cDNA cloning, genomic organization and expression analysis during somatic embryogenesis of the translationally controlled tumor protein (TCTP) gene from Japanese larch (Larix leptolepis)

Establishment of embryogenic Pinus thunbergii Parl. suspension cultures: growth parameters, dynamic analysis, and plant regenerative capacities

BACKGROUND

Pinus thunbergii is an economically important conifer species that plays a fundamental role in forest ecosystems. However, the population has declined dramatically in recent years as a result of the pine wilt disease outbreak. Thus, developing pine wilt-resistant P. thunbergii is an effective strategy for combating this epidemic.

RESULTS

The somatic embryogenesis of nematode-resistant P. thunbergii was previously reported by our group. The current study looked into the potential commercialization of suspension cultures as a means of large-scale production of nematode-resistant P. thunbergii seedlings. According to our findings, P. thunbergii suspension cultures were suitable for an initial inoculum of embryogenic tissue (2 g) and a subculture inoculum (6.7% (v/v)). Suspension cultures were cultivated for 8-10 days in a 30 mL liquid medium (Gupta and Durzan medium, DCR medium) to facilitate their maturation. The suspension cultures produced a large number of high-quality somatic embryos, which were then used to regenerate the plants and move them into the field. A more accurate assessment of the quality of suspension cultures for somatic embryogenesis could come from the suspension's dynamics. The results showed that the medium's phosphate, ammonium, nitrate, and carbohydrates were quickly eaten from day 0 to day 10. In terms of the absorption of nitrogen sources, the ammonium (NH4+) was absorbed prior to nitrate (NO3-). Additionally, the activity of mitochondrial succinate dehydrogenase and superoxide dismutase was directly related to cell growth.

CONCLUSIONS

This study presents an approach for selecting appropriate suspension cultures for efficient somatic maturation of P. thunbergii that can also be applied to other conifers. Furthermore, it is possible to commercialize nematode-resistant P. thunbergii seedlings using bioreactors, according to the suspension culture system we describe. To the best of our knowledge, this is the first work to describe a P. thunbergii suspension culture.

Screening and Functional Evaluation of Four Larix kaempferi Promoters

Promoters are powerful tools for breeding new varieties using transgenic technology. However, the low and unstable expression of target genes is still a limiting factor in Larix kaempferi (Lamb.) Carr (Japanese larch) genetic transformation. In this study, we analyzed L. kaempferi transcriptome data, screened out highly expressed genes, cloned their promoters, and constructed plant expression vectors containing the β-glucuronidase (GUS) reporter gene driven by these promoters. Recombinant vectors were introduced into the L. kaempferi embryogenic callus by means of the Agrobacterium-mediated transient or stable genetic transformation method, and the promoter activity was then determined by measuring GUS expression and its enzyme activity in the transformed materials. Four highly expressed genes were identified: L. kaempferi Zhang Chen Yi-1 (LaZCY-1), Zhang Chen Yi-2 (LaZCY-2), Translationally Controlled Tumor Protein (LaTCTP), and ubiquitin (LaUBQ). The 2000 bp fragments upstream of ATG in these sequences were cloned as promoters and named pLaZCY-1, pLaZCY-2, pLaTCTP, and pLaUBQ. Semi-quantitative and quantitative RT-PCR analyses of transient genetic transformation materials showed that all four promoters could drive GUS expression, indicating that they have promoter activities. Semi-quantitative and quantitative RT-PCR analyses and the histochemical staining of stable genetic transformation materials showed that the pLaUBQ promoter had higher activity than the other three L. kaempferi promoters and the CaMV35S promoter. Thus, the pLaUBQ promoter was suggested to be used in larch genetic transformation.

Genome-wide identification of YABBY transcription factors in Brachypodium distachyon and functional characterization of Bd DROOPING LEAF

YABBY transcription factors (TFs) are plant-specific and are characterized by a C2-C2 zinc finger domain at the N-terminus and a YABBY domain at the C-terminus. In this study, eight YABBY genes were identified in the Brachypodium distachyon genome and were unevenly distributed across four chromosomes. Phylogenetic analysis classified BdYABBYs into FIL/YAB3, YAB2, CRC, and INO clades. Sixty-two putative cis-elements were identified in BdYABBY gene putative promoters, among them, CAAT-box, TATA-box, MYB, MYC, ARE, and Box_4 were shared by all. BdYABBY genes are highly expressed in inflorescences, and abiotic stresses regulate their expression. In addition, three transcripts of BdDL were identified. Over-expression in Arabidopsis has shown their different functions in reproductive development, as well as in response to cold stress. Our study lays the foundation for the functional elucidation of BdYABBY genes.

Genome-wide identification, expression analyses of Wuschel-related homeobox (WOX) genes in Brachypodium distachyon and functional characterization of BdWOX12

As one kind of plant-specific transcription factors (TFs), WOX (Wuschel-related homeobox) plays an essential role in plant growth and development. In this study, 21 WOX TFs were identified in Brachypodium distachyon. They were divided into ancient, intermediate, and WUS clades based on phylogenetic analysis. These 21 BdWOX genes are mapped on 5 chromosomes unevenly. In the promoters, the most abundant cis-elements are ABRE, TGACG-motif, and G-box. qRT-PCR results showed that most BdWOX genes are expressed in vegetative and reproductive organs. Meanwhile, the expression of 14, 12, and 15 BdWOX genes are up-regulated by exogenous 6-BA, NAA, and GA, respectively. These results indicated that BdWOX genes participate in hormone signaling and regulate plant growth and development. Overexpression of BdWOX12 in Arabidopsis improved the root system, further indicating the functions of BdWOX genes in growth and development. This study provided a basis for the functional elucidation of BdWOX genes.

Multiple Methods Synergistically Promote the Synchronization of Somatic Embryogenesis Through Suspension Culture in the New Hybrid Between Pinus elliottii and Pinus caribaea

Pinus elliottii × Pinus caribaea is an interspecific pine hybrid of major economic importance. Somatic embryogenesis and plant regeneration in P. elliottii × P. caribaea on solid medium have been reported previously; however, a current limitation is the lack of a stable and effective method for its commercial use. The objective of this study was to establish a suspension culture system and evaluate the effect of multiple methods synergistically on the synchronization of embryo development in P. elliottii × P. caribaea. For the former, a protocol to initiate and establish a suspension culture system of P. elliottii × P. caribaea was presented. Based on biomass growth, the growth of embryogenic calli (EC) followed an S-shape curve in suspensions grown for a 15-day period, and the exponential phase of cell suspensions was reached between days 3 and 6. The initial packed cell volume (PCV) and revolutions per minute (rpm) have a significant effect on the proliferation of EC, and the highest proliferation multiple reached 6.86 (±0.06) at the initial density of 5 ml PCV under a 9-10 days transfer interval in the dark on a rotary shaker at 70 rpm. For the latter, the influence of abscisic acid (ABA), ammonium (NH4 +), nitrate (NO3 -), low temperature, and polyethylene glycol (PEG) on somatic embryogenesis was very significant. When EC were suspended in the medium at a presence of 37.84 μM/L ABA, as many as 274 mature cotyledonary embryos/ml PCV of cells were thereafter formed in the mature medium, and 266 somatic embryos were obtained on mature medium after suspension culture in liquid medium containing 10 mmol/L NH4 + and 30 mmol/L NO3 -. Furthermore, reducing the concentration of 2,4-dichlorophenoxyacetic acid gradually and at 4°C incubation for 12 h in the initial exponential phase could promote the synchronization of somatic embryogenesis, which resulted in 260 mature cotyledonary embryos. This suspension culture system and method of synchronic control can be used in the large-scale production of P. elliottii × P. caribaea seedlings.

MYB transcription factor family in sweet cherry (Prunus avium L.): genome-wide investigation, evolution, structure, characterization and expression patterns

BACK GROUND

MYB Transcription factors (TFs) are most imperative and largest gene family in plants, which participate in development, metabolism, defense, differentiation and stress response. The MYB TFs has been studied in various plant species. However, comprehensive studies of MYB gene family in the sweet cherry (Prunus avium L.) are still unknown.

RESULTS

In the current study, a total of 69 MYB genes were investigated from sweet cherry genome and classified into 28 subfamilies (C1-C28 based on phylogenetic and structural analysis). Microcollinearity analysis revealed that dispersed duplication (DSD) events might play an important role in the MYB genes family expansion. Chromosomal localization, the synonymous (Ks) and nonsynonymous (Ka) analysis, molecular characteristics (pI, weight and length of amino acids) and subcellular localization were accomplished using several bioinformatics tools. Furthermore, the members of distinct subfamilies have diverse cis-acting regions, conserved motifs, and intron-exon architectures, indicating functional heterogeneity in the MYB family. Moreover, the transcriptomic data exposed that MYB genes might play vital role in bud dormancy. The quantitative real-time qRT-PCR was carried out and the expression pattern indicated that MYB genes significantly expressed in floral bud as compared to flower and fruit.

CONCLUSION

Our comprehensive findings provide supportive insights into the evolutions, expansion complexity and functionality of PavMYB genes. These PavMYB genes should be further investigated as they seem to be brilliant candidates for dormancy manipulation in sweet cherry.

Over-Expression of the Cell-Cycle Gene LaCDKB1;2 Promotes Cell Proliferation and the Formation of Normal Cotyledonary Embryos during Larix kaempferi Somatic Embryogenesis

Somatic embryogenesis is an effective tool for the production of forest tree seedlings with desirable characteristics; however, the low initiation frequency and productivity of high-quality mature somatic embryos are still limiting factors for Larix kaempferi (Japanese larch). Here, we analyzed the expression pattern of L. kaempferi cyclin-dependent kinase B 1;2 (LaCDKB1;2) during somatic embryogenesis in L. kaempferi and its relationship with the cell proliferation rate. We also analyzed the effect of LaCDKB1;2 over-expression on somatic embryo quality. The results revealed a positive correlation between LaCDKB1;2 expression and the cell proliferation rate during the proliferation stage. After LaCDKB1;2 over-expression, the proliferation rate of cultures increased, and the number of somatic embryos in transgenic cultures was 2.69 times that in non-transformed cultures. Notably, the number of normal cotyledonary embryos in transgenic cultures was 3 times that in non-transformed cultures, indicating that LaCDKB1;2 not only increases the proliferation of cultures and the number of somatic embryos but also improves the quality of somatic embryos. These results provide insight into the regulatory mechanisms of somatic embryogenesis as well as new Larix breeding material.

Genome-wide analysis of BpDof genes and the tolerance to drought stress in birch (Betula platyphylla)

Background

DNA binding with one finger (Dof) proteins are plant-specific transcription factors playing vital roles in developmental processes and stress responses in plants. Nevertheless, the characterizations, expression patterns, and functions of the Dof family under drought stress (a key determinant of plant physiology and metabolic homeostasis) in woody plants remain unclear.

Methods

The birch (Betula platyphylla var. mandshuric) genome and plant TFDB database were used to identify Dof gene family members in birch plants. ClustalW2 of BioEdit v7.2.1, MEGA v7.0, ExPASy ProtParam tool, Subloc, TMHMM v2.0, GSDS v2.0, MEME, TBtools, KaKs Calculator v2.0, and PlantCARE were respectively used to align the BpDof sequences, build a phylogenetic tree, identify the physicochemical properties, analyze the chromosomal distribution and synteny, and identify the cis-elements in the promoter regions of the 26 BpDof genes. Additionally, the birch seedlings were exposed to PEG6000-simulated drought stress, and the expression patterns of the BpDof genes in different tissues were analyzed by qRT-PCR. The histochemical staining and the evaluation of physiological indexes were performed to assess the plant tolerance to drought with transient overexpression of BpDof4, BpDof11, and BpDof17 genes. SPSS software and ANOVA were used to conduct all statistical analyses and determine statistically significant differences between results.

Results

A total of 26 BpDof genes were identified in birch via whole-genome analysis. The conserved Dof domain with a C(x)2C(x)21C(x)2C zinc finger motif was present in all BpDof proteins. These birch BpDofs were classified into four groups (A to D) according to the phylogenetic analysis of Arabidopsis thaliana Dof genes. BpDof proteins within the same group mostly possessed similar motifs, as detected by conserved motif analysis. The exon–intron analysis revealed that the structures of BpDof genes differed, indicating probable gene gain and lose during the BpDof evolution. The chromosomal distribution and synteny analysis showed that the 26 BpDofs were unevenly distributed on 14 chromosomes, and seven duplication events among six chromosomes were found. Cis-acting elements were abundant in the promoter regions of the 26 BpDof genes. qRT-PCR revealed that the expression of the 26 BpDof genes was differentially regulated by drought stress among roots, stems, and leaves. Most BpDof genes responded to drought stress, and BpDof4, BpDof11, and BpDof17­ were significantly up-regulated. Therefore, plants overexpressing these three genes were generated to investigate drought stress tolerance. The BpDof4-, BpDof11-, and BpDof17­-overexpressing plants showed promoted reactive oxygen species (ROS) scavenging capabilities and less severe cell damage, suggesting that they conferred enhanced drought tolerance in birch. This study provided an in-depth insight into the structure, evolution, expression, and function of the Dof gene family in plants.

Identification and characterization of a natural SNP variant in ALTERNATIVE OXIDASE gene associated with cold stress tolerance in watermelon

Alternative oxidase (AOX) is a mitochondrial enzyme encoded by a small nuclear gene family, which contains the two subfamilies, AOX1 and AOX2. In the present study on watermelon (Citrullus lanatus), only one ClAOX gene, belonging to AOX2 subfamily but having a similar gene structure to AtAOX1a, was found in the watermelon genome. The expression analysis suggested that ClAOX had the constitutive expression feature of AOX2 subfamily, but was cold inducible, which is normally considered an AOX1 subfamily feature. Moreover, one single nucleotide polymorphism (SNP) in ClAOX sequence, which led to the change from Lys (N) to Asn (K) in the 96^th amino acids, was found among watermelon subspecies. Ectopic expression of two ClAOX alleles in the Arabidopsis aox1a knock-out mutant indicated that ClAOX^K-expressing plants had stronger cold tolerance than aox1a mutant and ClAOX^N-expressing plants. Our findings suggested watermelon genome contained a single ClAOX that possessed the expression features of both AOX1 and AOX2 subfamilies. A naturally existing SNP in ClAOX differentiated the cold tolerance of transgenic Arabidopsis plants, impling a possibility this gene might be a functional marker for stress-tolerance breeding.

Early nodulin 93 protein gene: essential for induction of somatic embryogenesis in oil palm

Transcript profiling during the early induction phase of oil palm tissue culture and RNAi studies in a model somatic embryogenesis system showed that EgENOD93 expression is essential for somatic embryogenesis. Micropropagation of oil palm through tissue culture is vital for the generation of superior and uniform elite planting materials. Studies were carried out to identify genes to distinguish between leaf explants with the potential to develop into embryogenic or non-embryogenic callus. Oil palm cDNA microarrays were co-hybridized with cDNA probes of reference tissue, separately with embryo forming (media T527) and non-embryo (media T694) forming leaf explants sampled at Day 7, Day 14 and Day 21. Analysis of the normalized datasets has identified 77, 115 and 127 significantly differentially expressed genes at Day 7, Day 14, and Day 21, respectively. An early nodulin 93 protein gene (ENOD93), was highly expressed at Day 7, Day 14, and Day 21 and in callus (media T527), as assessed by RT-qPCR. Validation of EgENOD93 across tissue culture lines of different genetic background and media composition showed the potential of this gene as an embryogenic marker. In situ RNA hybridization and functional characterization in Medicago truncatula provided additional evidence that ENOD93 is essential for somatic embryogenesis. This study supports the suitability of EgENOD93 as a marker to predict the potential of leaf explants to produce embryogenic callus. Crosstalk among stresses, auxin, and Nod-factor like signalling molecules likely induces the expression of EgENOD93 for embryogenic callus formation.

Genome-wide identification and characterization of SRO gene family in wheat: Molecular evolution and expression profiles during different stresses

SRO (SIMILAR TO RCD ONE), a type of plant-specific small protein family, play important roles in plant growth and development, as well as in response to biotic/abiotic stresses. Although characterization of SROs have been performed in model plants, little is known about their function in wheat, especially under stress conditions. In this study, 30 SRO genes were identified from the wheat genome (TaSRO). They were phylogenetically separated into two groups with distinct structures. The cis-regulatory elements in the promoter region of TaSROs were analyzed and numerous elements functionally associated with stress responding and hormones were interpreted, implying the reason for induction expression patterns of TaSROs during abiotic and biotic stresses in wheat. Whole-genome replication events in the SRO gene family of wheat and seven other species (Arabidopsis thaliana, rice, maize, barley, soybean, upland cotton, and cucumber) were analyzed, resulting in 1, 12, 9, 23, 6, 5, and 3 of gene pairs, respectively. The tissue-specific expression pattern profiling revealed that most TaSROs are highly expressed in one or more tissues and may play an important role in wheat growth and development. In addition, qRT-PCR results further confirmed that these TaSRO genes are involved in wheat stress response. In summary, our study laid a theoretical basis for molecular function deciphering of TaSROs, especially in plant hormones and biotic/abiotic stress responses.

Genome-wide identification of expansin genes in Brachypodium distachyon and functional characterization of BdEXPA27

Plant expansin belongs to a group of cell wall proteins and functions in plant growth and development. However, limited data are available on the contributions of expansins in Brachypodium distachyon. In the present study, a total of 38 expansins were identified in B. distachyon genome. Phylogenetic analysis divided the expansins into four groups, namely EXPA, EXPB, EXLA, and EXLB. Chromosomal distribution showed that they were unevenly distributed on 4 chromosomes. A total of six tandem duplication pairs and four segmental duplication pairs were detected, which contributed to the expansion of the B. distachyon expansin gene family. Expansins in the same group shared similar gene structure and motif composition. Three types of cis-elements, development-related, hormone-related, and abiotic stresses-related elements were found in the B. distachyon expansin gene promoters. Expression profiles indicated that most of B. distachyon expansin genes participate in plant development and abiotic stress responses. Overexpression of BdEXPA27 increased seed width and length, root length, root hair number and length in Arabidopsis and showed higher germination rate in transgenic lines. This study establishes a foundation for further investigation of B. distachyon expansin genes and provides novel insights into their biological functions.

Characteristics and Expression Pattern of MYC Genes in Triticum aestivum, Oryza sativa, and Brachypodium distachyon

Myelocytomatosis oncogenes (MYC) transcription factors (TFs) belong to basic helix-loop-helix (bHLH) TF family and have a special bHLH_MYC_N domain in the N-terminal region. Presently, there is no detailed and systematic analysis of MYC TFs in wheat, rice, and Brachypodium distachyon. In this study, 26 TaMYC, 7 OsMYC, and 7 BdMYC TFs were identified and their features were characterized. Firstly, they contain a JAZ interaction domain (JID) and a putative transcriptional activation domain (TAD) in the bHLH_MYC_N region and a BhlH region in the C-terminal region. In some cases, the bHLH region is followed by a leucine zipper region; secondly, they display tissue-specific expression patterns: wheat MYC genes are mainly expressed in leaves, rice MYC genes are highly expressed in stems, and B. distachyon MYC genes are mainly expressed in inflorescences. In addition, three types of cis-elements, including plant development/growth-related, hormone-related, and abiotic stresses-related were identified in different MYC gene promoters. In combination with the previous studies, these results indicate that MYC TFs mainly function in growth and development, as well as in response to stresses. This study laid a foundation for the further functional elucidation of MYC genes.

Genome-wide identification of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) family in grape (Vitis vinifera L.)

Background

CLE genes play various biological roles in plant growth and development, as well as in responses to environmental stimuli.

Results

In the present study, we identified nine CLE genes in the grape genome using an effective identification method. We analyzed the expression profiles of grape CLE genes in different tissues and under environmental different stimuli. VvCLE3 was expressed in shoot apical meristem (SAM) enriched regions, and VvCLE6 was expressed in shoot tissue without SAM. When grapes were infected with bois noir, VvCLE2 was up-regulated. Under ABA treatment, VvCLE3 was down-regulated. VvCLE6 was up-regulated under high temperature stress. We found that VvCLE6 and VvCLE1 were highly expressed in root tissue. In addition, we compared the characteristics of CLEs from grape and other plant species. The CLE family in Sphagnum fallax underwent positive selection, while the CLE family in grape underwent purifying selection. The frequency of optimal codons and codon adaptation index of rice and grape CLE family members were positively correlated with GC content at the third site of synonymous codons, indicating that the dominant evolutionary pressure acting on rice and grape CLE genes was mutation pressure. We also found that closely related species had higher levels of similarity in relative synonymous codon usage in CLE genes. The rice CLE family was biased toward C and G nucleotides at third codon positions. Gene duplication and loss events were also found in grape CLE genes.

Conclusion

These results demonstrate an effective identification method for CLE motifs and increase the understanding of grape CLEs. Future research on CLE genes may have applications for grape breeding and cultivation to better understand root and nodulation development.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5944-2) contains supplementary material, which is available to authorized users.

Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization

BACKGROUND

Polyploidization is a common event in the evolutionary history of angiosperms, and there will be some changes in the genomes of plants other than a simple genomic doubling after polyploidization. Allotetraploid Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are a good group for studying the problems associated with polyploidization. On the other hand, the EIN3/EIL gene family is an important gene family in plants, all members of which are key genes in the ethylene signaling pathway. Until now, the EIN3/EIL gene family in B. napus and its diploid progenitors have been largely unknown, so it is necessary to comprehensively identify and analyze this gene family.

RESULTS

In this study, 13, 7 and 7 EIN3/EIL genes were identified in B. napus (2n = 4x = 38, A_nC_n), B. rapa (2n = 2x = 20, A_r) and B. oleracea (2n = 2x = 18, C_o). All of the identified EIN3/EIL proteins were divided into 3 clades and further divided into 8 sub-clades. Ka/Ks analysis showed that all identified EIN3/EIL genes underwent purifying selection after the duplication events. Moreover, gene structure analysis showed that some EIN3/EIL genes in B. napus acquired introns during polyploidization, and homolog expression bias analysis showed that B. napus was biased towards its diploid progenitor B. rapa. The promoters of the EIN3/EIL genes in B. napus contained more cis-acting elements, which were mainly involved in endosperm gene expression and light responsiveness, than its diploid progenitors. Thus, B. napus might have potential advantages in some biological aspects.

CONCLUSIONS

The results indicated allotetraploid B. napus might have potential advantages in some biological aspects. Moreover, our results can increase the understanding of the evolution of the EIN3/EIL gene family in B. napus, and provided more reference for future research about polyploidization.

Stearoyl-ACP Δ9 Desaturase 6 and 8 (GhA-SAD6 and GhD-SAD8) Are Responsible for Biosynthesis of Palmitoleic Acid Specifically in Developing Endosperm of Upland Cotton Seeds

Palmitoleic acid (16:1Δ⁹) is one kind of ω-7 fatty acids (ω-7 FAs) widely used in food, nutraceutical and industry. However, such high-valued ω-7 FA only has a trace level in mature seeds of cotton and other common oil crops. We found that palmitoleic acid (>10.58 Mol%) was specially enriched in developing cotton endosperm which is disappeared in its mature seed. The present study was conducted to investigate the mechanism underlying high accumulation of palmitoleic acid in developing endosperm but not in embryo of upland cotton (Gossypium hirsutum L.) seed. Of 17 stearoyl-ACP Δ⁹ desaturases (SAD) gene family members identified in upland cotton, six GhSADs may specifically work in the desaturation of palmitic acid (16:0-ACP) to produce palmitoleic acid (16:1Δ⁹-ACP), which were revealed by examining the key amino acids in the catalytic center and their cis-elements. Gene expression analysis showed that spatial patterns of these GhSADs were different in developing ovules, with GhA-SAD6 and GhD-SAD8 preferentially expressed in developing endosperms. Functional analysis by transient expression in Nicotiana benthamiana leaves and genetic complementary assay using yeast mutant BY4389 strain unable to synthesize unsaturated fatty acids demonstrated that GhA-SAD6 and GhD-SAD8 have strong substrate specificity for 16:0-ACP. In contrast, GhA-SAD5 and GhA-SAD7 exhibited high specific activity on 18:0-ACP. Taken together, these data evidence that GhA-SAD6 and GhD-SAD8 are responsible for making palmitoleic acid in developing cotton endosperms, and provide endogenous gene targets for genetic modification to enrich ω-7 FAs in cotton seed oil required for sustainable production of functionality-valued products.

Silencing of an α-dioxygenase gene, Ca-DOX, retards growth and suppresses basal disease resistance responses in Capsicum annum

Alpha-dioxygenases (α-DOX) catalyzing the primary oxygenation of fatty acids to oxylipins were recently found in plants. Here, the biological roles of the pepper α-DOX (Ca-DOX) gene, which is strongly induced during non-host pathogen infection in chili pepper, were examined. Virus-induced gene silencing demonstrated that down-regulation of Ca-DOX enhanced susceptibility to bacterial pathogens and suppressed the hypersensitive response via the suppression of pathogenesis-related genes such as PR4, proteinase inhibitor II and lipid transfer protein (PR14). Ca-DOX-silenced pepper plants also exhibited more retarded growth with lower epidermal cell numbers and reduced cell wall thickness than control plants. To better understand regulation of Ca-DOX, transgenic Arabidopsis plants harboring the β-glucuronidase (GUS) reporter gene driven from a putative Ca-DOX promoter were generated. GUS expression was significantly induced upon avirulent pathogen infection in transgenic Arabidopsis leaves, whereas GUS induction was relatively weak upon virulent pathogen treatment. After treatment with plant hormones, early and strong GUS expression was seen after treatment of salicylic acid, whereas ethylene and methyl jasmonate treatments produced relatively weak and late GUS signals. These results will enable us to further understand the role of α-DOX, which is important in lipid metabolism, defense responses, and growth development in plants.

Roles of the Translationally Controlled Tumor Protein (TCTP) in Plant Development

The Translationally Controlled Tumor Protein (TCTP) is a conserved protein which expression was associated with several biochemical and cellular functions. Loss-of-function mutants are lethal both in animals and in plants, making the identification of its exact role difficult. Recent data using the model plant Arabidopsis thaliana provided the first viable adult knockout for TCTP and helped addressing the biological role of TCTP during organ development and the functional conservation between plants and animals. This chapter summarizes our up to date knowledge about the role of TCTP in plants and discuss about conserved functions and mechanisms between plants and animals.

Identification and expression dynamics of three WUSCHEL related homeobox 13 (WOX13) genes in peanut

WUSCHEL-related homeobox (WOX) genes play key roles in plant stem cell maintenance and development. WOX genes showed specific expression patterns which are important for their functions. WOX13 subfamily genes as the ancestor genes of this family were less studied in the past. In this study, we cloned three Arachis hypogaea (peanut) WOX13 (AhWOX13) subfamily genes from peanut: WOX13A and WOX13B1, 2. WOX13B1 encoded a same protein as WOX13B2, and there were only two-base difference between these two genes. Differential expression patterns were observed for these three AhWOX13 subfamily genes in different tissues and developmental stages. Phylogenic trees analysis showed that these AhWOX13 subfamily genes were the most conserved WOX genes and belonged to the ancient clade of WOX family. This was also supported by the conserved motif analysis. Selective pressure analysis showed that the WOX family genes mainly underwent weak purifying selection (ω = 0.58097), while many positive mutations accumulated during the evolution history. Under the purifying selection, gene duplication event and loss of duplicated gene play important roles in the expansion and evolution of WOX family.

The alternative Medicago truncatula defense proteome of ROS-defective transgenic roots during early microbial infection

ROP-type GTPases of plants function as molecular switches within elementary signal transduction pathways such as the regulation of ROS synthesis via activation of NADPH oxidases (RBOH-respiratory burst oxidase homolog in plants). Previously, we reported that silencing of the Medicago truncatula GTPase MtROP9 led to reduced ROS production and suppressed induction of ROS-related enzymes in transgenic roots (MtROP9i) infected with pathogenic (Aphanomyces euteiches) and symbiotic microorganisms (Glomus intraradices, Sinorhizobium meliloti). While fungal infections were enhanced, S. meliloti infection was drastically impaired. In this study, we investigate the temporal proteome response of M. truncatula MtROP9i transgenic roots during the same microbial interactions under conditions of deprived potential to synthesize ROS. In comparison with control roots (Mtvector), we present a comprehensive proteomic analysis using sensitive MS protein identification. For four early infection time-points (1, 3, 5, 24 hpi), 733 spots were found to be different in abundance: 213 spots comprising 984 proteins (607 unique) were identified after S. meliloti infection, 230 spots comprising 796 proteins (580 unique) after G. intraradices infection, and 290 spots comprising 1240 proteins (828 unique) after A. euteiches infection. Data evaluation by GelMap in combination with a heatmap tool allowed recognition of key proteome changes during microbial interactions under conditions of hampered ROS synthesis. Overall, the number of induced proteins in MtROP9i was low as compared with controls, indicating a dual function of ROS in defense signaling as well as alternative response patterns activated during microbial infection. Qualitative analysis of induced proteins showed that enzymes linked to ROS production and scavenging were highly induced in control roots, while in MtROP9i the majority of proteins were involved in alternative defense pathways such as cell wall and protein degradation.