Validation of Reference Genes for Relative Quantitative Gene Expression Studies in Cassava (Manihot esculenta Crantz) by Using Quantitative Real-Time PCR

A high-affinity potassium transporter (MeHKT1) from cassava (Manihot esculenta) negatively regulates the response of transgenic Arabidopsis to salt stress

BACKGROUND

High-affinity potassium transporters (HKTs) are crucial in facilitating potassium uptake by plants. Many types of HKTs confer salt tolerance to plants through regulating K+ and Na+ homeostasis under salinity stress. However, their specific functions in cassava (Manihot esculenta) remain unclear.

RESULTS

Herein, an HKT gene (MeHKT1) was cloned from cassava, and its expression is triggered by exposure to salt stress. The expression of a plasma membrane-bound protein functions as transporter to rescue a low potassium (K+) sensitivity of yeast mutant strain, but the complementation of MeHKT1 is inhibited by NaCl treatment. Under low K+ stress, transgenic Arabidopsis with MeHKT1 exhibits improved growth due to increasing shoot K+ content. In contrast, transgenic Arabidopsis accumulates more Na+ under salt stress than wild-type (WT) plants. Nevertheless, the differences in K+ content between transgenic and WT plants are not significant. Additionally, Arabidopsis expressing MeHKT1 displayed a stronger salt-sensitive phenotype.

CONCLUSION

These results suggest that under low K+ condition, MeHKT1 functions as a potassium transporter. In contrast, MeHKT1 mainly transports Na+ into cells under salt stress condition and negatively regulates the response of transgenic Arabidopsis to salt stress. Our results provide a reference for further research on the function of MeHKT1, and provide a basis for further application of MeHKT1 in cassava by molecular biological means.

Positive Regulatory Roles of Manihot esculenta HAK5 under K+ Deficiency or High Salt Stress

HAK/KUP/KT family members have been identified as playing key roles in K+ uptake and salt tolerance in numerous higher plants. However, their functions in cassava (Manihot esculenta Cantz) remain unknown. In this study, a gene encoding for a high-affinity potassium transporter (MeHAK5) was isolated from cassava and its function was investigated. Subcellular localization analysis showed that MeHAK5 is a plasma membrane-localized transporter. RT-PCR and RT-qPCR indicated that MeHAK5 is predominantly expressed in cassava roots, where it is upregulated by low potassium or high salt; in particular, its highest expression levels separately increased by 2.2 and 2.9 times after 50 µM KCl and 150 mM NaCl treatments. When heterologously expressed in yeast, MeHAK5 mediated K+ uptake within the cells of the yeast strain CY162 and rescued the salt-sensitive phenotype of AXT3K yeast. MeHAK5 overexpression in transgenic Arabidopsis plants exhibited improved growth and increased shoot K+ content under low potassium conditions. Under salt stress, MeHAK5 transgenic Arabidopsis plants accumulated more K+ in the shoots and roots and had reduced Na+ content in the shoots. As a result, MeHAK5 transgenic Arabidopsis demonstrated a more salt-tolerant phenotype. These results suggest that MeHAK5 functions as a high-affinity K+ transporter under K+ starvation conditions, improving K+/Na+ homeostasis and thereby functioning as a positive regulator of salt stress tolerance in transgenic Arabidopsis. Therefore, MeHAK5 may be a suitable candidate gene for improving K+ utilization efficiency and salt tolerance.

Improving cassava bacterial blight resistance by editing the epigenome

Pathogens rely on expression of host susceptibility (S) genes to promote infection and disease. As DNA methylation is an epigenetic modification that affects gene expression, blocking access to S genes through targeted methylation could increase disease resistance. Xanthomonas phaseoli pv. manihotis, the causal agent of cassava bacterial blight (CBB), uses transcription activator-like20 (TAL20) to induce expression of the S gene MeSWEET10a. In this work, we direct methylation to the TAL20 effector binding element within the MeSWEET10a promoter using a synthetic zinc-finger DNA binding domain fused to a component of the RNA-directed DNA methylation pathway. We demonstrate that this methylation prevents TAL20 binding, blocks transcriptional activation of MeSWEET10a in vivo and that these plants display decreased CBB symptoms while maintaining normal growth and development. This work therefore presents an epigenome editing approach useful for crop improvement.

Genome-wide identification, expression profiling, and functional analysis of ammonium transporter 2 (AMT2) gene family in cassava (Manihot esculenta crantz)

Background: Nitrogen (N), absorbed primarily as ammonium (NH₄ ⁺) from soil by plant, is a necessary macronutrient in plant growth and development. Ammonium transporter (AMT) plays a vital role in the absorption and transport of ammonium (NH₄ ⁺). Cassava (Manihot esculenta Crantz) has a strong adaptability to nitrogen deprivation. However, little is known about the functions of ammonium transporter AMT2 in cassava. Methods: The cassava AMT2-type genes were identified and their characteristics were analyzed using bioinformatic techniques. The spatial expression patterns were analyzed based on the public RNA-seq data and their expression profiles under low ammonium treatment were studied using Real-time quantitative PCR (RT-qPCR) method. The cassava AMT2 genes were transformed into yeast mutant strain TM31019b by PEG/LiAc method to investigate their functions. Results: Seven AMT2-type genes (MeAMT2.1-2.7) were identified in cassava and they were distributed on 6 chromosomes and included two segmental duplication events (MeAMT2.2/MeAMT2.4 and MeAMT2.3/MeAMT2.5). Based on their amino acid sequences, seven MeAMT2 were further divided into four subgroups, and each subgroup contained similar motif constitution and protein structure. Synteny analysis showed that two and four MeAMT2 genes in cassava were collinear with those in the Arabidopsis and soybean genomes, respectively. Sixteen types of cis-elements were identified in the MeAMT2 promoters, and they were related to light-, hormone-, stress-, and plant growth and development-responsive elements, respectively. Most of the MeAMT2 genes displayed tissue-specific expression patterns according to the RNA-seq data, of them, three MeAMT2 (MeAMT2.3, MeAMT2.5, and MeATM2.6) expressions were up-regulated under ammonium deficiency. Complementation experiments showed that yeast mutant strain TM31019b transformed with MeAMT2.3, MeAMT2.5, or MeATM2.6 grew better than untransgenic yeast cells under ammonium deficiency, suggesting that MeAMT2.3, MeAMT2.5, and MeATM2.6 might be the main contributors in response to ammonium deficiency in cassava. Conclusion: This study provides a basis for further study of nitrogen efficient utilization in cassava.

MeGATAs, functional generalists in interactions between cassava growth and development, and abiotic stresses

The proteins with DNA-binding preference to the consensus DNA sequence (A/T) GATA (A/G) belong to a GATA transcription factor family, with a wide array of biological processes in plants. Cassava (Manihot esculenta) is an important food crop with high production of starch in storage roots. Little was however known about cassava GATA domain-containing genes (MeGATAs). Thirty-six MeGATAs, MeGATA1 to MeGATA36, were found in this study. Some MeGATAs showed a collinear relationship with orthologous genes of Arabidopsis, poplar and potato, rice, maize and sorghum. Eight MeGATA-encoded proteins (MeGATAs) analysed were all localized in the nucleus. Some MeGATAs had potentials of binding ligands and/or enzyme activity. One pair of tandem-duplicated MeGATA17-MeGATA18 and 30 pairs of whole genome-duplicated MeGATAs were found. Fourteen MeGATAs showed low or no expression in the tissues. Nine analysed MeGATAs showed expression responses to abiotic stresses and exogenous phytohormones. Three groups of MeGATA protein interactions were found. Fifty-three miRNAs which can target 18 MeGATAs were identified. Eight MeGATAs were found to target other 292 cassava genes, which were directed to radial pattern formation and phyllome development by gene ontology enrichment, and autophagy by Kyoto Encyclopaedia of Genes and Genomes enrichment. These data suggest that MeGATAs are functional generalists in interactions between cassava growth and development, abiotic stresses and starch metabolism.

Ethanol treatment enhances drought stress avoidance in cassava (Manihot esculenta Crantz)

External application of ethanol enhances tolerance to high salinity, drought, and heat stress in various plant species. However, the effects of ethanol application on increased drought tolerance in woody plants, such as the tropical crop "cassava," remain unknown. In the present study, we analyzed the morphological, physiological, and molecular responses of cassava plants subjected to ethanol pretreatment and subsequent drought stress treatment. Ethanol pretreatment induced a slight accumulation of abscisic acid (ABA) and stomatal closure, resulting in a reduced transpiration rate, higher water content in the leaves during drought stress treatment and the starch accumulation in leaves. Transcriptomic analysis revealed that ethanol pretreatment upregulated the expression of ABA signaling-related genes, such as PP2Cs and AITRs, and stress response and protein-folding-related genes, such as heat shock proteins (HSPs). In addition, the upregulation of drought-inducible genes during drought treatment was delayed in ethanol-pretreated plants compared with that in water-pretreated control plants. These results suggest that ethanol pretreatment induces stomatal closure through activation of the ABA signaling pathway, protein folding-related response by activating the HSP/chaperone network and the changes in sugar and starch metabolism, resulting in increased drought avoidance in plants.

Analysis of controlling genes for tiller growth of Psathyrostachys juncea based on transcriptome sequencing technology

BACKGROUND

Tillering is a complicated process in plant and is a significant trait that affects biomass and seed yield of bunch grass Psathyrostachys juncea, a typical perennial forage species. To clarify the regulatory mechanisms of tillering in P. juncea and to explore related candidate genes could be helpful to improve the seed and forage yield of perennial gramineous forages. We selected the tiller node tissues of P. juncea for transcriptome sequencing to determine the differentially expressed genes (DEG) between dense and sparse tillering genotypes. The metabolic pathway was studied, candidate genes were screened, and reference genes stability were evaluated.

RESULTS

The results showed that approximately 5466 DEGs were identified between the two genotypes with dense and sparse tillers of P. juncea, which significantly differed in tiller number. Tillering regulation pathways analysis suggested that DEGs closely related to the biosynthesis of three plant hormones, namely auxin (IAA), cytokinin (CTK), and strigolactones (SLs), while "biosynthesis of lignin" and "nitrogen metabolism" have remarkable differences between the dense and sparse tillering genotypes. Meanwhile, the reference gene Actin1, having the best stability, was screened from twelve genes with highest expression level and was used in verification of ten tillering related candidate genes.

CONCLUSIONS

The tillering mechanism of perennial grass P. juncea was expounded by transcriptome analysis of tiller node tissues. We demonstrated that dense-tillering genotypes may be distinguished by their low expression patterns of genes involved in SL, IAA, and high expression patterns of genes involved in CTK biosynthesis at the tillering stage, and nitrogen metabolism and lignin biosynthesis can also affect the number of tillers. Furthermore, the expression level of ten tillering related candidate genes were verified using Actin1 as reference gene. These candidate genes provide valuable breeding resources for marker assisted selection and yield traits improvement of P. juncea.

Genome-wide identification of nitrate transporter 2 (NRT2) gene family and functional analysis of MeNRT2.2 in cassava (Manihot esculenta Crantz)

Nitrate transporter 2 (NRT2) proteins play an important role in nitrate uptake and utilization in plants. The NRT2 family has been identified and functionally characterized in many plants. However, no systematic identification of NRT2 family members has been reported in cassava (Manihot esculenta Crantz). In this study, six MeNRT2 genes were identified from cassava genome and named as MeNRT2.1-2.6 according to their chromosomal locations. Phylogenetic tree showed that NRT2 proteins were divided into four main subgroups, which was further supported by their gene structure and conserved motifs. All six MeNRT2 genes are randomly distributed on 4 chromosomes (LG8, LG11, LG13, and LG17), two tandem duplicated genes (MeNRT2.3/MeNRT2.4) and a pair of segmental duplicated gene (MeNRT2.1/MeNRT2.2) was detected. Subsequently, expression profiles of MeNRT2 genes in eight different tissues and in response to nitrate deficient treatment were analyzed. The results showed that the MeNRT2 genes had differential expression patterns. All of MeNRT2 genes induced by nitrate deficiency, of them the MeNRT2.2 had the highest expression level after treatment. Arabidopis transformed with MeNRT2.2 gene showed higher fresh weight than wild type plants in response to N starvation, suggesting that MeNRT2.2 play important role in adapting to low nitrogen. Taken together, our results provide the reference for further analyses of the molecular functions of the MeNRT2 gene family, but also some candidate genes for developing nitrogen efficient crops.

Genome-wide identification and expression analysis of ammonium transporter 1 (AMT1) gene family in cassava (Manihot esculenta Crantz) and functional analysis of MeAMT1;1 in transgenic Arabidopsis

Nitrogen (N), a fundamental macronutrient for plant growth and development, is absorbed from the soil primarily in the form of ammonium (NH₄ ⁺) and uptaken through a plant's ammonium transporters (AMTs). While AMT proteins have been documented within diverse plant taxa, there has been no systematic analysis of their activity in cassava (Manihot esculenta Crantz), which is highly resistant to nitrogen deficiency. Here, we perform a comprehensive genome-wide analysis to identify and characterize the functional dynamics of cassava ammonium transporters 1 (MeAMT1). We identified a total of six AMT1 genes in the cassava genome (MeAMT1;1 to MeAMT1;6), the phylogenetic analysis of which fell into three distinct subgroups based on the conserved motifs and gene structures. Collinearity analysis showed that segmental duplication events played a key role in expansion of the MeAMT1 gene family. Synteny analysis indicated that two MeAMT1 genes were orthologous to Arabidopsis and rice. MeAMT1 promoters were additionally found to include various cis-acting elements related to light responsiveness, hormones, stress, and development processes. According to the RNA-seq data, the majority of MeAMT1 genes displayed specific patterns in the tested tissues. qRT-PCR revealed that all the tested MeAMT1 genes were up-regulated by low ammonium exposure. Furthermore, Arabidopis transformed with MeAMT1;1 gene grew well than wild-type plants in response to ammonium deficiency, suggesting that MeAMT1s play important role in response to low ammonium. Overall, our work lays the groundwork for new understanding of the AMT1 gene family in cassava and provides a basis for breeding efficient nitrogen use in other plants.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03070-6.

An Improved Reference Gene for Detection of "Candidatus Liberibacter asiaticus" Associated with Citrus Huanglongbing by qPCR and Digital Droplet PCR Assays

Citrus huanglongbing (HLB) disease associated with the 'Candidatus Liberibacter asiaticus' (CLas) bacterium has caused significant financial damage to many citrus industries. Large-scale pathogen surveys are routinely conducted in California to detect CLas early in the disease cycle by lab-based qPCR assays. We have developed an improved reference gene for the sensitive detection of CLas from plants in diagnostic duplex qPCR and analytical digital droplet PCR (ddPCR) assays. The mitochondrial cytochrome oxidase gene (COX), widely used as a reference, is not ideal because its high copy number can inhibit amplification of small quantities of target genes. In ddPCRs, oversaturation of droplets complicates data normalization and quantification. The variable copy numbers of COX gene in metabolically active young tissue, greenhouse plants, and citrus relatives suggest the need for a non-variable, nuclear, low copy, universal reference gene for analysis of HLB hosts. The single-copy nuclear gene, malate dehydrogenase (MDH), developed here as a reference gene, is amenable to data normalization, suitable for duplex qPCR and ddPCR assays. The sequence of MDH fragment selected is conserved in most HLB hosts in the taxonomic group Aurantioideae. This study emphasizes the need to develop standard guidelines for reference genes in DNA-based PCR assays.

Expression of potential reference genes in response to macronutrient stress in rice and soybean

Given the complexity of nutrient stress responses and the availability of a few validated reference genes, we aimed to identify robust and stable reference genes for macronutrient stress in rice and soybean. Ten potential reference genes were evaluated using geNorm, NormFinder, BestKeeper, Comparative ΔCt method, and RefFinder algorithms under low and completely starved conditions of nitrogen (N), phosphorus (P), potassium (K), and sulphur (S). Results revealed distinct sets of reference gene pairs, showing stable expression under different experimental conditions. The gene pairs TIP41/UBC(9/10/18) and F-box/UBC10 were most stable in rice and soybean, respectively under N stress. Under P stress, UBC9/UBC10 in rice and F-Box/UBC10 in soybean were most stable. Similarly, TIP41/UBC10 in rice and RING FINGER/UBC9 in soybean were the best gene pairs under K stress while F-Box/TIP41 in rice and UBC9/UBC10 in soybean were the most stable gene pairs under S stress. These reference gene pairs were validated by quantifying the expression levels of high-affinity transporters like NRT2.1/NRT2.5, PT1, AKT1, and SULTR1 for N, P, K, and S stress, respectively. This study reiterates the importance of choosing reference genes based on crop species and the experimental conditions, in order to obtain concrete answers to missing links of gene regulation in response to macronutrient deficiencies.

Cassava (Manihot esculenta) defensins: Prospection, structural analysis and tissue-specific expression under biotic/abiotic stresses

Defensins are a prominent family of antimicrobial peptides. They play sophisticated roles in the defense against pathogens in all living organisms, but few works address their expression under different conditions and plant tissues. The present work prospected defensins of Manihot esculenta Crantz, popularly known as cassava. Five defensin candidates (MeDefs) were retrieved from the genome sequences and characterized. Considering chromosome distribution, only MeDef1 and 2 occupy adjacent positions in the same chromosome arm. All 3D structures had antiparallel ß-sheets, an α-helix, and amphipathic residues distributed throughout the peptides with a predominance of cationic surface charge. MeDefs expression was validated by RT-qPCR, including two stress types (biotic: fungus Macrophomina pseudophaseolina, and abiotic: mechanical injury) and a combination of both stresses (fungus+injury) in three different tissues (root, stem, and leaf). For this purpose, ten reference genes (RGs) were tested, and three were chosen to characterize MeDef expression. MeDef3 was up-regulated at roots in all stress situations tested. MeDef1 and MeDef5 were induced in leaves under biotic and abiotic stresses, but not in both stress types simultaneously. Only MeDef2 was down-regulated in the stem tissue also with biotic/abiotic combined stresses. These results indicate that although defensins are known to be responsive to pathogen infection, they may act as preformed defense or, still, have tissue or stress specificities. Aspects of their structure, stability and evolution are also discussed.

Identification of New miRNA-mRNA Networks in the Development of Non-syndromic Cleft Lip With or Without Cleft Palate

Objective: To identify new microRNA (miRNA)-mRNA networks in non-syndromic cleft lip with or without cleft palate (NSCL/P).

Materials and Methods: Overlapping differentially expressed miRNAs (DEMs) were selected from cleft palate patients (GSE47939) and murine embryonic orofacial tissues (GSE20880). Next, the target genes of DEMs were predicted by Targetscan, miRDB, and FUNRICH, and further filtered through differentially expressed genes (DEGs) from NSCL/P patients and controls (GSE42589), MGI, MalaCards, and DECIPHER databases. The results were then confirmed by in vitro experiments. NSCL/P lip tissues were obtained to explore the expression of miRNAs and their target genes.

Results: Let-7c-5p and miR-193a-3p were identified as DEMs, and their overexpression inhibited cell proliferation and promoted cell apoptosis. PIGA and TGFB2 were confirmed as targets of let-7c-5p and miR-193a-3p, respectively, and were involved in craniofacial development in mice. Negative correlation between miRNA and mRNA expression was detected in the NSCL/P lip tissues. They were also associated with the occurrence of NSCL/P based on the MGI, MalaCards, and DECIPHER databases.

Conclusions: Let-7c-5p-PIGA and miR-193a-3p-TGFB2 networks may be involved in the development of NSCL/P.

Optimization of reference genes for qRT-PCR analysis of microRNA expression under abiotic stress conditions in sweetpotato

Sweetpotato (Ipomoea batatas. L) is an important food crop, harvested for its nutrient-rich tuberous roots. Drought and salt stresses are two major factors limiting the sweetpotato production. Since microRNAs (miRNAs) are well known to play crucial roles in regulation of plant stress responses, quantitative profiling of miRNA expression under stress conditions will facilitate identification and genetic manipulation of novel miRNAs to improve stress tolerance. Real-time quantitative reverse transcription PCR (qRT-PCR) is a commonly used tool for this purpose, but not without challenges. Although stem-loop and poly(A)-tail modified qRT-PCR methods were developed for characterizing miRNA expression, accurate profiling of miRNAs is still difficult in many plant species because of a lack of reliable reference genes for normalizing miRNA transcripts. To identify reference genes that are suitable for normalizing miRNA expression in sweetpotato, the expression stability of eight candidate miRNAs and two commonly used reference genes were tested in 96 samples involving four tissues and two cultivars under drought and salt stress treatments. Data analysis using the geNorm, NormFinder and Bestkeeper algorithms demonstrated that miRn60, miR482, and their combination were reliable references. We further validated the reference genes by expression analysis of the well-characterized miR319 and miR156 that regulate drought and salt stress responses, respectively. The reference genes identified in this study will facilitate future miRNA analysis under abiotic stress conditions in sweetpotato.

Decrypting tubby-like protein gene family of multiple functions in starch root crop cassava

Tubby-like proteins (TLPs) are ubiquitous in eukaryotes and function in abiotic stress tolerance of some plants. Cassava (Manihot esculenta Crantz) is a high-yield starch root crop and has a high tolerance to poor soil conditions and abiotic stress. However, little is known about TLP gene characteristics and their expression in cassava. We identified cassava TLP genes, MeTLPs, and further analysed structure, duplication, chromosome localization and collinearity, cis-acting elements in the promoter regions and expression patterns of MeTLPs, and three-dimensional structure of the encoded proteins MeTLPs. In conclusion, there is a MeTLP family containing 13 members, which are grouped into A and C subfamilies. There are 11 pairs of MeTLPs that show the duplication which took place between 10.11 and 126.69 million years ago. Two MeTLPs 6 and 9 likely originate from one gene in an ancestral species, may be common ancestors for other MeTLPs and would most likely not be eligible for ubiquitin-related protein degradation because their corresponding proteins (MeTLPs 6 and 9) have no the F-box domain in the N-terminus. MeTLPs feature differences in the number from TLPs in wheat, apple, Arabidopsis, poplar and maize, and are highlighted by segmental duplication but more importantly by the chromosomal collinearity with potato StTLPs. MeTLPs are at least related to abiotic stress tolerance in cassava. However, the subtle differences in function among MeTLPs are predictable partly because of their differential expression profiles, which are coupled with various cis‑acting elements existing in the promoter regions depending on genes.

Cassava AGPase genes and their encoded proteins are different from those of other plants

Cassava AGPase and AGPase genes have some unique characteristics. ADP-glucose pyrophosphorylase (AGPase) is a rate-limiting enzyme for starch synthesis. In this study, cassava AGPase genes (MeAGP) were analyzed based on six cultivars and one wild species. A total of seven MeAGPs was identified, including four encoding AGPase large subunits (MeAGPLs 1, 2, 3 and 4) and three encoding AGPase small subunits (MeAGPSs 1, 2 and 3). The copy number of MeAGPs varied in cassava germplasm materials. There were 14 introns for MeAGPLs 1, 2 and 3, 13 introns for MeAGPL4, and 8 introns for other three MeAGPSs. Multiple conservative amino acid sequence motifs were found in the MeAGPs. There were differences in amino acids at binding sites of substrates and regulators among different MeAGP subunits and between MeAGPs and a potato AGPase small subunit (1YP2:B). MeAGPs were all located in chloroplasts. MeAGP expression was not only associated with gene copy number and types/combinations, regions and levels of the DNA methylation but was also affected by environmental factors with the involvement of various transcription factors in multiple regulation networks and in various cis-elements in the gene promoter regions. The MeAGP activity also changed with environmental conditions and had potential differences among the subunits. Taken together, MeAGPs differ in number from those of Arabidopsis, potato, maize, banana, sweet potato, and tomato.

Transcriptomic and proteomic response of Manihot esculenta to Tetranychus urticae infestation at different densities

Tetranychus urticae (Acari: Tetranychidae) is an extremely serious cassava (Manihot esculenta) pest. Building a genomic resource to investigate the molecular mechanisms of cassava responses to T. urticae is vital for characterizing cassava resistance to mites. Based on the tolerance of cassava varieties to mite infestation (focusing on mite development rate, fecundity and physiology), cassava variety SC8 was selected to analyze transcriptomic and proteomic changes after 5 days of T. urticae feeding. Transcriptomic analysis revealed 698 and 2140 genes with significant expression changes under low and high mite infestation, respectively. More defense-related genes were found in the enrichment pathways at high mite density than at low density. In addition, iTRAQ-labeled proteomic analysis revealed 191 proteins with significant expression changes under low mite infestation. Differentially expressed genes and proteins were mainly found in the following defense-related pathways: flavonoid biosynthesis, phenylpropanoid biosynthesis, and glutathione metabolism under low-density mite feeding and plant hormone signal transduction and plant-pathogen interaction pathways under high-density mite feeding. The plant hormone signal transduction network, involving ethylene, jasmonic acid, and salicylic acid transduction pathways, was explored in relation to the M. esculenta response to T. urticae. Correlation analysis of the transcriptome and proteome generated a Pearson correlation coefficients of R = 0.2953 (P < 0.01), which might have been due to post-transcriptional or post-translational regulation resulting in many genes being inconsistently expressed at both the transcript and protein levels. In summary, the M. esculenta transcriptome and proteome changed in response to T. urticae, providing insight into the general activation of plant defense pathways in response to mite infestation.

Selection and validation of reference genes for target gene analysis with quantitative real-time PCR in the leaves and roots of Carex rigescens under abiotic stress

Carex rigescens is an ornamental turfgrass in northern China which has a relatively low maintenance cost and robust tolerance to many adverse environmental conditions, so it could be considered a new material for researching into plant stress resistance. However, suitable reference genes are vacant for obtaining reliable results in quantitative real-time PCR (qRT-PCR) analysis of C. rigescens in adversity research. In this study, we tested the expression stability of nine potential reference genes in leaves and roots under five different abiotic stress conditions, including cold, salt, heat, osmotic and cadmium (Cd). We then selected the best reference genes according to the analysis results calculated by three algorithmic programs (geNorm, NormFinder and BestKeeper) and used the RankAggreg package to merge the outputted data. The results showed that combinations of at least two reference genes should be used for reliable normalization except in heat-treated root samples, which require three reference genes. eIF-4α, GADPH, SAND and PEPKR1 and their combination were found to be the most stably expressed reference genes, while SAM, TUA-α and UPL7 were the three least stable reference genes among most of experimental samples. In addition, five stress-induced genes (Cu-Zn SOD, P5CS, LEA, GST, and APX) were chosen to verify the stability of the selected reference genes in various tissues and under various stress conditions. The results of this study will provide an important fundamental basis both for gene expression verification for transcriptomic and proteomic analyses and for gene expression analysis for future gene function research in C. rigescens.

Transcriptome Comparison Reveals Distinct Selection Patterns in Domesticated and Wild Agave Species, the Important CAM Plants

Agave species are an important family of crassulacean acid metabolism (CAM) plants with remarkable tolerance to heat and drought stresses (Agave deserti) in arid regions and multiple agricultural applications, such as spirit (Agave tequilana) and fiber (Agave sisalana) production. The agave genomes are commonly too large to sequence, which has significantly restricted our understanding to the molecular basis of stress tolerance and economic traits in agaves. In this study, we collected three transcriptome databases for comparison to reveal the phylogenic relationships and evolution patterns of the three agave species. The results indicated the close but distinctly domesticated relations between A. tequilana and A. sisalana. Natural abiotic and biotic selections are very important factors that have contributed to distinct economic traits in agave domestication together with artificial selection. Besides, a series of candidate unigenes regulating fructan, fiber, and stress response-related traits were identified in A. tequilana, A. sisalana, and A. deserti, respectively. This study represents the first transcriptome comparison within domesticated and wild agaves, which would serve as a guidance for further studies on agave evolution, environmental adaptation, and improvement of economically important traits.

MePHD1 as a PHD-Finger Protein Negatively Regulates ADP-Glucose Pyrophosphorylase Small Subunit1a Gene in Cassava

ADP-glucose pyrophosphorylase (AGPase) is an important enzyme in the starch synthesis pathway. Its enzyme activity can determine the efficiency of starch biosynthesis. Cassava (Manihot esculenta Crantz) is the main staple crop worldwide and has a high starch content in its storage root. However, the inner regulatory mechanism of AGPase gene family is unclear. MePHD1; a plant homeodomain transcription factor; was isolated through a yeast one-hybrid screening using the promoter of ADP-glucose pyrophosphorylase small subunit1a (MeAGPS1a) as bait, and cassava storage root cDNA library as prey. This factor could bind to the MeAGPS1a promoter in vitro and in vivo, and its predicted binding region ranged from −400 bp to −201 bp, at the translation initiation site. The transcript level of MePHD1 could be induced by five plant hormones, and a temperature of 42 °C. This was down-regulated during the maturation process of the storage root. MePHD1 protein could repress the promoter activity of MeAGPS1a gene by a dual-luciferase assay; which indicated that MePHD1 is a negative regulator for the transcript level of MeAGPS1a gene.

MeSAUR1, Encoded by a Small Auxin-Up RNA Gene, Acts as a Transcription Regulator to Positively Regulate ADP-Glucose Pyrophosphorylase Small Subunit1a Gene in Cassava

Cassava, being one of the top three tuberous crops, features highly efficient starch accumulation in the storage root to adapt the tropical resources and environments. The molecular mechanism for the process, however, is still unclear. ADP-glucose pyrophosphorylase, the first and rate-limited enzyme in starch biosynthesis pathway, is a heterotetramer comprised of two small/catalytic and two large/modulatory subunits. To understand the regulation of MeAGPase, the promoter of a highly expressed small subunit, MeAGPs1a, was used as bait for a yeast one-hybrid assay to screen storage root cDNA library. One cDNA, coding for a small auxin-up RNA protein, named MeSAUR1, was isolated from cassava. MeSAUR1 could bind to the promoter of MeAGPS1a in yeast one-hybrid test and in vitro, and was located in cell nucleus. MeSAUR1 displayed a higher transcript level in cassava root cortex, and its expression was induced by indole-3-acetic acid, gibberellin and ethylene, but repressed by abscisic acid. A dual-luciferase interaction test further convinced that MeSAUR1 could bind to the promoter of MeAGPS1a, and positively regulate the transcription of MeAGPS1a in cassava.

Evaluation of Reference Genes for Quantitative Real-Time PCR Analysis of the Gene Expression in Laticifers on the Basis of Latex Flow in Rubber Tree (Hevea brasiliensis Muell. Arg.)

Latex exploitation-caused latex flow is effective in enhancing latex regeneration in laticifer cells of rubber tree. It should be suitable for screening appropriate reference gene for analysis of the expression of latex regeneration-related genes by quantitative real-time PCR (qRT-PCR). In the present study, the expression stability of 23 candidate reference genes was evaluated on the basis of latex flow by using geNorm and NormFinder algorithms. Ubiquitin-protein ligase 2a (UBC2a) and ubiquitin-protein ligase 2b (UBC2b) were the two most stable genes among the selected candidate references in rubber tree clones with differential duration of latex flow. The two genes were also high-ranked in previous reference gene screening across different tissues and experimental conditions. By contrast, the transcripts of latex regeneration-related genes fluctuated significantly during latex flow. The results suggest that screening reference gene during latex flow should be an efficient and effective clue for selection of reference genes in qRT-PCR.