed (DE) during the leaf senescence process. Moreover, 4601 (69.59%) circRNAs were derived from the exons or introns of their parental genes, while 2110 (71%) of the parental genes produced only one circRNA. The sequence alignment analysis showed that hundreds of rice circRNAs were conserved among different plant species. Gene Ontology (GO) enrichment analysis revealed that parental genes of DE circRNAs were enriched in many biological processes closely related to leaf senescence. Through weighted gene co-expression network analysis (WGCNA), six continuously down-expressed circRNAs, 18 continuously up-expressed circRNAs and 15 turn-point high-expressed circRNAs were considered to be highly associated with leaf senescence. Additionally, a total of 17 senescence-associated circRNAs were predicted to have parental genes, in which, regulations of three circRNAs to their parental genes were validated by qRT-PCR. The competing endogenous RNA (ceRNA) networks were also constructed. And a total of 11 senescence-associated circRNAs were predicted to act as miRNA sponges to regulate mRNAs, in which, regulation of two circRNAs to eight mRNAs was validated by qRT-PCR. It is discussed that senescence-associated circRNAs were involved in flag leaf senescence probably through mediating their parental genes and ceRNA networks, to participate in several well-studied senescence-associated processes, mainly including the processes of transcription, translation, and posttranslational modification (especially protein glycosylation), oxidation-reduction process, involvement of senescence-associated genes, hormone signaling pathway, proteolysis, and DNA damage repair. This study not only showed the systematic identification of circRNAs involved in leaf senescence of rice, but also laid a foundation for functional research on candidate circRNAs.

Genome-wide identification and characterization of small auxin-up RNA (SAUR) gene family in plants: evolution and expression profiles during normal growth and stress response

BACKGROUND

Auxin is critical to plant growth and development, as well as stress responses. Small auxin-up RNA (SAUR) is the largest family of early auxin responsive genes in higher plants. However, the function of few SAUR genes is known owing to functional redundancy among the many family members.

RESULTS

In this study, we conducted a phylogenetic analysis using protein sequences of 795 SAURs from Anthoceros angustus, Marchantia polymorpha, Physcomitrella patens, Selaginella moellendorffii, Ginkgo biloba, Gnetum montanum, Amborella trichopoda, Arabidopsis thaliana, Oryza sativa, Zea mays, Glycine max, Medicago truncatula and Setaria italica. The phylogenetic trees showed that the SAUR proteins could be divided into 10 clades and three subfamilies, and that SAUR proteins of three bryophyte species were only located in subfamily III, which suggested that they may be ancestral. From bryophyta to anthophyta, SAUR family have appeared very large expansion. The number of SAUR gene in Fabaceae species was considerably higher than that in other plants, which may be associated with independent whole genome duplication event in the Fabaceae lineages. The phylogenetic trees also showed that SAUR genes had expanded independently monocotyledons and dicotyledons in angiosperms. Conserved motif and protein structure prediction revealed that SAUR proteins were highly conserved among higher plants, and two leucine residues in motif I were observed in almost all SAUR proteins, which suggests the residues plays a critical role in the stability and function of SAUR proteins. Expression analysis of SAUR genes using publicly available RNA-seq data from rice and soybean indicated functional similarity of members in the same clade, which was also further confirmed by qRT-PCR. Summarization of SAUR functions also showed that SAUR functions were usually consistent within a subclade.

CONCLUSIONS

This study provides insights into the evolution and function of the SAUR gene family from bryophyta to anthophyta, particularly in Fabaceae plants. Future investigation to understand the functions of SAUR family members should employ a clade as the study unit.

Comparative Transcriptome Profiling Reveals Defense-Related Genes Against Ralstonia solanacearum Infection in Tobacco

Bacterial wilt (BW) caused by Ralstonia solanacearum (R. solanacearum), is a vascular disease affecting diverse solanaceous crops and causing tremendous damage to crop production. However, our knowledge of the mechanism underlying its resistance or susceptibility is very limited. In this study, we characterized the physiological differences and compared the defense-related transcriptomes of two tobacco varieties, 4411-3 (highly resistant, HR) and K326 (moderately resistant, MR), after R. solanacearum infection at 0, 10, and 17 days after inoculation (dpi). A total of 3967 differentially expressed genes (DEGs) were identified between the HR and MR genotypes under mock condition at three time points, including1395 up-regulated genes in the HR genotype and 2640 up-regulated genes in the MR genotype. Also, 6,233 and 21,541 DEGs were induced in the HR and MR genotypes after R. solanacearum infection, respectively. Furthermore, GO and KEGG analyses revealed that DEGs in the HR genotype were related to the cell wall, starch and sucrose metabolism, glutathione metabolism, ABC transporters, endocytosis, glycerolipid metabolism, and glycerophospholipid metabolism. The defense-related genes generally showed genotype-specific regulation and expression differences after R. solanacearum infection. In addition, genes related to auxin and ABA were dramatically up-regulated in the HR genotype. The contents of auxin and ABA in the MR genotype were significantly higher than those in the HR genotype after R. solanacearum infection, providing insight into the defense mechanisms of tobacco. Altogether, these results clarify the physiological and transcriptional regulation of R. solanacearum resistance infection in tobacco, and improve our understanding of the molecular mechanism underlying the plant-pathogen interaction.

Genetic architecture to cause dynamic change in tiller and panicle numbers revealed by genome-wide association study and transcriptome profile in rice

Panicle number (PN) is one of the three yield components in rice. As one of the most unstable traits, the dynamic change in tiller number (DCTN) may determine the final PN. However, the genetic basis of DCTN and its relationship with PN remain unclear. Here, 377 deeply re-sequenced rice accessions were used to perform genome-wide association studies (GWAS) for tiller/PN. It was found that the DCTN pattern rather than maximum tiller number or effective tiller ratio is the determinant factor of high PN. The DCTN pattern that affords more panicles exhibits a period of stable tillering peak between 30 and 45 days after transplant (called DT30 and DT45, respectively), which was believed as an ideal pattern contributing to the steady transition from tiller development to panicle development (ST-TtP). Consistently, quantitative trait loci (QTL) expressed near DT30-DT45 were especially critical to the rice DCTN and in supporting the ST-TtP. The spatio-temporal expression analysis showed that the expression pattern of keeping relatively high expression in root at 24:00 (R24-P2) from about DT30 to DT45 is a typical expression pattern of cloned tiller genes, and the candidate genes with R24-P2 can facilitate the prediction of PN. Moreover, gene OsSAUR27 was identified by an integrated approach combining GWAS, bi-parental QTL mapping and transcription. These findings related to the genetic basis underlying the DCTN will provide the genetic theory in making appropriate decisions on field management, and in developing new varieties with high PN and ideal dynamic plant architecture.

A study of leaf-senescence genes in rice based on a combination of genomics, proteomics and bioinformatics

Leaf senescence is a highly complex, genetically regulated and well-ordered process with multiple layers and pathways. Delaying leaf senescence would help increase grain yields in rice. Over the past 15 years, more than 100 rice leaf-senescence genes have been cloned, greatly improving the understanding of leaf senescence in rice. Systematically elucidating the molecular mechanisms underlying leaf senescence will provide breeders with new tools/options for improving many important agronomic traits. In this study, we summarized recent reports on 125 rice leaf-senescence genes, providing an overview of the research progress in this field by analyzing the subcellular localizations, molecular functions and the relationship of them. These data showed that chlorophyll synthesis and degradation, chloroplast development, abscisic acid pathway, jasmonic acid pathway, nitrogen assimilation and ROS play an important role in regulating the leaf senescence in rice. Furthermore, we predicted and analyzed the proteins that interact with leaf-senescence proteins and achieved a more profound understanding of the molecular principles underlying the regulatory mechanisms by which leaf senescence occurs, thus providing new insights for future investigations of leaf senescence in rice.

SAUR15 Promotes Lateral and Adventitious Root Development via Activating H+-ATPases and Auxin Biosynthesis

SMALL AUXIN-UP RNAs (SAURs) comprise the largest family of early auxin response genes. Some SAURs have been reported to play important roles in plant growth and development, but their functional relationships with auxin signaling remain unestablished. Here, we report Arabidopsis (Arabidopsis thaliana) SAUR15 acts downstream of the auxin response factors ARF6,8 and ARF7,19 to regulate auxin signaling-mediated lateral root (LR) and adventitious root (AR) formation. The loss-of-function mutant saur15-1 exhibits fewer LRs and ARs. By contrast, plants overexpressing SAUR15 exhibit more LRs and ARs. We find that the SAUR15 promoter contains four tandem auxin-responsive elements, which are directly bound by ARF6 and ARF7 and are essential for SAUR15 expression. LR and AR impairment in arf6 and arf7 mutants is partially reduced by ectopic expression of SAUR15 Additionally, we demonstrate that the ARF6,7-upregulated SAUR15 promotes LR and AR development using two mechanisms. On the one hand, SAUR15 interacts with PP2C-D subfamily type 2C protein phosphatases to inhibit their activities, thereby stimulating plasma membrane H+-ATPases, which drives cell expansion and facilitates LR and AR formation. On the other hand, SAUR15 promotes auxin accumulation, potentially by inducing the expression of auxin biosynthesis genes. A resulting increase in free auxin concentration likely triggers LR and AR formation, forming a feedback loop. Our study provides insights and a better understanding of how SAURs function at the molecular level in regulating auxin-mediated LR and AR development.

Integrating transcriptomic and metabolomic analysis of hormone pathways in Acer rubrum during developmental leaf senescence

BACKGROUND

To fully elucidate the roles and mechanisms of plant hormones in leaf senescence, we adopted an integrated analysis of both non-senescing and senescing leaves from red maple with transcriptome and metabolome data.

RESULTS

Transcription and metabolite profiles were generated through a combination of deep sequencing, third-generation sequencing data analysis, and ultrahigh-performance liquid chromatograph Q extractive mass spectrometry (UHPLC-QE-MS), respectively. We investigated the accumulation of compounds and the expression of biosynthesis and signaling genes for eight hormones. The results revealed that ethylene and abscisic acid concentrations increased during the leaf senescence process, while the contents of cytokinin, auxin, jasmonic acid, and salicylic acid continued to decrease. Correlation tests between the hormone content and transcriptional changes were analyzed, and in six pathways, genes closely linked with leaf senescence were identified.

CONCLUSIONS

These results will enrich our understanding of the mechanisms of plant hormones that regulate leaf senescence in red maple, while establishing a foundation for the genetic modification of Acer in the future.

Small Auxin Up RNAs influence the distribution of indole-3-acetic acid and play a potential role in increasing seed size in Euryale ferox Salisb

BACKGROUND

Aquatic Euryale ferox Salisb. is an economically important crop in China and India. Unfortunately, low yield limitations seriously hinder market growth. Unveiling the control of seed size is of remarkable importance in improvement of crops. Here, we generated a new hybrid line (HL) with larger seeds by crossing South Gordon Euryale and North Gordon Euryale (WT) which hasn't been reported before. However, the functional genes and molecular mechanisms controlling the seed size in Euryale ferox Salisb. remain unclear. In this study, we focused on the differentially expressed genes in the auxin signal transduction pathway during fruit development between HL and WT to explore candidate regulatory genes participated in regulating seed size.

RESULTS

Both concentration and localization of indole-3-acetic acid (IAA) at two growth stages of fruits of WT and HL were detected by LC-MS and immunofluorescence. Although IAA content between the two lines did not differ, IAA distribution was significantly different. To elucidate the mechanism and to seek the key genes underlying this difference, RNA-seq was performed on young fruits at the two selected growth stages, and differentially expressed genes related to the auxin transduction pathway were selected for further analysis.

CONCLUSION

Hybrid Euryale ferox Salisb. expressed significant heterosis, resulting in non-prickly, thin-coated, large seeds, which accounted for the significantly larger yield of HL than that of WT. Our study indicated that Small Auxin Up RNAs (SAURs) -mediated localization of IAA regulates seed size in Euryale ferox Salisb. We found that some SAURs may act as a positive mediator of the auxin transduction pathway, thereby contributing to the observed heterosis.

The SAUR41 subfamily of SMALL AUXIN UP RNA genes is abscisic acid inducible to modulate cell expansion and salt tolerance in Arabidopsis thaliana seedlings

BACKGROUND AND AIMS

Most primary auxin response genes are classified into three families: AUX/IAA, GH3 and SAUR genes. Few studies have been conducted on Arabidopsis thaliana SAUR genes, possibly due to genetic redundancy among different subfamily members. Data mining on arabidopsis transcriptional profiles indicates that the SAUR41 subfamily members of SMALL AUXIN UP RNA genes are, strikingly, induced by an inhibitory phytohormone, abscisic acid (ABA). We aimed to reveal the physiological roles of arabidopsis SAUR41 subfamily genes containing SAUR40, SAUR41, SAUR71 and SAUR72.

METHODS

Transcriptional responses of arabidopsis SAUR41 genes to phytohormones were determined by quantitative real-time PCR. Knock out of SAUR41 genes was carried out with the CRISPR/Cas9 (clustered regulatory interspaced short palindromic repeats/CRISPR-associated protein 9) genome editing technique. The saur41/40/71/72 quadruple mutants, SAUR41 overexpression lines and the wild type were subjected to ultrastructural observation, transcriptome analysis and physiological characterization.

KEY RESULTS

Transcription of arabidopsis SAUR41 subfamily genes is activated by ABA but not by gibberellic acids and brassinosteroids. Quadruple mutations in saur41/40/71/72 led to reduced cell expansion/elongation in cotyledons and hypocotyls, opposite to the overexpression of SAUR41; however, an irregular arrangement of cell size and shape was observed in both cases. The quadruple mutants had increased transcription of calcium homeostasis/signalling genes in seedling shoots, and the SAUR41 overexpression lines had decreased transcription of iron homeostasis genes in roots and increased ABA biosynthesis in shoots. Notably, both the quadruple mutants and the SAUR41 overexpression lines were hypersensitive to salt stress during seedling establishment, whereas specific expression of SAUR41 under the ABA-responsive RD29A (Responsive to Desiccation 29A) promoter in the quadruple mutants rescued the inhibitory effect of salt stress.

CONCLUSIONS

The SAUR41 subfamily genes of arabidopsis are ABA inducible to modulate cell expansion, ion homeostasis and salt tolerance. Our work may provide new candidate genes for improvement of plant abiotic stress tolerance.

SAUR49 Can Positively Regulate Leaf Senescence by Suppressing SSPP in Arabidopsis

The involvement of SMALL AUXIN-UP RNA (SAUR) proteins in leaf senescence has been more and more acknowledged, but the detailed mechanisms remain unclear. In the present study, we performed yeast two-hybrid assays and identified SAUR49 as an interactor of SENESCENCE SUPPRESSED PROTEIN PHOSPHATASE (SSPP), which is a PP2C protein phosphatase that negatively regulates Arabidopsis leaf senescence by suppressing the leucine-rich repeat receptor-like protein kinase SENESCENCE-ASSOCIATED RECEPTOR-LIKE KINASE (SARK), as reported previously by our group. The interaction between SAUR49 and SSPP was further confirmed in planta. Functional characterization revealed that SAUR49 is a positive regulator of leaf senescence. The accumulation level of SAUR49 protein increased during natural leaf senescence in Arabidopsis. The transcript level of SAUR49 was upregulated during SARK-induced premature leaf senescence but downregulated during SSPP-mediated delayed leaf senescence. Overexpression of SAUR49 significantly accelerated both natural and dark-induced leaf senescence in Arabidopsis. More importantly, SAUR49 overexpression completely reversed SSPP-induced delayed leaf senescence. In addition, overexpression of SAUR49 reversed the decreased plasma membrane H+-ATPase activity mediated by SSPP. Taken together, the results showed that SAUR49 functions in accelerating the leaf senescence process via the activation of SARK-mediated leaf senescence signaling by suppressing SSPP. We further identified four other SSPP-interacting SAURs, SAUR30, SAUR39, SAUR41 and SAUR72, that may act redundantly with SAUR49 in regulating leaf senescence. All these observations indicated that certain members of the SAUR family may serve as an important hub that integrates various hormonal and environmental signals with senescence signals in Arabidopsis.

Indoleacetic Acid Levels in Wheat and Rice Seedlings under Oxygen Deficiency and Subsequent Reoxygenation

The lack of oxygen and post-anoxic reactions cause significant alterations of plant growth and metabolism. Plant hormones are active participants in these alterations. This study focuses on auxin-a phytohormone with a wide spectrum of effects on plant growth and stress tolerance. The indoleacetic acid (IAA) content in plants was measured by ELISA. The obtained data revealed anoxia-induced accumulation of IAA in wheat and rice seedlings related to their tolerance of oxygen deprivation. The highest IAA accumulation was detected in rice roots. Subsequent reoxygenation was accompanied with a fast auxin reduction to the control level. A major difference was reported for shoots: wheat seedlings contained less than one-third of normoxic level of auxin during post-anoxia, while IAA level in rice seedlings rapidly recovered to normoxic level. It is likely that the mechanisms of auxin dynamics resulted from oxygen-induced shift in auxin degradation and transport. Exogenous IAA treatment enhanced plant survival under anoxia by decreased electrolyte leakage, production of hydrogen peroxide and lipid peroxidation. The positive effect of external IAA application coincided with improvement of tolerance to oxygen deprivation in the 35S:iaaM × 35S:iaaH lines of transgene tobacco due to its IAA overproduction.

Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour

BACKGROUND

Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system for studying embryogenesis in woody plants, SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. To understand the molecular mechanisms during longan SE, we examined the transcriptome changes by using Illumina HiSeq from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), globular embryos (GE).

RESULTS

RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to longan genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22,743, 19,745, 21,144, 21,102 expressed transcripts, 1935, 1710, 1816, 1732 novel transcripts, 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis showed that a total of 10,642, 4180, 5846 and 1785 genes were differentially expressed in the pairwise comparisons of NEC_vs_EC, EC_vs_ICpEC, EC_vs_GE, ICpEC_vs_GE, respectively. Among them, plant hormones signalling related genes were significantly enriched, especially the auxin and cytokinin signalling components. The transcripts of flavonoid biosynthesis related genes were mainly expressed in NEC, while fatty acid biosynthesis related genes mainly accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Combined with the FPKM value of longan nine tissues transcription, 27 SE specific or preferential genes (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC preferential genes (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2-1, POD-P7 and POD5 et al.) were characterized as molecular markers for longan early SE. qRT-PCR validation of SE-related genes showed a high correlation between RNA-seq and qRT-PCR data.

CONCLUSION

This study provides new insights into the role of the transcriptome during early SE in longan. Differentially expressed genes reveal that plant hormones signalling, flavonoid and fatty acid biosynthesis, and extracelluar protein related genes were involved in longan early SE. It could serve as a valuable platform resource for further functional studies addressing embryogenesis in woody plants.

Direct comparison of Arabidopsis gene expression reveals different responses to melatonin versus auxin

BACKGROUND

Melatonin (N-acetyl-5-methoxytryptamine) in plants, regulates shoot and root growth and alleviates environmental stresses. Melatonin and the phyto-hormone auxin are tryptophan-derived compounds. However, it largely remains controversial as to whether melatonin and auxin act through similar or overlapping signalling and regulatory pathways.

RESULTS

Here, we have used a promoter-activation study to demonstrate that, unlike auxin (1-naphthalene acetic acid, NAA), melatonin neither induces Direct repeat 5 DR5 expression in Arabidopsis thaliana roots under normal growth conditions nor suppresses the induction of Alternative oxidase 1a AOX1a in leaves upon Antimycin A treatment, both of which are the hallmarks of auxin action. Additionally, comparative global transcriptome analysis conducted on Arabidopsis treated with melatonin or NAA revealed differences in the number and types of differentially expressed genes. Auxin (4.5 μM) altered the expression of a diverse and large number of genes whereas melatonin at 5 μM had no significant effect but melatonin at 100 μM had a modest effect on transcriptome compared to solvent-treated control. Interestingly, the prominent category of genes differentially expressed upon exposure to melatonin trended towards biotic stress defence pathways while downregulation of key genes related to photosynthesis was observed.

CONCLUSION

Together these findings indicate that though they are both indolic compounds, melatonin and auxin act through different pathways to alter gene expression in Arabidopsis thaliana. Furthermore, it appears that effects of melatonin enable Arabidopsis thaliana to prioritize biotic stress defence signalling rather than growth. These findings clear the current confusion in the literature regarding the relationship of melatonin and auxin and also have greater implications of utilizing melatonin for improved plant protection.

Role of auxin homeostasis and response in nitrogen limitation and dark stimulation of adventitious root formation in petunia cuttings

BACKGROUND AND AIMS

Adventitious root (AR) formation in Petunia hybrida is inhibited by low nitrogen fertilization of stock plants but promoted by dark incubation of cuttings before planting. We investigated whether the plant hormone auxin is involved in nitrogen- and dark-mediated AR formation.

METHODS

Concentrations of indole-3-acetic acid (IAA) and RNA accumulation of genes controlling auxin homeostasis and function were monitored in the stem base in response to high versus low nitrogen supply to stock plants and to temporal dark vs. light exposure of cuttings by use of GC-MS/MS, a petunia-specific microarray and quantitative RT-PCR. Auxin source capacity, polar auxin transport in cuttings and auxin concentration in the rooting zone were manipulated to investigate the functional contribution of auxin homeostasis and response to the effects of nitrogen fertilization and dark exposure on rooting.

KEY RESULTS

The nitrogen content of cuttings had only a marginal effect on IAA concentration in the stem base. Dark incubation enhanced the accumulation of IAA in the stem base during AR induction independent of nitrogen level. Early IAA accumulation in the dark depended on the upper shoot as an auxin source and was enhanced after apical IAA supply. Dark exposure stimulated RNA accumulation of auxin-related genes. In particular, expression of Ph-PIN1 and of genes controlling auxin signalling, including Ph-IAA14, Ph-ARF8, Ph-ARF10 and Ph-SAUR14, was enhanced, while the latter four were repressed in nitrogen-limited cuttings, particularly in the dark. Dark stimulation of rooting depended on polar auxin transport. Basal auxin application partially substituted the effect of dark exposure on rooting, whereas the auxin response of AR formation was strongly depressed by nitrogen limitation.

CONCLUSIONS

Increased auxin delivery from the upper shoot and enhanced auxin signalling in the stem base contribute to dark-stimulated AR formation, while nitrogen limitation inhibits AR formation downstream of the auxin signal.

Identification of plant hormones and candidate hub genes regulating flag leaf senescence in wheat response to water deficit stress at the grain-filling stage

In order to clarify the transcriptional regulatory network and physiological mechanisms governing leaf senescence response to drought stress in wheat, experiments were performed using two wheat varieties with contrasting drought tolerance: Fu287 (F287, a drought-sensitive genotype) and Shannong20 (SN20, a drought-resistant genotype). The latter has higher SPAD values, salicylic acid (SA), jasmonic acid (JA), zeatin (Z), zeatin riboside (ZR), and gibberellin (GA 3) content as well as higher expression levels of Cu/Zn-SOD, Mn-SOD, Fe-SOD,POD,CAT, and APX under various water deficit conditions. Conjoint analysis of physiological and biochemical indicators and transcriptome data by weighted gene co-expression network analysis (WGCNA) in the present study provides a useful genomic and molecular resource for studying drought adaptation in wheat. The flag leaf senescence process was changed by altering the concentration of phytohormones. SA, JA, abscisic acid (ABA), Z, ZR, and GA 3 coordinate with each other to control leaf senescence and plant adaptation under drought stress. Further, the leaf senescence process was divided into two phases: the persistence phase and the rapid loss phase. Shorter Chltotal (duration of the flag leaf being photosynthetically active), shorter Chlper (persistence phase), reduced M (inflection point cumulative temperature when senescence rate is the maximum), decreased r max (the maximum senescence rate), larger r 0 (the initial senescence rate), and increased r aver (the average senescence rate) were slightly associated with low grain mass. We speculated that extending the period of the persistence phase by cultivation or chemical control measures could further increase the drought survivability and productivity of wheat.

Transcriptome analysis of roots from resistant and susceptible rice varieties infected with Hirschmanniella mucronata

Hirschmanniella mucronata is a plant-parasitic nematode that is widespread in rice production areas and causes 10-25% yield losses a year on average. Here, we investigated the mechanism of resistance to this nematode by comparing the transcriptomes of roots from resistant (Jiabali) and susceptible (Bawangbian) varieties of rice. Of 39 233 unigenes, 2243. exhibited altered total expression levels between control and infected resistant and susceptible varieties. Significant differences were observed in the expression levels of genes related to stress, peptidase regulation or inhibition, oxidoreductase activity, peroxidase activity and antioxidant activity. The up-regulated genes related to plant secondary metabolites, such as phenylpropanoid, lignin, cellulose or hemicellulose, may result in an increase in the degree of resistance of Jiabali to the H. mucronata infection compared with that of Bawangbian by affecting cell wall organization or biogenesis. Of the genes that responded similarly to H. mucronata infection, ~252 (~76.59%) showed greater changes (whether induced or suppressed) in RN155 (susceptible varieties infected by rice root nematode) than in RN51 (resistance varieties infected by rice root nematode). Nineteen pathogenesis-related genes belonging to nine pathogenesis-related gene families were significantly induced by H. mucronata in the infected roots of Jiabali and Bawangbian, and 13 differentially expressed genes showed changes in their abundance only in the susceptible Bawangbian variety. This study may help enhance our understanding of the mechanisms underlying plant resistance to nematodes.

Signal Transduction in Leaf Senescence: Progress and Perspective

Leaf senescence is a degenerative process that is genetically controlled and involves nutrient remobilization prior to the death of leaf tissues. Age is a key developmental determinant of the process along with other senescence inducing factors. At the cellular level, different hormones, signaling molecules, and transcription factors contribute to the regulation of senescence. This review summarizes the recent progress in understanding the complexity of the senescence process with primary focuses on perception and transduction of senescence signals as well as downstream regulatory events. Future directions in this field and potential applications of related techniques in crop improvement will be discussed.

Auxin and Cell Wall Crosstalk as Revealed by the Arabidopsis thaliana Cellulose Synthase Mutant Radially Swollen 1

Plant cells sheath themselves in a complex lattice of polysaccharides, proteins and enzymes forming an integral matrix known as the cell wall. Cellulose microfibrils, the primary component of cell walls, are synthesized at the plasma membrane by CELLULOSE SYNTHASE A (CESA) proteins throughout cellular growth and are responsible for turgor-driven anisotropic expansion. Associations between hormone signaling and cell wall biosynthesis have long been suggested, but recently direct links have been found revealing hormones play key regulatory roles in cellulose biosynthesis. The radially swollen 1 (rsw1) allele of Arabidopsis thaliana CESA1 harbors a single amino acid change that renders the protein unstable at high temperatures. We used the conditional nature of rsw1 to investigate how auxin contributes to isotropic growth. We found that exogenous auxin treatment reduces isotropic swelling in rsw1 roots at the restrictive temperature of 30�C. We also discovered decreases in auxin influx between rsw1 and wild-type roots via confocal imaging of AUX1-YFP, even at the permissive temperature of 19�C. Moreover, rsw1 displayed mis-expression of auxin-responsive and CESA genes. Additionally, we found altered auxin maxima in rsw1 mutant roots at the onset of swelling using DII-VENUS and DR5:vYFP auxin reporters. Overall, we conclude disrupted cell wall biosynthesis perturbs auxin transport leading to altered auxin homeostasis impacting both anisotropic and isotropic growth that affects overall root morphology.

The study of hormonal metabolism of Trincadeira and Syrah cultivars indicates new roles of salicylic acid, jasmonates, ABA and IAA during grape ripening and upon infection with Botrytis cinerea

Hormones play an important role in fruit ripening and in response to biotic stress. Nevertheless, analyses of hormonal profiling during plant development and defense are scarce. In this work, changes in hormonal metabolism in grapevine (Vitis vinifera) were compared between a susceptible (Trincadeira) and a tolerant (Syrah) variety during grape ripening and upon infection with Botrytis cinerea. Infection of grapes with the necrotrophic pathogen Botrytis cinerea leads to significant economic losses worldwide. Peppercorn-sized fruits were infected in the field and mock-treated and infected berries were collected at green, veraison and harvest stages for hormone analysis and targeted qPCR analysis of genes involved in hormonal metabolism and signaling. Results indicate a substantial reprogramming of hormonal metabolism during grape ripening and in response to fungal attack. Syrah and Trincadeira presented differences in the metabolism of abscisic acid (ABA), indole-3-acetic acid (IAA) and jasmonates during grape ripening that may be connected to fruit quality. On the other hand, high basal levels of salicylic acid (SA), jasmonates and IAA at an early stage of ripening, together with activated SA, jasmonates and IAA signaling, likely enable a fast defense response leading to grape resistance/ tolerance towards B. cinerea. The balance among the different phytohormones seems to depend on the ripening stage and on the intra-specific genetic background and may be fundamental in providing resistance or susceptibility. In addition, this study indicated the involvement of SA and IAA in defense against necrotrophic pathogens and gains insights into possible strategies for conventional breeding and/or gene editing aiming at improving grape quality and grape resistance against Botrytis cinerea.

Transcriptional Profile Corroborates that bml Mutant Plays likely Role in Premature Leaf Senescence of Rice (Oryza sativa L.)

Leaf senescence is the last period of leaf growth and a dynamic procedure associated with its death. The adaptability of the plants to changing environments occurs thanks to leaf senescence. Hence, transcriptional profiling is important to figure out the exact mechanisms of inducing leaf senescence in a particular crop, such as rice. From this perspective, leaf samples of two different rice genotypes, the brown midrib leaf (bml) mutant and its wild type (WT) were sampled for transcriptional profiling to identify differentially-expressed genes (DEGs). We identified 2670 DEGs, among which 1657 genes were up- and 1013 genes were down-regulated. These DEGs were enriched in binding and catalytic activity, followed by the single organism process and metabolic process through gene ontology (GO), while the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DEGs were related to the plant hormone signal transduction and photosynthetic pathway enrichment. The expression pattern and the clustering of DEGs revealed that the WRKY and NAC family, as well as zinc finger transcription factors, had greater effects on early-senescence of leaf compared to other transcription factors. These findings will help to elucidate the precise functional role of bml rice mutant in the early-leaf senescence.

miR1432-OsACOT (Acyl-CoA thioesterase) module determines grain yield via enhancing grain filling rate in rice

Rice grain filling rate contributes largely to grain productivity and accumulation of nutrients. MicroRNAs (miRNAs) are key regulators of development and physiology in plants and become a novel key target for engineering grain size and crop yield. However, there is little studies, so far, showing the miRNA regulation of grain filling and rice yield, in consequence. Here, we show that suppressed expression of rice miR1432 (STTM1432) significantly improves grain weight by enhancing grain filling rate and leads to an increase in overall grain yield up to 17.14% in a field trial. Molecular analysis identified rice Acyl-CoA thioesterase (OsACOT), which is conserved with ACOT13 in other species, as a major target of miR1432 by cleavage. Moreover, overexpression of miR1432-resistant form of OsACOT (OXmACOT) resembled the STTM1432 plants, that is, a large margin of an increase in grain weight up to 46.69% through improving the grain filling rate. Further study indicated that OsACOT was involved in biosynthesis of medium-chain fatty acids. In addition, RNA-seq based transcriptomic analyses of transgenic plants with altered expression of miR1432 demonstrated that downstream genes of miR1432-regulated network are involved in fatty acid metabolism and phytohormones biosynthesis and also overlap with the enrichment analysis of co-expressed genes of OsACOT, which is consistent with the increased levels of auxin and abscisic acid in STTM1432 and OXmACOT plants. Overall, miR1432-OsACOT module plays an important role in grain filling in rice, illustrating its capacity for engineering yield improvement in crops.

The RIN-regulated Small Auxin-Up RNA SAUR69 is involved in the unripe-to-ripe phase transition of tomato fruit via enhancement of the sensitivity to ethylene

Ethylene is the main hormone controlling climacteric fruit ripening; however, the mechanisms underlying the developmental transition leading to the initiation of the ripening process remain elusive, although the presumed role of active hormone interplay has often been postulated. To unravel the putative role of auxin in the unripe-to-ripe transition, we investigated the dynamics of auxin activity in tomato fruit and addressed the physiological significance of Sl-SAUR69, previously identified as a RIN target gene, using reverse genetics approaches. Auxin signalling undergoes dramatic decline at the onset of ripening in wild-type fruit, but not in the nonripening rin mutant. Sl-SAUR69 exhibits reduced expression in rin and its up-regulation results in premature initiation of ripening, whereas its down-regulation extends the time to ripening. Overexpression of Sl-SAUR69 reduces proton pump activity and polar auxin transport, and ectopic expression in Arabidopsis alters auxin transporter abundance, further arguing for its active role in the regulation of auxin transport. The data support a model in which Sl-SAUR69 represses auxin transport, thus generating auxin minima, which results in enhanced ethylene sensitivity. This defines a regulation loop, fed by ethylene and auxin as the main hormonal signals and by RIN and Sl-SAUR69 as modulators of the balance between the two hormones.

Roles of potential plant hormones and transcription factors in controlling leaf senescence and drought tolerance

Plant leaves offer an exclusive windowpane to uncover the changes in organs, tissues, and cells as they advance towards the process of senescence and death. Drought-induced leaf senescence is an intricate process with remarkably coordinated phases of onset, progression, and completion implicated in an extensive reprogramming of gene expression. Advancing leaf senescence remobilizes nutrients to younger leaves thereby contributing to plant fitness. However, numerous mysteries remain unraveled concerning leaf senescence. We are not still able to correlate leaf senescence and drought stress to endogenous and exogenous environments. Furthermore, we need to decipher how molecular mechanisms of the leaf senescence and levels of drought tolerance are advanced and how is the involvement of SAGs in drought tolerance and plant fitness. This review provides the perspicacity indispensable for facilitating our coordinated point of view pertaining to leaf senescence together with inferences on progression of whole plant aging. The main segments discussed in the review include coordination between hormonal signaling, leaf senescence, drought tolerance, and crosstalk between hormones in leaf senescence regulation.

The SAUR gene family: the plant's toolbox for adaptation of growth and development

The family of small auxin up-regulated RNA (SAUR) genes is a family of auxin-responsive genes with ~60-140 members in most higher plant species. Despite the early discovery of their auxin responsiveness, their function and mode of action remained unknown for a long time. In recent years, the importance of SAUR genes in the regulation of dynamic and adaptive growth, and the molecular mechanisms by which SAUR proteins act are increasingly well understood. SAURs play a central role in auxin-induced acid growth, but can also act independently of auxin, tissue specifically regulated by various other hormone pathways and transcription factors. In this review, we summarize recent advances in the characterization of the SAUR genes in Arabidopsis and other plant species. We particularly elaborate on their capacity to fine-tune growth in response to internal and external signals, and discuss the breakthroughs in understanding the mode of action of SAURs in relation to their complex regulation.

SMALL AUXIN UP RNA62/75 Are Required for the Translation of Transcripts Essential for Pollen Tube Growth

Successful pollen tube elongation is critical for double fertilization, but the biological functions of pollen tube genes and the regulatory machinery underlying this crucial process are largely unknown. A previous translatomic study revealed two Arabidopsis (Arabidopsis thaliana) SAUR (SMALL AUXIN UP RNA) genes, SAUR62 and SAUR75, whose expression is up-regulated by pollination. Here, we found that both SAUR62 and SAUR75 localized mainly to pollen tube nuclei. The siliques of homozygous saur62 (saur62/-), saur75 (saur75/-), and the SAUR62/75 RNA interference (RNAi) knockdown line had many aborted seeds. These lines had normal pollen viability but defective in vitro and in vivo pollen tube growth, with branching phenotypes. Immunoprecipitation with transgenic SAUR62/75-GFP flowers revealed ribosomal protein RPL12 family members as potential interacting partners, and their individual interactions were confirmed further by yeast two-hybrid and bimolecular fluorescence complementation assays. Polysome profiling showed reduced 80S ribosome abundance in homozygous saur62, saur75, ribosomal large subunit12c, and SAUR62/75 RNAi flowers, suggesting that SAUR62/75 play roles in ribosome assembly. To clarify their roles in translation, we analyzed total proteins from RNAi versus wild-type flowers by isobaric tags for relative and absolute quantitation, revealing significantly reduced expression of factors participating in pollen tube wall biogenesis and F-actin dynamics, which are critical for the elastic properties of tube elongation. Indeed, RNAi pollen tubes showed mislocalization of deesterified and esterified pectins and F-actin organization. Thus, the biological roles of SAUR62/75 and their RPL12 partners are critical in ribosomal pre-60S subunit assembly for efficient pollen tube elongation and subsequent fertilization.

Transcriptome dynamics associated with resistance and susceptibility against fusarium head blight in four wheat genotypes

Background

Fusarium head blight (FHB) of wheat in North America is caused mostly by the fungal pathogen Fusarium graminearum (Fg). Upon exposure to Fg, wheat initiates a series of cellular responses involving massive transcriptional reprogramming. In this study, we analyzed transcriptomics data of four wheat genotypes (Nyubai, Wuhan 1, HC374, and Shaw), at 2 and 4 days post inoculation (dpi) with Fg, using RNA-seq technology.

Results

A total of 37,772 differentially expressed genes (DEGs) were identified, 28,961 from wheat and 8811 from the pathogen. The susceptible genotype Shaw exhibited the highest number of host and pathogen DEGs, including 2270 DEGs associating with FHB susceptibility. Protein serine/threonine kinases and LRR-RK were associated with susceptibility at 2 dpi, while several ethylene-responsive, WRKY, Myb, bZIP and NAC-domain containing transcription factors were associated with susceptibility at 4 dpi. In the three resistant genotypes, 220 DEGs were associated with resistance. Glutathione S-transferase (GST), membrane proteins and distinct LRR-RKs were associated with FHB resistance across the three genotypes. Genes with unique, high up-regulation by Fg in Wuhan 1 were mostly transiently expressed at 2 dpi, while many defense-associated genes were up-regulated at both 2 and 4 dpi in Nyubai; the majority of unique genes up-regulated in HC374 were detected at 4 dpi only. In the pathogen, most genes showed increased expression between 2 and 4 dpi in all genotypes, with stronger levels in the susceptible host; however two pectate lyases and a hydrolase were expressed higher at 2 dpi, and acetyltransferase activity was highly enriched at 4 dpi.

Conclusions

There was an early up-regulation of LRR-RKs, different between susceptible and resistant genotypes; subsequently, distinct sets of genes associated with defense response were up-regulated. Differences in expression profiles among the resistant genotypes indicate genotype-specific defense mechanisms. This study also shows a greater resemblance in transcriptomics of HC374 to Nyubai, consistent with their sharing of two FHB resistance QTLs on 3BS and 5AS, compared to Wuhan 1 which carries one QTL on 2DL in common with HC374.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5012-3) contains supplementary material, which is available to authorized users.

Transcriptome dynamics associated with resistance and susceptibility against fusarium head blight in four wheat genotypes

BACKGROUND

Fusarium head blight (FHB) of wheat in North America is caused mostly by the fungal pathogen Fusarium graminearum (Fg). Upon exposure to Fg, wheat initiates a series of cellular responses involving massive transcriptional reprogramming. In this study, we analyzed transcriptomics data of four wheat genotypes (Nyubai, Wuhan 1, HC374, and Shaw), at 2 and 4 days post inoculation (dpi) with Fg, using RNA-seq technology.

RESULTS

A total of 37,772 differentially expressed genes (DEGs) were identified, 28,961 from wheat and 8811 from the pathogen. The susceptible genotype Shaw exhibited the highest number of host and pathogen DEGs, including 2270 DEGs associating with FHB susceptibility. Protein serine/threonine kinases and LRR-RK were associated with susceptibility at 2 dpi, while several ethylene-responsive, WRKY, Myb, bZIP and NAC-domain containing transcription factors were associated with susceptibility at 4 dpi. In the three resistant genotypes, 220 DEGs were associated with resistance. Glutathione S-transferase (GST), membrane proteins and distinct LRR-RKs were associated with FHB resistance across the three genotypes. Genes with unique, high up-regulation by Fg in Wuhan 1 were mostly transiently expressed at 2 dpi, while many defense-associated genes were up-regulated at both 2 and 4 dpi in Nyubai; the majority of unique genes up-regulated in HC374 were detected at 4 dpi only. In the pathogen, most genes showed increased expression between 2 and 4 dpi in all genotypes, with stronger levels in the susceptible host; however two pectate lyases and a hydrolase were expressed higher at 2 dpi, and acetyltransferase activity was highly enriched at 4 dpi.

CONCLUSIONS

There was an early up-regulation of LRR-RKs, different between susceptible and resistant genotypes; subsequently, distinct sets of genes associated with defense response were up-regulated. Differences in expression profiles among the resistant genotypes indicate genotype-specific defense mechanisms. This study also shows a greater resemblance in transcriptomics of HC374 to Nyubai, consistent with their sharing of two FHB resistance QTLs on 3BS and 5AS, compared to Wuhan 1 which carries one QTL on 2DL in common with HC374.

Ectopic expression of a Brassica rapa AINTEGUMENTA gene (BrANT-1) increases organ size and stomatal density in Arabidopsis

The AINTEGUMENTA-like (AIL) family plays a central role in regulating the growth and development of organs in many plants. However, little is known about the characteristics and functions of the AIL family in Chinese cabbage (Brassica rapa L. ssp. pekinensis). In this study, a genome-wide analysis was performed to identify the members of the AIL family in Chinese cabbage. We identified three ANT genes and six ANT-like genes of Chinese cabbage, most of which were differentially expressed in different organs or tissues. Furthermore, compared with the wild-type line, the size of different organs in the 35S-BrANT-1 line was significantly increased by promoting cell proliferation. Meanwhile, over-expression of BrANT-1 also increases the stomatal number and delays the leaf senescence. Transcriptome analyses revealed that a set of cell proliferation and stoma development genes were up-regulated, while the senescence-associated genes were down-regulated, suggesting these genes may be involved in BrANT-1 regulated processes for controlling organ size, stomatal density and leaf senescence. In summary, this study offers important insights into the characteristics and functions of the ANT genes in Chinese cabbage, and provides a promising strategy to improve yield or head size in Chinese cabbage breeding programs.

Genome-wide analysis of poplar SAUR gene family and expression profiles under cold, polyethylene glycol and indole-3-acetic acid treatments

Small auxin-up RNA (SAUR) proteins play an important role in the regulation of plant growth and development. Here, we identified 105 SAUR genes and comprehensively analyzed them in Populus trichocarpa. Based on the phylogenetic relationships, the PtSAURs were classified into ten subfamilies. Of the 105 PtSAURs, 100 were randomly distributed along the nineteen chromosomes, while the remaining genes were located along unassigned scafoolds. These genes mainly evolved through segmental duplications. In total, 94 PtSAURs contained no introns, and each group had a similar conserved motif structure. A promoter analysis revealed various cis-elements related to growth, development and stress responses, and a synteny analysis established orthologous relationships among SAURs in Arabidopsis, rice, grape and poplar. The qRT-PCR and tissue expression analyses indicated that PtSAURs show different expression levels in various tissues in response to different treatments. PtSAUR53 was located on the nuclear and plasma membrane by conducting subcellular localization analysis. This study provides a comprehensive overview of poplar SAUR proteins and a foundation for further investigations for functional analysis of SAURs in poplar growth and development. At the same time, it will be valuable to further study the poplar SAUR genes to reveal their biological effects.

CIN-TCP transcription factors: Transiting cell proliferation in plants

Leaves are the most conspicuous planar organs in plants, designed for efficient capture of sunlight and its conversion to energy that is channeled into sustaining the entire biosphere. How a few founder cells derived from the shoot apical meristem give rise to diverse leaf forms has interested naturalists and developmental biologists alike. At the heart of leaf morphogenesis lie two simple cellular processes, division and expansion, that are spatially and temporally segregated in a developing leaf. In leaves of dicot model species, cell division occurs predominantly at the base, concomitant with the expansion and differentiation of cells at the tip of the lamina that drives increase in leaf surface area. The timing of the transition from one cell fate (division) to the other (expansion) within a growing leaf lamina is a critical determinant of final leaf shape, size, complexity and flatness. The TCP proteins, unique to plant kingdom, are sequence-specific DNA-binding transcription factors that control several developmental and physiological traits. A sub-group of class II TCPs, called CINCINNATA-like TCPs (CIN-TCPs henceforth), are key regulators of the timing of the transition from division to expansion in dicot leaves. The current review highlights recent advances in our understanding of how the pattern of CIN-TCP activity is translated to the dynamic spatio-temporal control of cell-fate transition through the transactivation of cell-cycle regulators, growth-repressing microRNAs, and interactions with the chromatin remodeling machinery to modulate phytohormone responses. Unravelling how environmental inputs influence CIN-TCP-mediated growth control is a challenge for future studies. © 2018 IUBMB Life, 70(8):718-731, 2018.

The root transcriptome of Achyranthes bidentata and the identification of the genes involved in the replanting benefit

The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis. The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called "replanting benefit" is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit. The analysis of RNA-seq libraries prepared from mRNA extracted from the roots of first year planting (normal growth, NG) and second year replanting (consecutive monoculture, CM) yielded about 40.22 GB sequencing data. After de novo assembly, 87,256 unigenes were generated with an average length of 1060 bp. Among these unigenes, 55,604 were annotated with public databases, and 52,346 encoding sequences and 2881 transcription factors were identified. A contrast between the NG and CM libraries resulted in a set of 3899 differentially transcribed genes (DTGs). The DTGs related to the replanting benefit and their expression profiles were further analyzed by bioinformatics and qRT-PCR approaches. The major differences between the NG and CM transcriptomes included genes encoding products involved in glycolysis/gluconeogenesis, glutathione metabolism and antioxidant defense, in aspects of the plant/pathogen interaction, phytohormone signaling and phenylpropanoid biosynthesis. The indication was that replanting material enjoyed a stronger level of defense systems, a balance regulation of hormone signals and a suppression of lignin formation, thereby promoting root growth and development. The study provides considerable significant insights for a better understanding of the molecular mechanism of the replanting benefit and suggests their possible application in developing methods to reinforce the effects in medicinal plants.

Transcriptome analysis of Brassica juncea var. tumida Tsen responses to Plasmodiophora brassicae primed by the biocontrol strain Zhihengliuella aestuarii

Mustard clubroot, caused by Plasmodiophora brassicae, is a serious disease that affects Brassica juncea var. tumida Tsen, a mustard plant that is the raw material for a traditional fermented food manufactured in Chongqing, China. In our laboratory, we screened the antagonistic bacteria Zhihengliuella aestuarii against P. brassicae. To better understand the biocontrol mechanism, three transcriptome analyses of B. juncea var. tumida Tsen were conducted using Illumina HiSeq 4000, one from B. juncea only inoculated with P. brassicae (P), one inoculated with P. brassica and the biocontrol agent Z. aestuarii at the same time (P + B), and the other was the control (H), in which P. brassicae was replaced by sterile water. A total of 19.94 Gb was generated by Illumina HiSeq sequencing. The sequence data were de novo assembled, and 107,617 unigenes were obtained. In total, 5629 differentially expressed genes between biocontrol-treated (P + B) and infected (P) samples were assigned to 126 KEGG pathways. Using multiple testing corrections, 20 pathways were significantly enriched with Qvalue ≤ 0.05. The resistance-related genes, involved in the production of pathogenesis-related proteins, pathogen-associated molecular pattern-triggered immunity, and effector-triggered immunity signaling pathways, calcium influx, salicylic acid pathway, reactive oxygen intermediates, and mitogen-activated protein kinase cascades, and cell wall modification, were obtained. The various defense responses induced by the biocontrol strain combatted the P. brassicae infection. The genes and pathways involved in plant resistance were induced by a biocontrol strain. The transcriptome data explained the molecular mechanism of the potential biocontrol strain against P. brassicae. The data will also serve as an important public information platform to study B. juncea var. tumida Tsen and will be useful for breeding mustard plants resistant to P. brassicae.

Transcriptome Analysis of a Premature Leaf Senescence Mutant of Common Wheat (Triticum aestivum L.)

Leaf senescence is an important agronomic trait that affects both crop yield and quality. In this study, we characterized a premature leaf senescence mutant of wheat (Triticum aestivum L.) obtained by ethylmethane sulfonate (EMS) mutagenesis, named m68. Genetic analysis showed that the leaf senescence phenotype of m68 is controlled by a single recessive nuclear gene. We compared the transcriptome of wheat leaves between the wild type (WT) and the m68 mutant at four time points. Differentially expressed gene (DEG) analysis revealed many genes that were closely related to senescence genes. Gene Ontology (GO) enrichment analysis suggested that transcription factors and protein transport genes might function in the beginning of leaf senescence, while genes that were associated with chlorophyll and carbon metabolism might function in the later stage. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the genes that are involved in plant hormone signal transduction were significantly enriched. Through expression pattern clustering of DEGs, we identified 1012 genes that were induced during senescence, and we found that the WRKY family and zinc finger transcription factors might be more important than other transcription factors in the early stage of leaf senescence. These results will not only support further gene cloning and functional analysis of m68, but also facilitate the study of leaf senescence in wheat.

Analysis of the genetic basis of plant height-related traits in response to ethylene by QTL mapping in maize (Zea mays L.)

Ethylene (ET) is critical importance in the growth, development, and stress responses of plants. Plant hormonal stress responses have been extensively studied, however, the role of ET in plant growth, especially plant height (PH) remains unclear. Understanding the genetic control for PH in response to ET will provide insights into the regulation of maize development. To clarify the genetic basis of PH-related traits of maize in response to ET, we mapped QTLs for PH, ear height (EH), and internode length above the uppermost ear (ILAU) in two recombinant inbred line (RIL) populations of Zea mays after ET treatment and in an untreated control (CK) group. Sixty QTLs for the three traits were identified. Twenty-two QTLs were simultaneously detected under both ET treatment and untreated control, and five QTLs were detected at two geographic locations under ET treatment only. Individual QTL can be explained 3.87-17.71% of the phenotypic variance. One QTL (q2PH9-1, q1PH9, q1EH9/q1ILAU9-1, q2ILAU9, and q2EH9) for the measured traits (PH, EH, ILAU) was consistent across both populations. Two QTLs (q2PH2-5, q2ILAU2-2, q1PH2-2, and q1ILAU2-2; q1PH8-1, q1EH8-1, q2PH8-1) were identified for up to two traits in both locations and populations under both ET treatment and untreated control. These consistent and stable regions are important QTLs of potential hot spots for PH, ear height (EH), and internode length above the uppermost ear (ILAU) response to ET in maize; therefore, QTL fine-mapping and putative candidate genes validation should enable the cloning of PH, EH, and ILAU related genes to ET response. These results will be valuable for further fine-mapping and quantitative trait nucleotides (QTNs) determination, and elucidate the underlying molecular mechanisms of ET responses in maize.

Phloem fibres as motors of gravitropic behaviour of flax plants: level of transcriptome

Restoration of stem vertical position after plant inclination is a widely spread version of plant orientation in accordance with gravity vector direction. Gravitropic behaviour of flax plants involves the formation of curvature in stem region that has ceased elongation long in advance of stem inclination. The important participants of such behaviour are phloem fibres with constitutively formed tertiary cell wall (G-layer). We performed the large-scale transcriptome profiling of phloem fibres isolated from pulling and opposite sides of gravitropic curvature and compared with control plant fibres. Significant changes in transcript abundance take place for genes encoding proteins of several ion channels, transcription factors and other regulating elements. The largest number of upregulated genes belonged to the cell wall category; many of those were specifically upregulated in fibres of pulling stem side. The obtained data permit to suggest the mechanism of fibre participation in gravitropic reaction that involves the increase of turgor pressure and the rearrangements of cell wall structure in order to improve contractile properties, and to identify the regulatory elements that operate specifically in the fibres of the pulling stem side making gelatinous phloem fibres an important element of gravitropic response in herbaceous plants.