Phylogeny and expression profiling of CAD and CAD-like genes in hybrid Populus (P. deltoides x P. nigra): evidence from herbivore damage for subfunctionalization and functional divergence

Regulation of lignin biosynthesis by GhCAD37 affects fiber quality and anther vitality in upland cotton

Cotton stands as a pillar in the textile industry due to its superior natural fibers. Lignin, a complex polymer synthesized from phenylalanine and deposited in mature cotton fibers, is believed to be essential for fiber quality, although the precise effects remain largely unclear. In this study, we characterized two ubiquitously expressed cinnamyl alcohol dehydrogenases (CAD), GhCAD37A and GhCAD37D (GhCAD37A/D), in Gossypium hirsutum. GhCAD37A/D possess CAD enzymatic activities, to catalyze the generation of monolignol products during lignin biosynthesis. Analysis of transgenic cotton knockout and overexpressing plants revealed that GhCAD37A/D are important regulators of fiber quality, positively impacting breaking strength but negatively affecting fiber length and elongation percentage by modulating lignin biosynthesis in fiber cells. Moreover, GhCAD37A/D are shown to modulate anther vitality and affect stem lodging trait in cotton by influencing lignin biosynthesis in the vascular bundles of anther and stem, respectively. Additionally, our study revealed that Ghcad37A/D knockout plants displayed red stem xylem, likely due to the overaccumulation of aldehyde intermediates in the phenylpropanoid metabolism pathway, as indicated by metabolomics analysis. Thus, our work illustrates that GhCAD37A/D are two important enzymes of lignin biosynthesis in different cotton organs, influencing fiber quality, anther vitality, and stem lodging.

Impaired Brown midrib12 function orchestrates sorghum resistance to aphids via an auxin conjugate indole-3-acetic acid-aspartic acid

Lignin, a complex heterogenous polymer present in virtually all plant cell walls, plays a critical role in protecting plants from various stresses. However, little is known about how lignin modifications in sorghum will impact plant defense against sugarcane aphids (SCA), a key pest of sorghum. We utilized the sorghum brown midrib (bmr) mutants, which are impaired in monolignol synthesis, to understand sorghum defense mechanisms against SCA. We found that loss of Bmr12 function and overexpression (OE) of Bmr12 provided enhanced resistance and susceptibility to SCA, respectively, as compared with wild-type (WT; RTx430) plants. Monitoring of the aphid feeding behavior indicated that SCA spent more time in reaching the first sieve element phase on bmr12 plants compared with RTx430 and Bmr12-OE plants. A combination of transcriptomic and metabolomic analyses revealed that bmr12 plants displayed altered auxin metabolism upon SCA infestation and specifically, elevated levels of auxin conjugate indole-3-acetic acid-aspartic acid (IAA-Asp) were observed in bmr12 plants compared with RTx430 and Bmr12-OE plants. Furthermore, exogenous application of IAA-Asp restored resistance in Bmr12-OE plants, and artificial diet aphid feeding trial bioassays revealed that IAA-Asp is associated with enhanced resistance to SCA. Our findings highlight the molecular underpinnings that contribute to sorghum bmr12-mediated resistance to SCA.

Dynamic Metabolic Responses of Resistant and Susceptible Poplar Clones Induced by Hyphantria cunea Feeding

Poplar trees are significant for both economic and ecological purposes, and the fall webworm (Hyphantria cunea Drury) poses a major threat to their plantation in China. The preliminary resistance assessment in the previous research indicated that there were differences in resistance to the insect among these varieties, with '2KEN8' being more resistant and 'Nankang' being more susceptible. The present study analyzed the dynamic changes in the defensive enzymes and metabolic profiles of '2KEN8' and 'Nankang' at 24 hours post-infestation (hpi), 48 hpi, and 96 hpi. The results demonstrated that at the same time points, compared to susceptible 'Nankang', the leaf consumption by H. cunea in '2KEN8' was smaller, and the larval weight gain was slower, exhibiting clear resistance to the insect. Biochemical analysis revealed that the increased activity of the defensive enzymes in '2KEN8' triggered by the feeding of H. cunea was significantly higher than that of 'Nankang'. Metabolomics analysis indicated that '2KEN8' initiated an earlier and more intense reprogramming of the metabolic profile post-infestation. In the early stages of infestation, the differential metabolites induced in '2KEN8' primarily included phenolic compounds, flavonoids, and unsaturated fatty acids, which are related to the biosynthesis pathways of phenylpropanoids, flavonoids, unsaturated fatty acids, and jasmonates. The present study is helpful for identifying the metabolic biomarkers for inductive resistance to H. cunea and lays a foundation for the further elucidation of the chemical resistance mechanism of poplar trees against this insect.

Multi-omics analysis of Populus simonii × P. nigra leaves under Hyphantria cunea stress

Poplar is an important greening and timber tree species in China, which has great economic and ecological values. However, the spread of Hyphantria cunea has become increasingly serious in recent years, resulting in huge economic loss of poplar production. Exploring the molecular mechanism of poplar reponse to H. cunea stress has significant implications for future development of new insect-resistant poplar varieties using genetic engineering technology. In this study, a total of 1039 differentially expressed genes (DEGs), 106 differentially expressed proteins (DEPs) and 212 differentially expressed metabolites (DEMs) were screened from Populus simonii × P. nigra leaves under H. cunea stress by transcriptome, proteomics and metabolomics analysis, respectively. GO and KEGG analysis showed that the DEGs and DEPs are associated with endopeptidase inhibitor activity, stress response, α-linolenic acid metabolism, phenylpropanoid biosynthesis and metabolic pathways, cysteine and methionine metabolism pathways and MAKP signaling pathway. Metabolomics analysis showed the most of DEMs were lipids and lipid molecules, and the pathways associated with transcriptome mainly include plant hormone signal transduction, α-linolenic acid metabolic pathway, amino sugar and nucleotide sugar metabolism, and phenylpropanoid biosynthesis. In particular, multi-omics analysis showed that several pathways such as α-linolenic acid metabolic, phenylpropanoid biosynthesis and metabolic pathway and cysteine and methionine metabolic pathway were significantly enriched in the three omics, which may play an important role in the resistance to pests in poplar.

Genome-wide identification of the CAD gene family and functional analysis of putative bona fide CAD genes in tobacco (Nicotiana tabacum L.)

Cinnamyl alcohol dehydrogenase (CAD) plays a crucial role in lignin biosynthesis, and the gene family encoding various CAD isozymes has been cloned and characterized in numerous plant species. However, limited information regarding the CAD gene family in tobacco is currently available. In this study, we identified 10 CAD genes in Nicotiana tabacum, four in N. tomentosiformis, and six in N. sylvestris. The nucleotide and amino acid sequences of these tobacco CADs demonstrate high levels of similarity, whereas the putative protein sequences conservatively possessed two Zn2+ binding motifs and an NADP(H) cofactor binding motif. Both NtCAD1 and NtCAD2 had conservative substrate binding sites, similar to those possessed by bona fide CADs, and evidence from phylogenetic analysis as well as expression profiling supported their role as bona fide CADs involved in lignin biosynthesis. NtCAD1 has two paralogous genes, NtCAD1-1 and NtCAD1-2. Enzyme activity analysis revealed that NtCAD1-1 and NtCAD1-2 had a high affinity to coniferyl aldehyde, p-coumaryl aldehyde, and sinapyl aldehyde, whereas NtCAD2 preferred coniferyl aldehyde and p-coumaryl aldehyde as substrates. The kinetic parameter assay revealed that NtCAD1-2 functions as the most efficient enzyme. Downregulation of both NtCAD1-1 and NtCAD1-2 resulted in reddish-brown stems without significant changes in lignin content. Furthermore, NtCAD1-1, NtCAD1-2, and NtCAD2 showed distinct expression patterns in response to biotic and abiotic stresses, as well as different phytohormones. Our findings suggest that NtCAD1-1 and NtCAD1-2 are involved in lignin biosynthesis, with NtCAD1-2 also participating in both biological and abiotic stresses, whereas NtCAD2 plays a distinct role mainly in responding to biological and abiotic stresses in tobacco.

Functional Diversification and the Plant Secondary Cell Wall

Much evidence exists suggesting the presence of genetic functional diversification in plants, though literature associated with the role of functional diversification in the evolution of the plant secondary cell wall (SCW) has sparsely been compiled and reviewed in a recent context. This review aims to elucidate, through the examination of gene phylogenies associated with its biosynthesis and maintenance, the role of functional diversification in shaping the critical, dynamic, and characteristic organelle, the secondary cell wall. It will be asserted that gene families resulting from gene duplication and subsequent functional divergence are present and are heavily involved in SCW biosynthesis and maintenance. Furthermore, diversification will be presented as a significant driver behind the evolution of the many functional characteristics of the SCW. The structure and function of the plant cell wall and its constituents will first be explored, followed by a discussion on the phenomenon of gene duplication and the resulting genetic functional divergence that can emerge. Finally, the major constituents of the SCW and their individual relationships with duplication and divergence will be reviewed to the extent of current knowledge on the subject.

Assessment of genetic diversity and phylogenetic relationship of local coffee populations in southwestern Saudi Arabia using DNA barcoding

The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southwestern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci: atpB-rbcl, trnL-trnF, trnT-trnL, and trnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while trnT-trnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, trnT-trnL recorded the highest singleton variable sites, while trnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts.

Morpho-physiological characterization and metabolic profiling of rice lines for immunity to counter Helminthosporiumoryzae

Heliminthosporium oryzae is a necrotrophic fungal pathogen that effect rice crops grown on millions of hectares. We evaluated nine newly establishing rice lines and one local variety for resistance against H. oryzae. Significant (P ≤ 0.05) differences in response to pathogen attack were recorded in all rice lines. Maximum disease resistance was recorded in Kharamana under pathogen attack as compared to uninfected plants. A comparison of decline in shoot length revealed that Kharamana and Sakh experienced minimum lost (9.21%, 17.23%) in shoot length respectively against control while Binicol exhibited highest reduction (35.04%) in shoot length due to H. oryzae attack. Post-infection observations of shoot fresh weight revealed 63% decline in Binicol and declared it as the most susceptible rice line. Sakh, Kharamana and Gervex exhibited minimum fresh weight decrease (19.86%, 19.24% and 17.64% respectively) as compared to other lines under pathogen attack. Maximum chlorophyll-a contents were recorded in Kharamana under control and post pathogen attackconditions. Following the inoculation of H. oryzae, SOD was increased up to 35% and 23% in Kharamana and Sakh. However, minimum POD activity was recorded in Gervex followed by Swarnalata, Kaosen and C-13 in non-inoculated and pathogen-inoculated plants. Significant decrease in ascorbic acid contents (73.7% and 70.8%) was observed in Gervex and Binicol that later contributed in their susceptibility to H. oryzae attack. Pathogen attack caused Significant (P ≤ 0.05) changes in secondary metabolites in all rice lines but minimum total flavonoids, anthocyanin and lignin were observed in Binicol in uninfected plants and attested its susceptibility to pathogen. In post-pathogen attack conditions, Kharamana showed best resistance against pathogen by exhibiting a significantly high and maximum value of morpho-physiological, and biochemical attributes. Our findings suggest that tested resistant lines can be further explored for multiple traits including molecular regulation of defense responses to breed immunity in rice varieties.

The impact of spring wheat species and sowing density on soil biochemical properties, content of secondary plant metabolites and the presence of Oulema ssp

The physical and chemical properties of the soil are important factors influencing the yield of crops. One of the agrotechnical factors influencing the biochemical properties of soil is sowing density. It affects the yield components, light, moisture and thermal conditions in the canopy and the pressure of pests. Secondary metabolites, many of which are known to act as a defense mechanism against insects, are of importance in the interaction between the crop and abiotic and biotic factors of the habitat. To the best of our knowledge, the studies conducted so far do not sufficiently reveal the impacts of the wheat species and the sowing density, together with the biochemical properties of the soil, on the accumulation of bioactive ingredients in the crop plants, and the subsequent impacts on the occurrence of phytophagic entomofauna in various management systems. Explaining these processes creates an opportunity for more sustainable development of agriculture. The study aimed to determine the effect of wheat species and sowing density on the biochemical properties of the soil, concentrations of biologically active compounds in the plant and the occurrence of insect pests in organic (OPS) and conventional (CPS) production systems. The research was conducted on spring wheat species (Indian dwarf wheat-Triticum sphaerococcum Percival and Persian wheat-Triticum persicum Vavilov) grown in OPS and CPS at sowing densities 400, 500, 600 (seeds m^-2). The following analyzes were performed: (i) soil analysis: the activity of catalases (CAT), dehydrogenases (DEH), peroxidases (PER); (ii) plant analysis: total phenolic compounds (TP), chlorogenic acid (CA), antioxidant capacity (FRAP); (iii) entomological analysis of the number of insects-Oulema spp. adults and larvae. Performing analyzes in such a wide (interdisciplinary) scope will allow for a comprehensive understanding of the soil-plant-insect biological transformation evaluation. Our results showed that an increase in soil enzyme activity caused a decrease in TP contents in the wheat grown the OPS. Despite this, both the content of TP and the anti-oxidative activity of the ferric reducing ability of plasma (FRAP) were higher in these wheats. Bioactive compound contents and FRAP were most favoured by the lowest sowing density. Regardless of the production system, the occurrence of the Oulema spp. adults on T. sphaerococcum was the lowest at a sowing density of 500 seeds m^-2. The occurrence of this pest's larvae was lowest at a sowing density of 400 seeds m^-2. Research on bioactive compounds in plants, biochemical properties of soil and the occurrence of pests make it possible to comprehensively assess the impact of the sowing density of ancient wheat in the ecological and conventional production system, which is necessary for the development of environmentally sustainable agriculture.

Qualitative and quantitative phytochemical screening of Nerium oleander L. extracts associated with toxicity profile

In this study, phytochemical analysis and toxicity profile of leaf and flower extracts of Nerium oleander L. species collected from Giresun province (Turkey) were investigated. In phytochemical analyzes, the cardiac glycoside, alkaloid, saponin and tannin contents of the extracts were analyzed qualitatively and quantitatively. The physiological effects of extracts were determined by examining root elongation, weight gain and germination rates. Biochemical effects were determined by measuring the levels of malondialdehyde (MDA), glutathione (GSH), superoxide dismutase (SOD) and catalase (CAT), which are indicators of oxidative stress. Cytotoxic and genotoxic effects were investigated by mitotic index (MI), micronucleus (MN) and chromosomal abnormality (CA) tests. N. oleander leaf and flower extract applications caused significant decreases in the physiological parameters of Allium bulbs. SOD and CAT activity in root tip cells increased significantly after the application of leaf extract compared to the control group. Similar changes were observed in the application of flower extract, but these increases were found to be at a lower level compared to the increases induced by the leaf extract. An increase in MDA levels and a decrease in GSH levels were observed in groups treated with leaf and flower extracts. These changes show that the extracts cause deterioration in antioxidant/oxidant balance. It was determined that the extracts, which caused a decrease in MI rates and an increase in MN and CAs frequencies, showed the most prominent cytotoxic and genotoxic effects at 250 μg/mL doses. These toxic effects were associated with the phytochemical content of the extracts, and it was thought that cardiac glycosides and alkaloids, whose presence were detected in qualitative and quantitative analyzes, may play an important role in toxicity. Studies investigating the therapeutic properties of plants as well as their toxic effects are insufficient, which leads to the fact that plants exhibiting potential toxicity are not well known. Therefore, this study will lead many studies on the toxicity profile of the phytochemical contents of plants. Therefore, this study will draw attention to the investigation of the toxicity profile and phytochemical contents of plants and will lead to similar studies.

S. M, Rakesh G, B. S, Joseph J, H. P. M, P. S. P. Deciphering the role of polyphenol in defence mechanism against tea mosquito bug (Helopeltis theivora Waterhouse.) in cocoa (Theobroma cocoa L.)

Tea mosquito bug (TMB) is a serious pest of cocoa whose prevalence is high, mostly during summer and post monsoon season. Three species of tea mosquito bug have been reported on cocoa: Helopeltis antonii Signoret, H. theivora Waterhouse, and H. bradyi Waterhouse. H. theivora is the most prevalent one causing damage to young shoots, cherelles and pods. Rearing of tea mosquito bug on cocoa was found to be a failure in the present study hence Helopeltis theivora Waterhouse was maintained on the alternate host mile-a-minute (Mikania micrantha Kunth) under laboratory condition in insect rearing cages. Using freshly reared tea mosquito bugs twenty cocoa hybrids were screened for resistance and were ranked after 72 hours of screening. All the hybrids having less than three lesions per plant in seedlings and less than 33 lesions on pods were ranked as highly resistant. It was observed that hybrids classified as highly resistant had significantly higher phenol content than those classified as susceptible. The significantly low phenol content in the susceptible hybrids suggests that phenolics have a function in mediating resistance to tea mosquito bug in cocoa. From correlation and regression analysis it is confirmed that phenol content can be used as a potential marker indicating the level of resistance of cocoa hybrids against tea mosquito bug resistance.

Identification and Characterization of Cinnamyl Alcohol Dehydrogenase Encoding Genes Involved in Lignin Biosynthesis and Resistance to Verticillium dahliae in Upland Cotton (Gossypium hirsutum L.)

Verticillium wilt, caused by the soil-borne fungus Verticillium dahliae, is one of the most devastating diseases in cotton (Gossypium spp.). Lignin in the cell wall forms a physical barrier to inhibit pathogen invasion, and defense-induced lignification reinforces secondary cell wall to prevent pathogens from further spreading. Cinnamyl alcohol dehydrogenases (CADs) catalyze the production of three main monolignols, p-coumaryl- (H), coniferyl- (G), and sinapyl-alcohols (S), which are the fundamental blocks of lignin. Here, we identified CAD genes in G. hirsutum, analyzed their expression profiles in cotton leaf, stem, and root from different developmental stages, and selected GhCAD35, GhCAD45, and GhCAD43, which were consistently induced by V. dahliae inoculation in G. hirsutum cultivars resistant or susceptible to V. dahliae. On the basis of confirmation of the in vitro enzymatic activity of the three proteins in generation of the three monolignols, we used virus-induced gene silencing (VIGS) to investigate the effects of silencing of GhCAD35, GhCAD45, or GhCAD43 on resistance to V. dahliae as well as on deposition and the composition of lignin. Silencing each of the three CADs impaired the defense-induced lignification and salicylic acid biosynthesis in stem, and compromised resistance to V. dahliae. Moreover, our study showed that silencing the three GhCADs severely affected the biosynthesis of S-lignin, leading to a decrease of the syringyl/guaiacyl (S/G) ratio. Heterogeneous overexpression of GhCAD35, GhCAD45, or GhCAD43 in Arabidopsis enhanced disease resistance. Taken together, our study demonstrates a role of the three GhCADs in defense-induced lignin biosynthesis and resistance to V. dahliae in G. hirsutum.

Responses to larval herbivory in the phenylpropanoid pathway of Ulmus minor are boosted by prior insect egg deposition

Elms, which have received insect eggs as a 'warning' of larval herbivory, enhance their anti-herbivore defences by accumulating salicylic acid and amplifying phenylpropanoid-related transcriptional and metabolic responses to hatching larvae. Plant responses to insect eggs can result in intensified defences against hatching larvae. In annual plants, this egg-mediated effect is known to be associated with changes in leaf phenylpropanoid levels. However, little is known about how trees-long-living, perennial plants-improve their egg-mediated, anti-herbivore defences. The role of phytohormones and the phenylpropanoid pathway in egg-primed anti-herbivore defences of a tree species has until now been left unexplored. Using targeted and untargeted metabolome analyses we studied how the phenylpropanoid pathway of Ulmus minor responds to egg-laying by the elm leaf beetle and subsequent larval feeding. We found that when compared to untreated leaves, kaempferol and quercetin concentrations increased in feeding-damaged leaves with prior egg deposition, but not in feeding-damaged leaves without eggs. PCR analyses revealed that prior insect egg deposition intensified feeding-induced expression of phenylalanine ammonia lyase (PAL), encoding the gateway enzyme of the phenylpropanoid pathway. Salicylic acid (SA) concentrations were higher in egg-treated, feeding-damaged leaves than in egg-free, feeding-damaged leaves, but SA levels did not increase in response to egg deposition alone-in contrast to observations made of Arabidopsis thaliana. Our results indicate that prior egg deposition induces a SA-mediated response in elms to feeding damage. Furthermore, egg deposition boosts phenylpropanoid biosynthesis in subsequently feeding-damaged leaves by enhanced PAL expression, which results in the accumulation of phenylpropanoid derivatives. As such, the elm tree shows similar, yet distinct, responses to insect eggs and larval feeding as the annual model plant A. thaliana.

Insects-plants-pathogens: Toxicity, dependence and defense dynamics

In a natural ecosystem, the pathogen-plant-insect relationship has diverse implications for each other. The pathogens as well as insect-pests consume plant tissues as their feed that mostly results in damage. In turn, plant species have evolved specialized defense system to not only protect themselves but reduce the damage also. Such tripartite interactions involve toxicity, metabolic modulations, resistance etc. among all participants of interaction. These attributes result in selection pressure among participants. Coevolution of such traits reveals need to focus and unravel multiple hidden aspects of insect-plant-pathogen interactions. The definite modulations during plant responses to biotic stress and the operating defense network against herbivores are vital to research areas. Different types of plant pathogens and herbivores are tackled with various changes in plants, e.g. changes in genes expression, glucosinolate metabolism detoxification, signal transduction, cell wall modifications, Ca²⁺dependent signaling. It is essential to clarify which chemical in plants can work as a defense signal or weapon in plant-pathogen-herbivore interactions. In spite of increased knowledge regarding signal transduction pathways regulating growth-defense balance, much more is needed to unveil the coordination of growth rate with metabolic modulations in bi-trophic interactions. Here, we addressed plant-pathogen-insect interaction for toxicity as well as dependnce along with plant defense dynamics against pathogens and insects with broad range effects at the physio-biochemical and molecular level. We have reviewed interfaces in plant-pathogen-insect research to show pulsating regulation of plant immunity for attuning survival and ecological equilibrium. An improved understanding of the systematic foundation of growth-defense stability has vital repercussions for enhancing crop yield, including insights into uncoupling of host-parasite tradeoffs for ecological and environmental sustainability.

Drought-induced ABA, H2O2 and JA positively regulate CmCAD genes and lignin synthesis in melon stems

BACKGROUND

Cinnamyl alcohol dehydrogenase (CAD) is an important enzyme functions at the last step in lignin monomer synthesis pathway. Our previous work found that drought induced the expressions of CmCAD genes and promoted lignin biosynthesis in melon stems.

RESULTS

Here we studied the effects of abscisic acid (ABA), hydrogen peroxide (H2O2) and jasmonic acid (JA) to CmCADs under drought stress. Results discovered that drought-induced ABA, H2O2 and MeJA were prevented efficiently from increasing in melon stems pretreated with fluridone (Flu, ABA inhibitor), imidazole (Imi, H2O2 scavenger) and ibuprofen (Ibu, JA inhibitor). ABA and H2O2 are involved in the positive regulations to CmCAD1, 2, 3, and 5, and JA is involved in the positive regulations to CmCAD2, 3, and 5. According to the expression profiles of lignin biosynthesis genes, ABA, H2O2 and MeJA all showed positive regulations to CmPAL2-like, CmPOD1-like, CmPOD2-like and CmLAC4-like. In addition, positive regulations were also observed with ABA to CmPAL1-like, CmC4H and CmCOMT, with H2O2 to CmPAL1-like, CmC4H, CmCCR and CmLAC17-like, and with JA to CmCCR, CmCOMT, CmLAC11-like and CmLAC17-like. As expected, the signal molecules positively regulated CAD activity and lignin biosynthesis under drought stress. Promoter::GUS assays not only further confirmed the regulations of the signal molecules to CmCAD1~3, but also revealed the important role of CmCAD3 in lignin synthesis due to the strongest staining of CmCAD3 promoter::GUS.

CONCLUSIONS

CmCADs but CmCAD4 are positively regulated by ABA, H2O2 and JA under drought stress and participate in lignin synthesis.

SWATH-MS-based quantitative proteomics reveals a uniquely intricate defense response in Cnaphalocrocis medinalis-resistant rice

Cnaphalocrocis medinalis is a major insect pest of rice in Asia. A few defensive enzymes were reported to show higher activities in a resistant rice line (Qingliu) than in a susceptible rice line (TN1) upon leaffolder infestation. However, the overall molecular regulation of the rice defense response against leaffolder herbivory is unknown. Here, differential proteomic analysis by SWATH-MS was performed to identify differentially expressed proteins between the two rice varieties, Qingliu and TN1, at four time points of leaffolder herbivory, 0, 6, 24, and 72 h. Gene Ontology (GO) enrichment of the differentially expressed proteins indicated overrepresentation of (1) photosynthesis, (2) amino acid and derivative metabolic process, and (3) secondary metabolic process. Phenylalanine ammonia lyase and chalcone synthase, which catalyze flavonoid biosynthesis, and lipoxygenase, which catalyzes jasmonic acid biosynthesis, exhibited higher expression in Qingliu than in TN1 even before insect herbivory. Momentary activation of the light reaction and Calvin cycle was detected in Qingliu at 6 h and 24 h of insect herbivory, respectively. At 72 h of insect herbivory, amino acid biosynthesis and glutathione-mediated antioxidation were activated in Qingliu. A defense response involving jasmonic acid signaling, carbon remobilization, and the production of flavonoids and glutathione could underlie the resistance of Qingliu to leaffolder.

Lignin synthesized by CmCAD2 and CmCAD3 in oriental melon (Cucumis melo L.) seedlings contributes to drought tolerance

CmCAD2 and CmCAD3 function more positively than CmCAD1 in oriental melon for lignin synthesis which is important to ensure internal water status and thus for drought tolerance. Well-lignification may be the guarantee of efficient axial water transport and barrier of lateral water flow in oriental melon tolerating drought stress, however remains to be verified. As an important enzyme in monolignol synthesis pathway, five cinnamyl alcohol dehydrogenase (CAD) genes were generally induced in melon seedlings by drought. Here we further revealed the roles of CmCAD1, 2, and 3 in lignin synthesis and for drought tolerance. Results found that overexpressing CmCAD2 or 3 strongly recovered CAD activities, lignin synthesis and composition in Arabidopsis cadc cadd, whose lignin synthesis is disrupted, while CmCAD1 functioned modestly. In melon seedlings, silenced CmCAD2 and 3 individually or collectively decreased CAD activities and lignin depositions drastically, resulting in dwarfed phenotypes. Reduced lignin, mainly composed by guaiacyl units catalyzed by CmCAD3, is mainly due to the limited lignification in tracheary elements and development of Casparion strip. While CmCAD1 and 2 exhibited catalysis to p-coumaraldehyde and sinapaldehyde, respectively. Compared with CmCAD1, drought treatments revealed higher sensitivity of CmCAD2 and/or 3 silenced melon seedlings, accompanying with lower relative water contents, water potentials and relatively higher total soluble sugar contents. Slightly up-regulated expressions of aquaporin genes together with limited lignification might imply higher lateral water loss in stems of silenced lines. In Arabidopsis, CmCAD2 and 3 transgenic lines enhanced cadc cadd drought tolerance through recovering lignin synthesis and root development, accompanying with decreased electrolyte leakage ratios and increased RWCs, thus improved survival rates. Briefly, lignin synthesized by CmCAD2 and 3 functions importantly for drought tolerance in melon.

Insight into the relationship between S-lignin and fiber quality based on multiple research methods

Cotton (Gossypium hirsutum) is an important cash crop, providing people with high quality natural fiber. Lignin is the main component of cotton fiber, second only to cellulose. As a main substance filled in the cellulose framework during the secondary wall thickening process, lignin plays a key role in the formation of cotton fiber quality. However, the mechanism behind it is still unclear. In this research, we screened candidate genes involved in lignin biosynthesis based on analysis of cotton genome and transcriptome sequence data. The authenticity of the transcriptome data was verified by qRT-PCR assay. Total 62 genes were identified from nine gene families. In the process, we found the key gene GhCAD7 that affects the biosynthesis of S-lignin and the ratio of syringyl/guaiacyl (S/G). In addition, in combination with the metabolites and transcriptome profiles of the line 0-153 with high fiber quality and the line sGK9708 with low fiber quality during cotton fiber development, we speculate that the ratio of syringyl/guaiacyl (S/G) is inseparable from the quality of cotton fiber. Finally, the S-type lignin synthesis branch may play a more important role in the formation of high-quality fiber. This work provides insights into the synthesis of lignin in cotton and lays the foundation for future research into improving fiber quality.

Neonicotinoid Insecticides Alter the Transcriptome of Soybean and Decrease Plant Resistance

Neonicotinoids are widely used systemic insecticides that have been associated with spider mite outbreaks on diverse plants. These insecticides have complex effects on plant physiology, which have been speculated to drive enhanced performance of spider mites. We used RNA-Seq to explore how neonicotinoids modify gene expression in soybean thereby lowering plant resistance. We exposed soybean (Glycine max L.) to two neonicotinoid insecticides, thiamethoxam applied to seeds and imidacloprid applied as a soil drench, and we exposed a subset of these plants to spider mites (Tetranychus cinnabarinus). Applications of both insecticides downregulated genes involved in plant-pathogen interactions, phytohormone pathways, phenylpropanoid pathway, and cell wall biosynthesis. These effects were especially pronounced in plants exposed to thiamethoxam. Introduction of spider mites restored induction of genes in these pathways in plants treated with imidacloprid, while expression of genes involved in phenylpropanoid synthesis, in particular, remained downregulated in thiamethoxam-treated plants. Our outcomes indicate that both insecticides suppress genes in pathways relevant to plant⁻arthropod interactions, and suppression of genes involved in cell wall synthesis may explain lower plant resistance to spider mites, cell-content feeders. These effects appear to be particularly significant when plants are exposed to neonicotinoids applied to soybean seeds.

Defense responses of Thuja orientalis to infestation of anholocyclic species aphid Cinara tujafilina

The aim of this study was to determine an interdependence between generation of semiquinone radicals, superoxide anion (O₂-), manganese ions (Mn²⁺) and phenolic content in leaves of Thuja orientalis in response to infestation by varying populations of Cinara tujafilina, i.e. 40 or 80 aphids per plant. Also, superoxide dismutase (SOD) and β-d-glucosidase activities in leaves of T. orientalis in a defense response to C. tujafilina was recorded. Analyses of electron paramagnetic resonance (EPR) showed generally a higher concentration of semiquinone radicals with g-values of 2.0051 ± 0.0005 and 20032 ± 0.0005 after C. tujafilina infestation in leaves in comparison to the control. Up to 48 h post-infestation in leaves infested by 80 aphids the level of semiquinone radicals was significantly higher than in the control, while in leaves infested by 40 aphids the highest concentrations of these radicals were recorded at later time points (i.e. at 72 and 96 hpi). In parallel, the highest total generation of O₂- and low activity of SOD were recorded in 24-h leaves infested by 80 aphids. Additionally, analysis of confocal images showed that the strongest yellow fluorescence indicating O₂- generation was detected in epidermal cells of leaves up to 48 hpi. Significant reduction of Mn²⁺ ions detected by EPR spectroscopy in relation to the control was observed in 4-w leaves infested by 80 and 40 aphids and in 48-h leaves infested by 40 aphids. Phenolic contents in leaves infested by 80 and 40 aphids at all time points were higher than in the control. The greatest β-d-glucosidase activity and phenolic contents were recorded at 96 h of feeding. These results indicate that the perception of C. tujafilina infestation by T. orientalis leaves induces a specified sequence of defense mechanisms in the course of time.

Host plant accessions determine bottom-up effect of snapmelon (Cucumis melo var. momordica) against melon fly (Bactrocera cucurbitae (Coquillett))

The melon fly, Bactrocera cucurbitae (Tephritidae: Diptera) is an important pest of snapmelon (Cucumis melo var. momordica), leading to significant losses in yield in the hot arid agro-climate of India. The accessions IC- 430190 (11.21%), DKS-AHS 2011/4 (14.97%) and DKS-AHS 2011/3 (18.57%) were found to be novel resistant accessions against melon fly, B. cucurbitae infestation. Free amino acid and total soluble solid (TSS) were in positive correlation with percent fruit infestation whereas phenols, tannin, total alkaloids and flavonoid contents had significant negative correlation with percent fruit infestation. The percent fruit infestation had significant positive correlation with fruit length, fruit diameter and flesh thickness and negative correlation with length of ovary pubescence, rind hardness at immature stage, rind hardness at mature stage and pericarp thickness. Based on Kaiser Normalization method, two principal components (PCs) were extracted explaining cumulative variation of 82.80% in melon fly infestation. PC1 explained 53.41% of the variation while PC2 explained 29.39% of variation. The flavonoid, total alkaloid, tannins, phenols content, length of ovary pubescence and rind hardness were the novel antibiosis and antixenotic characters found in snapmelon resistant melon fly, B. cucurbitae and therefore, could be used as marker traits in plant breeding programs to select resistant accessions.

Induction of Systemic Resistance against Insect Herbivores in Plants by Beneficial Soil Microbes

Soil microorganisms with growth-promoting activities in plants, including rhizobacteria and rhizofungi, can improve plant health in a variety of different ways. These beneficial microbes may confer broad-spectrum resistance to insect herbivores. Here, we provide evidence that beneficial microbes modulate plant defenses against insect herbivores. Beneficial soil microorganisms can regulate hormone signaling including the jasmonic acid, ethylene and salicylic acid pathways, thereby leading to gene expression, biosynthesis of secondary metabolites, plant defensive proteins and different enzymes and volatile compounds, that may induce defenses against leaf-chewing as well as phloem-feeding insects. In this review, we discuss how beneficial microbes trigger induced systemic resistance against insects by promoting plant growth and highlight changes in plant molecular mechanisms and biochemical profiles.

Regioselective Baeyer–Villiger oxidation of lignin model compounds with tin beta zeolite catalyst and hydrogen peroxide

One approach to lignin deconstruction involves oxidation of benzylic alcohol groups, followed by Baeyer–Villiger oxidation (BVO) and ester hydrolysis. In this study β-O-4 and β-1 lignin models were oxidized using a heterogeneous BVO system.

A novel zinc-binding alcohol dehydrogenase 2 from Arachis diogoi, expressed in resistance responses against late leaf spot pathogen, induces cell death when transexpressed in tobacco

A novel zinc-binding alcohol dehydrogenase 2 (AdZADH2) was significantly upregulated in a wild peanut, Arachis diogoi treated with conidia of late leaf spot (LLS) pathogen, Phaeoisariopsis personata. This upregulation was not observed in a comparative analysis of cultivated peanut, which is highly susceptible to LLS. This zinc-binding alcohol dehydrogenase possessed a Rossmann fold containing NADB domain in addition to the MDR domain present in all previously characterized plant ADH genes/proteins. Transient over-expression of AdZADH2 under an estradiol inducible promoter (XVE) resulted in hypersensitive response (HR)-like cell death in tobacco leaf. However, the same level of cell death was not observed when the domains were transiently expressed individually. Cell death observed in tobacco was associated with overexpression of cell death related proteins, antioxidative enzymes such as SOD, CAT and APX and pathogenesis-related (PR) proteins. In A. diogoi, AdZADH2 expression was significantly upregulated in response to the plant signaling hormones salicylic acid, methyl jasmonate, and sodium nitroprusside.

Lignin and lignans in plant defence: insight from expression profiling of cinnamyl alcohol dehydrogenase genes during development and following fungal infection in Populus

Cinnamyl alcohol dehydrogenase (CAD) catalyses the final step in the biosynthesis of monolignol, the main component of lignin. Lignins, deposited in the secondary cell wall, play a role in plant defence against pathogens. We re-analysed the phylogeny of CAD/CAD-like genes using sequences from recently sequenced genomes, and analysed the temporal and spatial expression profiles of CAD/CAD-like genes in Populus trichocarpa healthy and infected plants. Three fungal pathogens (Rhizoctonia solani, Fusarium oxysporum, and Cytospora sp.), varying in lifestyle and pathogenicity, were used for plant infection. Phylogenetic analyses showed that CAD/CAD-like genes were distributed in classes represented by all members from angiosperm lineages including basal angiosperms and Selaginella. The analysed genes showed different expression profiles during development and demonstrated that three genes were involved in primary xylem maturation while five may function in secondary xylem formation. Expression analysis following inoculation with fungal pathogens, showed that five genes were induced in either stem or leaves. These results add further evidence that CAD/CAD-like genes have evolved specialised functions in plant development and defence against various pest and pathogens. Two genes (PoptrCAD11 and PoptrCAD15), which were induced under various stresses, could be treated as universal markers of plant defence using lignification or lignan biosynthesis.

Molecular cloning and functional analysis of nine cinnamyl alcohol dehydrogenase family members in Populus tomentosa

Nine CAD/CAD-like genes in P. tomentosa were classified into four classes based on expression patterns, phylogenetic analysis and biochemical properties with modification for the previous claim of SAD. Cinnamyl alcohol dehydrogenase (CAD) functions in monolignol biosynthesis and plays a critical role in wood development and defense. In this study, we isolated and cloned nine CAD/CAD-like genes in the Populus tomentosa genome. We investigated differential expression using microarray chips and found that PtoCAD1 was highly expressed in bud, root and vascular tissues (xylem and phloem) with the greatest expression in the root. Differential expression in tissues was demonstrated for PtoCAD3, PtoCAD6 and PtoCAD9. Biochemical analysis of purified PtoCADs in vitro indicated PtoCAD1, PtoCAD2 and PtoCAD8 had detectable activity against both coniferaldehyde and sinapaldehyde. PtoCAD1 used both substrates with high efficiency. PtoCAD2 showed no specific requirement for sinapaldehyde in spite of its high identity with so-called PtrSAD (sinapyl alcohol dehydrogenase). In addition, the enzymatic activity of PtoCAD1 and PtoCAD2 was affected by temperature. We classified these nine CAD/CAD-like genes into four classes: class I included PtoCAD1, which was a bone fide CAD with the highest activity; class II included PtoCAD2, -5, -7, -8, which might function in monolignol biosynthesis and defense; class III genes included PtoCAD3, -6, -9, which have a distinct expression pattern; class IV included PtoCAD12, which has a distinct structure. These data suggest divergence of the PtoCADs and its homologs, related to their functions. We propose genes in class II are a subset of CAD genes that evolved before angiosperms appeared. These results suggest CAD/CAD-like genes in classes I and II play a role in monolignol biosynthesis and contribute to our knowledge of lignin biosynthesis in P. tomentosa.

Ectopic lignification in the flax lignified bast fiber1 mutant stem is associated with tissue-specific modifications in gene expression and cell wall composition

Histochemical screening of a flax ethyl methanesulfonate population led to the identification of 93 independent M2 mutant families showing ectopic lignification in the secondary cell wall of stem bast fibers. We named this core collection the Linum usitatissimum (flax) lbf mutants for lignified bast fibers and believe that this population represents a novel biological resource for investigating how bast fiber plants regulate lignin biosynthesis. As a proof of concept, we characterized the lbf1 mutant and showed that the lignin content increased by 350% in outer stem tissues containing bast fibers but was unchanged in inner stem tissues containing xylem. Chemical and NMR analyses indicated that bast fiber ectopic lignin was highly condensed and rich in G-units. Liquid chromatography-mass spectrometry profiling showed large modifications in the oligolignol pool of lbf1 inner- and outer-stem tissues that could be related to ectopic lignification. Immunological and chemical analyses revealed that lbf1 mutants also showed changes to other cell wall polymers. Whole-genome transcriptomics suggested that ectopic lignification of flax bast fibers could be caused by increased transcript accumulation of (1) the cinnamoyl-CoA reductase, cinnamyl alcohol dehydrogenase, and caffeic acid O-methyltransferase monolignol biosynthesis genes, (2) several lignin-associated peroxidase genes, and (3) genes coding for respiratory burst oxidase homolog NADPH-oxidases necessary to increase H2O2 supply.

Identification and validation of quantitative real-time reverse transcription PCR reference genes for gene expression analysis in teak (Tectona grandis L.f.)

Background

Teak (Tectona grandis L.f.) is currently the preferred choice of the timber trade for fabrication of woody products due to its extraordinary qualities and is widely grown around the world. Gene expression studies are essential to explore wood formation of vascular plants, and quantitative real-time reverse transcription PCR (qRT-PCR) is a sensitive technique employed for quantifying gene expression levels. One or more appropriate reference genes are crucial to accurately compare mRNA transcripts through different tissues/organs and experimental conditions. Despite being the focus of some genetic studies, a lack of molecular information has hindered genetic exploration of teak. To date, qRT-PCR reference genes have not been identified and validated for teak.

Results

Identification and cloning of nine commonly used qRT-PCR reference genes from teak, including ribosomal protein 60s (rp60s), clathrin adaptor complexes medium subunit family (Cac), actin (Act), histone 3 (His3), sand family (Sand), β-Tubulin (Β-Tub), ubiquitin (Ubq), elongation factor 1-α (Ef-1α), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Expression profiles of these genes were evaluated by qRT-PCR in six tissue and organ samples (leaf, flower, seedling, root, stem and branch secondary xylem) of teak. Appropriate gene cloning and sequencing, primer specificity and amplification efficiency was verified for each gene. Their stability as reference genes was validated by NormFinder, BestKeeper, geNorm and Delta Ct programs. Results obtained from all programs showed that TgUbq and TgEf-1α are the most stable genes to use as qRT-PCR reference genes and TgAct is the most unstable gene in teak. The relative expression of the teak cinnamyl alcohol dehydrogenase (TgCAD) gene in lignified tissues at different ages was assessed by qRT-PCR, using TgUbq and TgEf-1α as internal controls. These analyses exposed a consistent expression pattern with both reference genes.

Conclusion

This study proposes a first broad collection of teak tissue and organ mRNA expression data for nine selected candidate qRT-PCR reference genes. NormFinder, Bestkeeper, geNorm and Delta Ct analyses suggested that TgUbq and TgEf-1α have the highest expression stability and provided similar results when evaluating TgCAD gene expression, while the commonly used Act should be avoided.

The cinnamyl alcohol dehydrogenase gene family in melon (Cucumis melo L.): bioinformatic analysis and expression patterns

Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis. However, little was known about CADs in melon. Five CAD-like genes were identified in the genome of melons, namely CmCAD1 to CmCAD5. The signal peptides analysis and CAD proteins prediction showed no typical signal peptides were found in all CmCADs and CmCAD proteins may locate in the cytoplasm. Multiple alignments implied that some motifs may be responsible for the high specificity of these CAD proteins, and may be one of the key residues in the catalytic mechanism. The phylogenetic tree revealed seven groups of CAD and melon CAD genes fell into four main groups. CmCAD1 and CmCAD2 belonged to the bona fide CAD group, in which these CAD genes, as representative from angiosperms, were involved in lignin synthesis. Other CmCADs were distributed in group II, V and VII, respectively. Semi-quantitative PCR and real time qPCR revealed differential expression of CmCADs, and CmCAD5 was expressed in different vegetative tissues except mature leaves, with the highest expression in flower, while CmCAD2 and CmCAD5 were strongly expressed in flesh during development. Promoter analysis revealed several motifs of CAD genes involved in the gene expression modulated by various hormones. Treatment of abscisic acid (ABA) elevated the expression of CmCADs in flesh, whereas the transcript levels of CmCAD1 and CmCAD5 were induced by auxin (IAA); Ethylene induced the expression of CmCADs, while 1-MCP repressed the effect, apart from CmCAD4. Taken together, these data suggested that CmCAD4 may be a pseudogene and that all other CmCADs may be involved in the lignin biosynthesis induced by both abiotic and biotic stresses and in tissue-specific developmental lignification through a CAD genes family network, and CmCAD2 may be the main CAD enzymes for lignification of melon flesh and CmCAD5 may also function in flower development.

New insights into pioneer root xylem development: evidence obtained from Populus trichocarpa plants grown under field conditions

BACKGROUND AND AIMS

Effective programmed xylogenesis is critical to the structural framework of the plant root system and its central role in the acquisition and long-distance transport of water and nutrients. The process of xylem differentiation in pioneer roots under field conditions is poorly understood. In this study it is hypothesized that xylogenesis, an example of developmental programmed cell death (PCD), in the roots of woody plants demonstrates a clearly defined sequence of events resulting in cell death. A comprehensive analysis was therefore undertaken to identify the stages of xylogenesis in pioneer roots from procambial cells to fully functional vessels with lignified cell walls and secondary cell wall thickenings.

METHODS

Xylem differentiation was monitored in the pioneer roots of Populus trichocarpa at the cytological level using rhizotrons under field conditions. Detection and localization of the signalling molecule nitric oxide (NO) and hydrogen peroxide (H2O2) was undertaken and a detailed examination of nuclear changes during xylogenesis was conducted. In addition, analyses of the expression of genes involved in secondary cell wall synthesis were performed in situ.

KEY RESULTS

The primary event in initially differentiating tracheary elements (TEs) was a burst of NO in thin-walled cells, followed by H2O2 synthesis and the appearance of TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end labelling)-positive nuclei. The first changes in nuclear structure were observed in the early stages of xylogenesis of pioneer roots, prior to lignification; however, the nucleus was detectable under transmission electron microscopy in differentiating cells until the stage at which vacuole integrity was maintained, indicating that their degradation was slow and prolonged. The subsequent sequence of events involved secondary cell wall formation and autophagy. Potential gene markers from the cinnamyl alcohol dehydrogenase (CAD) gene family that were related to secondary wall synthesis were associated with primary xylogenesis, showing clear expression in cells that undergo differentiation into TEs and in the thin-walled cells adjacent to the xylem pole.

CONCLUSIONS

The early events of TE formation during pioneer root development are described, together with the timing of xylogenesis from signalling via NO, through secondary cell wall synthesis and autophagy events that are initiated long before lignification. This is the first work describing experiments conducted in planta on roots under field conditions demonstrating that the process of xylogenesis in vivo might be gradual and complex.

A high-resolution genetic map of yellow monkeyflower identifies chemical defense QTLs and recombination rate variation

Genotyping-by-sequencing methods have vastly improved the resolution and accuracy of genetic linkage maps by increasing both the number of marker loci as well as the number of individuals genotyped at these loci. Using restriction-associated DNA sequencing, we construct a dense linkage map for a panel of recombinant inbred lines derived from a cross between divergent ecotypes of Mimulus guttatus. We used this map to estimate recombination rate across the genome and to identify quantitative trait loci for the production of several secondary compounds (PPGs) of the phenylpropanoid pathway implicated in defense against herbivores. Levels of different PPGs are correlated across recombinant inbred lines suggesting joint regulation of the phenylpropanoid pathway. However, the three quantitative trait loci identified in this study each act on a distinct PPG. Finally, we map three putative genomic inversions differentiating the two parental populations, including a previously characterized inversion that contributes to life-history differences between the annual/perennial ecotypes.

Molecular cloning and biochemical characterization of two cinnamyl alcohol dehydrogenases from a liverwort Plagiochasma appendiculatum

Cinnamyl alcohol dehydrogenase (CAD) (EC 1.1.1.195) is a key enzyme in lignin biosynthesis. It catalyzes cinnamyl aldehydes as substrates to form corresponding alcohols, the last step in monolignol biosynthesis. Almost all CAD members of land plants could be divided into three classes according to the phylogenetic analysis, together with gene structure and function. In the present investigation, two cDNAs encoding CADs were obtained from a Chinese liverwort Plagiochasma appendiculatum thallus library and were designated as PaCAD1 and PaCAD2. Phylogenetic analysis showed that PaCAD1 and PaCAD2 belonged to Class II. Full length cDNAs were heterologously expressed in E. coli and the recombinant PaCAD proteins displayed high activity levels using p-coumaryl, caffeyl, coniferyl, 5-hydroxyconiferyl and sinapyl aldehydes as substrates to form corresponding alcohols. The enzyme kinetics results showed that PaCAD1 and PaCAD2 used coniferyl aldehyde as the favourite substrate and showed high catalytic efficiency towards p-coumaryl aldehyde but lowest catalytic efficiency towards 5-hydroxyconiferaldehyde. In accord with the higher lignin content in the thallus than in the callus, the expression level of PaCAD2 was also higher in thallus than in the callus. The expression of PaCAD1 and PaCAD2 was induced by Methyl jasmonic acid (MeJA) treatment. This suggested that these two PaCADs played twin roles in lignin biosynthesis and the defencedefence of abiotic stress in P. appendiculatum. This is the first time that the CADs in liverworts have been functionally characterized.

Molecular cloning, functional analysis of three cinnamyl alcohol dehydrogenase (CAD) genes in the leaves of tea plant, Camellia sinensis

Cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.195) is considered to be a key enzyme in lignin biosynthesis, but little was known about CADs in tea plants (Camellia sinensis). A full-length cDNA sequence (CsCAD2) was isolated by suppressive subtractive hybridization (SSH) in Ectropis oblique feeding-induced tea plants, and another two full-length cDNA sequences (CsCAD1 and CsCAD3) were obtained from a transcriptome obtained by deep sequencing. However, they showed only 20-54% identities. Phylogenetic analysis revealed that they belonged to three different families. DNA gel blotting analysis revealed that two copies of CsCAD1 and CsCAD2 genes existed in tea genome, but CsCAD3 likely had only one copy. Recombinant proteins of these CsCADs were produced in Escherichia coli. The activity of purified recombinant CsCAD2 protein was up to 0.43 μmol min(-1) mg(-1). However, the other two recombinant proteins had lower activities, probably due to incomplete refolding. qRT-PCR analysis indicated that while CsCAD3 was strongly up-regulated in tea plants after E. oblique attack and mechanical damage, CsCAD1 and CsCAD2 showed only moderate or no changes in transcript levels. Treatment of defence-related hormones methyl jasmonate (MeJA) and salicylic acid (SA) elevated the expression of CsCAD1 and CsCAD2, but decreased the transcript abundance of CsCAD3. The transcript levels of CsCAD2 did not change after applying abscisic acid (ABA), whereas CsCAD1 and CsCAD3 were induced. These results suggested that these three CsCAD genes in tea plants may play a role in defense against insects and pathogens and adaptation to abiotic stresses and these genes likely have divergant functions.

Expression patterns of a cinnamyl alcohol dehydrogenase gene involved in lignin biosynthesis and environmental stress in Ginkgo biloba

The cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis as it catalyzes the final step in the synthesis of monolignols. A cDNA sequence encoding the CAD gene was isolated from the leaves of Ginkgo biloba L, designated as GbCAD1. The full-length cDNA of GbCAD1 was 1,494 bp containing a 1,074 bp open reading frame encoding a polypeptide of 357 amino acids with a calculated molecular mass of 38.7 kDa and an isoelectric point of 5.74. Comparative and bioinformatic analyses revealed that GbCAD1 showed extensive homology with CADs from other gymnosperm species. Southern blot analysis indicated that GbCAD1 belonged to a multi-gene family. Phylogenetic tree analysis revealed that GbCAD1 shared the same ancestor in evolution with other CADs and had a further relationship with other gymnosperm species. GbCAD1 was an enzyme being pH-dependent and temperature-sensitive, and showing a selected catalyzing. Tissue expression pattern analysis showed that GbCAD1 was constitutively expressed in stems and roots, especially in the parts of the pest and disease infection, with the lower expression being found in two- to four-year-old stem. Further analysis showed the change in lignin content had some linear correlation with the expression level of GbCAD1 mRNA in different tissues. The increased expression of GbCAD1 was detected when the seedling were treated with exogenous abscisic acid, salicylic acid, ethephon, ultraviolet and wounding. These results indicate that the GbCAD1 gene may play a role in the resistance mechanism to biotic and abiotic stresses as well as in tissue-specific developmental lignification.

Phylogeny and structure of the cinnamyl alcohol dehydrogenase gene family in Brachypodium distachyon

Cinnamyl alcohol dehydrogenase (CAD) catalyses the final step of the monolignol biosynthesis, the conversion of cinnamyl aldehydes to alcohols, using NADPH as a cofactor. Seven members of the CAD gene family were identified in the genome of Brachypodium distachyon and five of these were isolated and cloned from genomic DNA. Semi-quantitative reverse-transcription PCR revealed differential expression of the cloned genes, with BdCAD5 being expressed in all tissues and highest in root and stem while BdCAD3 was only expressed in stem and spikes. A phylogenetic analysis of CAD-like proteins placed BdCAD5 on the same branch as bona fide CAD proteins from maize (ZmCAD2), rice (OsCAD2), sorghum (SbCAD2) and Arabidopsis (AtCAD4, 5). The predicted three-dimensional structures of both BdCAD3 and BdCAD5 resemble that of AtCAD5. However, the amino-acid residues in the substrate-binding domains of BdCAD3 and BdCAD5 are distributed symmetrically and BdCAD3 is similar to that of poplar sinapyl alcohol dehydrogenase (PotSAD). BdCAD3 and BdCAD5 expressed and purified from Escherichia coli both showed a temperature optimum of about 50 °C and molar weight of 49 kDa. The optimal pH for the reduction of coniferyl aldehyde were pH 5.2 and 6.2 and the pH for the oxidation of coniferyl alcohol were pH 8 and 9.5, for BdCAD3 and BdCAD5 respectively. Kinetic parameters for conversion of coniferyl aldehyde and coniferyl alcohol showed that BdCAD5 was clearly the most efficient enzyme of the two. These data suggest that BdCAD5 is the main CAD enzyme for lignin biosynthesis and that BdCAD3 has a different role in Brachypodium. All CAD enzymes are cytosolic except for BdCAD4, which has a putative chloroplast signal peptide adding to the diversity of CAD functions.

Mechanisms of plant defense against insect herbivores

Plants respond to herbivory through various morphological, biochemicals, and molecular mechanisms to counter/offset the effects of herbivore attack. The biochemical mechanisms of defense against the herbivores are wide-ranging, highly dynamic, and are mediated both by direct and indirect defenses. The defensive compounds are either produced constitutively or in response to plant damage, and affect feeding, growth, and survival of herbivores. In addition, plants also release volatile organic compounds that attract the natural enemies of the herbivores. These strategies either act independently or in conjunction with each other. However, our understanding of these defensive mechanisms is still limited. Induced resistance could be exploited as an important tool for the pest management to minimize the amounts of insecticides used for pest control. Host plant resistance to insects, particularly, induced resistance, can also be manipulated with the use of chemical elicitors of secondary metabolites, which confer resistance to insects. By understanding the mechanisms of induced resistance, we can predict the herbivores that are likely to be affected by induced responses. The elicitors of induced responses can be sprayed on crop plants to build up the natural defense system against damage caused by herbivores. The induced responses can also be engineered genetically, so that the defensive compounds are constitutively produced in plants against are challenged by the herbivory. Induced resistance can be exploited for developing crop cultivars, which readily produce the inducible response upon mild infestation, and can act as one of components of integrated pest management for sustainable crop production.

Environmental stresses of field growth allow cinnamyl alcohol dehydrogenase-deficient Nicotiana attenuata plants to compensate for their structural deficiencies

The organized lignocellulosic assemblies of cell walls provide the structural integrity required for the large statures of terrestrial plants. Silencing two CINNAMYL ALCOHOL DEHYDROGENASE (CAD) genes in Nicotiana attenuata produced plants (ir-CAD) with thin, red-pigmented stems, low CAD and sinapyl alcohol dehydrogenase activity, low lignin contents, and rubbery, structurally unstable stems when grown in the glasshouse (GH). However, when planted into their native desert habitat, ir-CAD plants produced robust stems that survived wind storms as well as the wild-type plants. Despite efficient silencing of NaCAD transcripts and enzymatic activity, field-grown ir-CAD plants had delayed and restricted spread of red stem pigmentation, a color change reflecting blocked lignification by CAD silencing, and attained wild-type-comparable total lignin contents. The rubbery GH phenotype was largely restored when field-grown ir-CAD plants were protected from wind, herbivore attack, and ultraviolet B exposure and grown in restricted rooting volumes; conversely, it was lost when ir-CAD plants were experimentally exposed to wind, ultraviolet B, and grown in large pots in growth chambers. Transcript and liquid chromatography-electrospray ionization-time-of-flight analysis revealed that these environmental stresses enhanced the accumulation of various phenylpropanoids in stems of field-grown plants; gas chromatography-mass spectrometry and nuclear magnetic resonance analysis revealed that the lignin of field-grown ir-CAD plants had GH-grown comparable levels of sinapaldehyde and syringaldehyde cross-linked into their lignins. Additionally, field-grown ir-CAD plants had short, thick stems with normal xylem element traits, which collectively enabled field-grown ir-CAD plants to compensate for the structural deficiencies associated with CAD silencing. Environmental stresses play an essential role in regulating lignin biosynthesis in lignin-deficient plants.

Chestnut resistance to the blight disease: insights from transcriptome analysis

BACKGROUND

A century ago, Chestnut Blight Disease (CBD) devastated the American chestnut. Backcross breeding has been underway to introgress resistance from Chinese chestnut into surviving American chestnut genotypes. Development of genomic resources for the family Fagaceae, has focused in this project on Castanea mollissima Blume (Chinese chestnut) and Castanea dentata (Marsh.) Borkh (American chestnut) to aid in the backcross breeding effort and in the eventual identification of blight resistance genes through genomic sequencing and map based cloning. A previous study reported partial characterization of the transcriptomes from these two species. Here, further analyses of a larger dataset and assemblies including both 454 and capillary sequences were performed and defense related genes with differential transcript abundance (GDTA) in canker versus healthy stem tissues were identified.

RESULTS

Over one and a half million cDNA reads were assembled into 34,800 transcript contigs from American chestnut and 48,335 transcript contigs from Chinese chestnut. Chestnut cDNA showed higher coding sequence similarity to genes in other woody plants than in herbaceous species. The number of genes tagged, the length of coding sequences, and the numbers of tagged members within gene families showed that the cDNA dataset provides a good resource for studying the American and Chinese chestnut transcriptomes. In silico analysis of transcript abundance identified hundreds of GDTA in canker versus healthy stem tissues. A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here. These DTA genes belong to various pathways involving cell wall biosynthesis, reactive oxygen species (ROS), salicylic acid (SA), ethylene, jasmonic acid (JA), abscissic acid (ABA), and hormone signalling. DTA genes were also identified in the hypersensitive response and programmed cell death (PCD) pathways. These DTA genes are candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica.

CONCLUSIONS

Our data allowed the identification of many genes and gene network candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica. The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection. Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.

Comparative and phylogenomic analyses of cinnamoyl-CoA reductase and cinnamoyl-CoA-reductase-like gene family in land plants

The biosynthesis of monolignols, the main components of lignin, involves many intermediates and enzymes. The cinnamoyl-CoA reductase (CCR) enzyme catalyzes the conversion of cinnamoyl-CoAs to cinnamaldehydes, i.e. the first specific step in lignin synthesis. The CCR and CCR-like gene family was studied partially in several plant species. This is a comprehensive study of the CCR and CCR-like gene family including genome organization, gene structure, phylogeny across land plant species, and, expression profiling in Populus. Analysis of amino acid motifs enabled the identification of sequence variations in the CCR catalytic site and annotates CCR and CCR-like genes. CCR and CCR-like genes were distributed in three major phylogenetic classes of which one includes the bona fide CCR genes. The other two classes include CCR and CCR-like, of which several genes present a high similarity to cinnamyl alcohol dehydrogenase, or dihydroflavonol reductase (DFR) genes. All CCR, CCR-like, and DFR classes were deeply rooted in the phylogeny of land plants suggesting that their evolution preceded the evolution of lycophytes. Over two thirds of CCR and CCR-like Populus genes were physically distributed on duplicated regions. This suggests that these duplication/retention processes contributed significantly to the size of the CCR and CCR-like gene family. The Populus CCR and CCR-like genes showed six expression patterns in the tissues studied with a preferential expression of PoptrCCR12 in xylem. The other genes present divergent expression profiles with some preferentially expressed in leaves, bark, or both. Several CCR and CCR-like genes were induced or repressed under various abiotic stresses suggesting that their duplication was followed by the evolution of divergent expression profiles and divergence of functions.

Correlating SNP genotype with the phenotypic response to exposure to cadmium in Populus spp

Species within the genus Populus include potential phytoextractors of heavy metal ions from contaminated soils, and genetic markers predictive of performance would be a useful tool for selection and breeding. Here, we have identified sequence variation within seven target and three nontarget genes among a set of 11 Populus spp. clones. Sequence variants were present in both the coding and noncoding regions; the former can potentially affect the functionality of the target genes. At the same time, the effect of exposure of the clones to cadmium ions on the morphology and the distribution of various metal ions was investigated by scanning electron microscopy microanalysis. A positive correlation was established between genetic variation, cadmium accumulation, and its bioconcentration in the root.

Comparative genomics and evolutionary analyses of the O-methyltransferase gene family in Populus

S-adenosyl-l-methionine (SAM) dependent O-methyltransferases (OMTs) proteins are involved in the methylation of various secondary metabolites. The OMT genes have been studied in various plants, but these studies focused either on a single or a small set of genes. Moreover, no comprehensive study was published yet on the OMT gene family in a tree species. To investigate the evolutionary history of this gene family and the functional diversification of its members, phylogenetic and several comparative genomics analyses were performed. Phylogeny across land plant lineages showed that OMT genes were distributed in two main classes deeply rooted in the phylogeny of land plants, suggesting that they have evolved by a gene duplication that had happen in the ancestor of land plants. COMT and COMT-like genes were clustering with few flavonoid and multifunctional OMT genes in class II. Class I included flavonoid, simple phenol, and multifunctional OMT genes. All 26 Populus OMT genes were located in segmental duplication blocks and two third of them were tandem duplicated, indicating the role of duplication processes in the expansion of this gene family. Expression profiling of OMT genes in Populus showed that only PoptrOMT25 was differentially expressed in xylem. The other genes were differentially expressed in leaves, bark, or both. Some OMT genes showed differential expression patterns under various biotic and abiotic stresses. The divergence of protein sequences, the phylogenetic distribution, and the expression of COMT and COMT-like genes suggest that they have evolved different functions or tissue specificities following duplications.