Altered carbohydrate metabolism in the storage roots of sweet potato plants overexpressing the SRF1 gene, which encodes a Dof zinc finger transcription factor

Genome-wide identification and molecular evolution of Dof gene family in Camellia oleifera

DNA binding with one finger(Dof) gene family is a class of transcription factors which play an important role on plant growth and development. Genome-wide identification results indicated that there were 45 Dof genes(ColDof) in C.oleifera genome. All 45 ColDof proteins were non-transmembrane and non-secretory proteins. Phosphorylation site analysis showed that biological function of ColDof proteins were mainly realized by phosphorylation at serine (Ser) site. The secondary structure of 44 ColDof proteins was dominated by random coil, and only one ColDof protein was dominated by α-helix. ColDof genes' promoter region contained a variety of cis-acting elements, including light responsive regulators, gibberellin responsive regulators, abscisic acid responsive regulators, auxin responsive regulators and drought induction responsive regulators. The SSR sites analysis showed that the proportion of single nucleotide repeats and the frequency of A/T in ColDof genes were the largest. Non-coding RNA analysis showed that 45 ColDof genes contained 232 miRNAs. Transcription factor binding sites of ColDof genes showed that ColDof genes had 5793 ERF binding sites, 4381 Dof binding sites, 2206 MYB binding sites, 3702 BCR-BPC binding sites. ColDof9, ColDof39 and ColDof44 were expected to have the most TFBSs. The collinearity analysis showed that there were 40 colinear locis between ColDof proteins and AtDof proteins. Phylogenetic analysis showed that ColDof gene family was most closely related to that of Camellia sinensis var. sinensis cv.Biyun and Camellia lanceoleosa. Protein-protein interaction analysis showed that ColDof34, ColDof20, ColDof28, ColDof35, ColDof42 and ColDof26 had the most protein interactions. The transcriptome analysis of C. oleifera seeds showed that 21 ColDof genes were involved in the growth and development process of C. oleifera seeds, and were expressed in 221 C. oleifera varieties. The results of qRT-PCR experiments treated with different concentrations NaCl and PEG6000 solutions indicated that ColDof1, ColDof2, ColDof14 and ColDof36 not only had significant molecular mechanisms for salt stress tolerance, but also significant molecular functions for drought stress tolerance in C. oleifera. The results of this study provide a reference for further understanding of the function of ColDof genes in C.oleifera.

Glucose uptake from the rhizosphere mediated by MdDOF3-MdHT1.2 regulates drought resistance in apple

In plants under drought stress, sugar content in roots increases, which is important for drought resistance. However, the molecular mechanisms for controlling the sugar content in roots during response to drought remain elusive. Here, we found that the MdDOF3-MdHT1.2 module-mediated glucose influx into the root is essential for drought resistance in apple (Malus × domestica). Drought induced glucose uptake from the rhizosphere and up-regulated the transcription of hexose transporter MdHT1.2. Compared with the wild-type plants, overexpression of MdHT1.2 promoted glucose uptake from the rhizosphere, thereby facilitating sugar accumulation in root and enhancing drought resistance, whereas silenced plants showed the opposite phenotype. Furthermore, ATAC-seq, RNA-seq and biochemical analysis demonstrated that MdDOF3 directly bound to the promoter of MdHT1.2 and was strongly up-regulated under drought. Overexpression of MdDOF3 in roots improved MdHT1.2-mediated glucose transport capacity and enhanced plant resistance to drought, but MdDOF3-RNAihr apple plants showed the opposite phenotype. Moreover, overexpression of MdDOF3 in roots did not attenuate drought sensitivity in MdHT1.2-RNAi plants, which was correlated with a lower glucose uptake capacity and glucose content in root. Collectively, our findings deciphered the molecular mechanism through which glucose uptake from the rhizosphere is mediated by MdDOF3-MdHT1.2, which acts to modulate sugar content in root and promote drought resistance.

Identification of Dof transcription factors in Dendrobium huoshanense and expression pattern under abiotic stresses

Introduction: DNA-binding with one finger (Dof) transcription factors (TFs) are a unique family of TFs found in higher plants that regulate plant responses to light, hormones, and abiotic stresses. The specific involvement of Dof genes in the response to environmental stresses remains unknown in D. huoshanense. Methods: A total of 22 Dof family genes were identified from the D. huoshanense genome. Results: Chromosome location analysis showed that DhDof genes were distributed on 12 chromosomes, with the largest number of Dof genes located on chromosome 8. The phylogenetic tree revealed that DhDofs could be categorized into 11 distinct subgroups. In addition to the common groups, DhDof4, DhDof5, DhDof17, and the AtDof1.4 ortholog were clustered into the B3 subgroup. Group E was a newly identified branch, among which DhDof6, DhDof7, DhDof8, and DhDof9 were in an independent branch. The conserved motifs and gene structure revealed the differences in motif number and composition of DhDofs. The dof domain near the N-terminus was highly conserved and contained a C2-C2-type zinc finger structure linked with four cysteines. Microsynteny and interspecies collinearity revealed gene duplication events and phylogenetic tree among DhDofs. Large-scale gene duplication had not occurred among the DhDofs genes and only in one pair of genes on chromosome 13. Synteny blocks were found more often between D. huoshanense and its relatives and less often between Oryza sativa and Arabidopsis thaliana. Selection pressure analysis indicated that DhDof genes were subject to purifying selection. Expression profiles and correlation analyses revealed that the Dof gene under hormone treatments showed several different expression patterns. DhDof20 and DhDof21 had the highest expression levels and were co-expressed under MeJA induction. The cis-acting element analysis revealed that each DhDof had several regulatory elements involved in plant growth as well as abiotic stresses. qRT-PCR analysis demonstrated that DhDof2 was the main ABA-responsive gene and DhDof7 was the main cold stress-related gene. IAA suppressed the expression of some Dof candidates, and SA inhibited most of the candidate genes. Discussion: Our results may provide new insights for the further investigation of the Dof genes and the screening of the core stress-resistance genes.

Different regions and environments have critical roles on yield, main quality and industrialization of an industrial purple-fleshed sweetpotato (Ipomoea batatas L. (Lam.)) "Xuzishu8"

Purple-fleshed sweetpotato (PFSP) (Ipomoea batatas (L.) Lam), whose flesh is purple to dark purple, is a special variety type of sweetpotato, which has the characteristics of food crop, industrial crop and medicinal crop. The storage root (SR) of PFSP is rich in anthocyanins, starch, protein, soluble sugar, mineral elements, polyphenol, dietary fiber and so on, which has balanced and comprehensive nutritional value. And in recent years, its unique nutritional elements are increasingly known for their health functions. At present, there is no article on the characteristics and quality analysis of industrial xz8 variety. To explore the influence of different environments on the processing quality of xz8, we selected nine regions (Xuzhou, Jiawang, Pizhou, Xinyi, Peixian, Sihong, Yanchen, Xiangyang and Tianshui) to measure its yield and quality changes. The data demonstrated that xz8 has a very consistent high yield performance. In Tianshui, the anthocyanins, protein and minerals contents were significantly higher and yield also above average. Moreover, the variety with the lowest starch content exhibited the best taste. On the basis of the above results, it suggested that quite practicable to promote xz8 cultivation and suitable for processing in these areas. Thus, our present findings improve our understanding of xz8 variety and provide the basis for the industrial production of PFSP with strong prospects for success.

Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato

The hexaploid sweetpotato (Ipomoea batatas) is one of the most important root crops worldwide. However, its genetic origin remains controversial, and its domestication history remains unknown. In this study, we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of sweetpotato. The diploid progenitor was likely closely related to Ipomoea aequatoriensis and contributed the B1 subgenome, IbT-DNA2, and the lineage 1 type of chloroplast genome to sweetpotato. The tetraploid progenitor of sweetpotato was most likely I. batatas 4x, which donated the B2 subgenome, IbT-DNA1, and the lineage 2 type of chloroplast genome. Sweetpotato most likely originated from reciprocal crosses between the diploid and tetraploid progenitors, followed by a subsequent whole-genome duplication. In addition, we detected biased gene exchanges between the subgenomes; the rate of B1 to B2 subgenome conversions was nearly three times higher than that of B2 to B1 subgenome conversions. Our analyses revealed that genes involved in storage root formation, maintenance of genome stability, biotic resistance, sugar transport, and potassium uptake were selected during the speciation and domestication of sweetpotato. This study sheds light on the evolution of sweetpotato and paves the way for improvement of this crop.

CRISPR/Cas9: an advanced platform for root and tuber crops improvement

Root and tuber crops (RTCs), which include cassava, potato, sweet potato, and yams, principally function as staple crops for a considerable fraction of the world population, in addition to their diverse applications in nutrition, industry, and bioenergy sectors. Even then, RTCs are an underutilized group considering their potential as industrial raw material. Complexities in conventional RTC improvement programs curb the extensive exploitation of the potentials of this group of crop species for food, energy production, value addition, and sustainable development. Now, with the advent of whole-genome sequencing, sufficient sequence data are available for cassava, sweet potato, and potato. These genomic resources provide enormous scope for the improvement of tuber crops, to make them better suited for agronomic and industrial applications. There has been remarkable progress in RTC improvement through the deployment of new strategies like gene editing over the last decade. This review brings out the major areas where CRISPR/Cas technology has improved tuber crops. Strategies for genetic transformation of RTCs with CRISPR/Cas9 constructs and regeneration of edited lines and the bottlenecks encountered in their establishment are also discussed. Certain attributes of tuber crops requiring focus in future research along with putative editing targets are also indicated. Altogether, this review provides a comprehensive account of developments achieved, future lines of research, bottlenecks, and major experimental concerns regarding the establishment of CRISPR/Cas9-based gene editing in RTCs.

Granule-bound starch synthase in plants: Towards an understanding of their evolution, regulatory mechanisms, applications, and perspectives

Amylose content (AC) is a significant quality trait in starchy crops, affecting their processing and application by the food and non-food industries. Therefore, fine-tuning AC in these crops has become a focus for breeders. Granule-bound starch synthase (GBSS) is the core enzyme that directly determines the AC levels. Several excellent reviews have summarized key progress in various aspects of GBSS research in recent years, but they mostly focus on cereals. Herein, we provide an in-depth review of GBSS research in monocots and dicots, focusing on the molecular characteristics, evolutionary relationships, expression patterns, molecular regulation mechanisms, and applications. We also discuss future challenges and directions for controlling AC in starchy crops, and found simultaneously increasing both the PTST and GBSS gene expression levels may be an effective strategy to increase amylose content.

Regulatory and functional divergence among members of Ibβfruct2, a sweet potato vacuolar invertase gene controlling starch and glucose content

Sweet potato [Ipomoea batatas (L.) Lam.] is an important food and industrial crop. Its storage root is rich in starch, which is present in the form of granules and represents the principal storage carbohydrate in plants. Starch content is an important trait of sweet potato controlling the quality and yield of industrial products. Vacuolar invertase encoding gene Ibβfruct2 was supposed to be a key regulator of starch content in sweet potato, but its function and regulation were unclear. In this study, three Ibβfruct2 gene members were detected. Their promoters displayed differences in sequence, activity, and cis-regulatory elements and might interact with different transcription factors, indicating that the three Ibβfruct2 family members are governed by different regulatory mechanisms at the transcription level. Among them, we found that only Ibβfruct2-1 show a high expression level and promoter activity, and encodes a protein with invertase activity, and the conserved domains and three conserved motifs NDPNG, RDP, and WEC are critical to this activity. Only two and six amino acid residue variations were detected in sequences of proteins encoded by Ibβfruct2-2 and Ibβfruct2-3, respectively, compared with Ibβfruct2-1; although not within key motifs, these variations affected protein structure and affinities for the catalytic substrate, resulting in functional deficiency and low activity. Heterologous expression of Ibβfruct2-1 in Arabidopsis decreased starch content but increased glucose content in leaves, indicating Ibβfruct2-1 was a negative regulator of starch content. These findings represent an important advance in understanding the regulatory and functional divergence among duplicated genes in sweet potato, and provide critical information for functional studies and utilization of these genes in genetic improvement.

Polyploid GWAS reveals the basis of molecular marker development for complex breeding traits including starch content in the storage roots of sweet potato

Given the importance of prioritizing genome-based breeding of sweet potato to enable the promotion of food and nutritional security for future human societies, here, we aimed to dissect the genetic basis of storage root starch content (SC) when associated with a complex set of breeding traits including dry matter (DM) rate, storage root fresh weight (SRFW), and anthocyanin (AN) content in a mapping population containing purple-fleshed sweet potato. A polyploid genome-wide association study (GWAS) was extensively exploited using 90,222 single-nucleotide polymorphisms (SNPs) obtained from a bi-parental 204 F₁ population between 'Konaishin' (having high SC but no AN) and 'Akemurasaki' (having high AN content but moderate SC). Through the comparison of polyploid GWAS on the whole set of the 204 F₁, 93 high-AN-containing F₁, and 111 low-AN-containing F₁ populations, a total of two (consists of six SNPs), two (14 SNPs), four (eight SNPs), and nine (214 SNPs) significantly associated signals were identified for the variations of SC, DM, SRFW, and the relative AN content, respectively. Of them, a novel signal associated with SC, which was most consistent in 2019 and 2020 in both the 204 F₁ and 111 low-AN-containing F₁ populations, was identified in homologous group 15. The five SNP markers associated with homologous group 15 could affect SC improvement with a degree of positive effect (~4.33) and screen high-starch-containing lines with higher efficiency (~68%). In a database search of 62 genes involved in starch metabolism, five genes including enzyme genes granule-bound starch synthase I (IbGBSSI), α-amylase 1D, α-amylase 1E, and α-amylase 3, and one transporter gene ATP/ADP-transporter were located on homologous group 15. In an extensive qRT-PCR of these genes using the storage roots harvested at 2, 3, and 4 months after field transplantation in 2022, IbGBSSI, which encodes the starch synthase isozyme that catalyzes the biosynthesis of amylose molecule, was most consistently elevated during starch accumulation in sweet potato. These results would enhance our understanding of the underlying genetic basis of a complex set of breeding traits in the starchy roots of sweet potato, and the molecular information, particularly for SC, would be a potential platform for molecular marker development for this trait.

Characterization of a novel mutant with inhibition of storage root formation in sweet potato

Sweet potato is a widely cultivated crop with storage roots. Although many studies have been conducted on the mechanism of its storage root formation, the details have not been fully elucidated. We screened mutant lines with inhibition of storage root formation to clarify parts of the mechanism. In this study, the process of storage root formation in one of the mutant lines, C20-8-1, was investigated. The inhibition of storage root formation was observed during the early stages of growth. The roots in C20-8-1 did not show histological differences compared to those in wild type. The transition from fibrous roots to pencil roots, which are the developmental stages prior to mature storage root formation, was delayed or inhibited in C20-8-1. The upregulation of starch biosynthesis-related genes and downregulation of lignin biosynthesis genes with storage root swelling were not confirmed in the root of C20-8-1 during the developmental transition stage, suggesting that most of the roots in C20-8-1 are in the pre-transition state toward the storage root swelling. C20-8-1 showed a mutant phenotype during the critical period of storage root swelling initiation, and further clarification of this mutation is expected to provide new insights into storage root formation.

DOF transcription factors: Specific regulators of plant biological processes

Plant biological processes, such as growth and metabolism, hormone signal transduction, and stress responses, are affected by gene transcriptional regulation. As gene expression regulators, transcription factors activate or inhibit target gene transcription by directly binding to downstream promoter elements. DOF (DNA binding with One Finger) is a classic transcription factor family exclusive to plants that is characterized by its single zinc finger structure. With breakthroughs in taxonomic studies of different species in recent years, many DOF members have been reported to play vital roles throughout the plant life cycle. They are not only involved in regulating hormone signals and various biotic or abiotic stress responses but are also reported to regulate many plant biological processes, such as dormancy, tissue differentiation, carbon and nitrogen assimilation, and carbohydrate metabolism. Nevertheless, some outstanding issues remain. This article mainly reviews the origin and evolution, protein structure, and functions of DOF members reported in studies published in many fields to clarify the direction for future research on DOF transcription factors.

Ectopic Expression of Arabidopsis thaliana zDof1.3 in Tomato (Solanum lycopersicum L.) Is Associated with Improved Greenhouse Productivity and Enhanced Carbon and Nitrogen Use

A large collection of transgenic tomato lines, each ectopically expressing a different Arabidopsis thaliana transcription factor, was screened for variants with alterations in leaf starch. Such lines may be affected in carbon partitioning, and in allocation to the sinks. We focused on ‘L4080’, which harbored an A. thaliana zDof (DNA-binding one zinc finger) isoform 1.3 (AtzDof1.3) gene, and which had a 2−4-fold higher starch-to-sucrose ratio in source leaves over the diel (p < 0.05). Our aim was to determine whether there were associated effects on productivity. L4080 plants were altered in nitrogen (N) and carbon (C) metabolism. The N-to-C ratio was higher in six-week-old L4080, and when treated with 1/10 N, L4080 growth was less inhibited compared to the wild-type and this was accompanied by faster root elongation (p < 0.05). The six-week-old L4080 acquired 42% more dry matter at 720 ppm CO2, compared to ambient CO2 (p < 0.05), while the wild-type (WT) remained unchanged. GC-MS-TOF data showed that L4080 source leaves were enriched in amino acids compared to the WT, and at 49 DPA, fruit had 25% greater mass, higher sucrose, and increased yield (25%; p < 0.05) compared to the WT. An Affymetrix cDNA array analysis suggested that only 0.39% of the 9000 cDNAs were altered by 1.5-fold (p < 0.01) in L4080 source leaves. 14C-labeling of fruit disks identified potential differences in 14-DPA fruit metabolism suggesting that post-transcriptional regulation was important. We conclude that AtzDof1.3 and the germplasm derived therefrom, should be investigated for their ‘climate-change adaptive’ potential.

Comparative Transcriptome Profiling Reveals the Genes Involved in Storage Root Expansion in Sweetpotato (Ipomoea batatas (L.) Lam.)

Sweetpotato (Ipomoea batatas (L.) Lam.) is recognized as one of the most important root crops in the world by the Food and Agriculture Organization of the United Nations. The yield of sweetpotato is closely correlated with the rate of storage root (SR) formation and expansion. At present, most of the studies on sweetpotato SR expansion are focused on the physiological mechanism. To explore the SR expansion mechanism of sweetpotato, we performed transcriptome sequencing of SR harvested at 60, 90, 120, and 150 days after planting (DAP) to analyze two sweetpotato lines, Xuzishu 8 and its crossing progenies named Xu 18-192, which were selected from an F1 segregation population of Xuzishu 8 and Meiguohong, in which SR expansion was delayed significantly. A total of 57,043 genes were produced using transcriptome sequencing, of which 1312 were differentially expressed genes (DEGs) in four SR growth periods of the sweetpotato lines. The combination of the KEGG and trend analysis revealed several key candidate genes involved in SR expansion. The SBEI gene involved in starch metabolism, and transcription factors ARF6, NF-YB3 and NF-YB10 were all significantly up-regulated during SR expansion. The data from this study provide insights into the complex mechanisms of SR formation and expansion in sweetpotato and identify new candidate genes for increasing the yield of sweetpotato.

The association of HpDof1.7 and HpDof5.4 with soluble sugar accumulation in pitaya fruit by transcriptionally activating sugar metabolic genes

Soluble sugar is one of the important factors affecting fruit flavor and quality. Here, we report the identification of two Dof (DNA-binding with one finger) transcription factors termed HpDof1.7 and HpDof5.4, and their roles in influencing sugar accumulation in pitayas. HpDof1.7 and HpDof5.4 shared a similar expression pattern with sugar metabolism-related genes HpSuSy1 and HpINV2, and sugar transporter genes HpTMT2 and HpSWEET14 during pitayas maturation, and their expression pattern was also consistent with the accumulation of glucose and fructose, which were the predominant sugars in pitayas. HpDof1.7 and HpDof5.4 were both typical nucleus-localized proteins with trans-activation ability. Gel mobility shift assay revealed that HpDof1.7 and HpDof5.4 were bound to promoters of HpSuSy1, HpINV2, HpTMT2 and HpSWEET14. Finally, transient expression assays in tobacco leaves showed that HpDof1.7 and HpDof5.4 increased the activities of HpSuSy1, HpINV2, HpTMT2 and HpSWEET14 promoters, thus facilitating sugar accumulation by transcriptionally enhancing sugar metabolic pathway genes. Our findings provide a new perspective on the regulatory mechanisms of Dof transcription factors in sugar accumulation and pitaya fruit quality formation.

Identification of Novel Mutations in Arabidopsis thaliana DOF 4.2 Coding Gene

Purpose: DOF (DNA-binding with One Finger) proteins are plant-specific transcription factors which mediate numerous biological processes. The purpose of the current study is to report new naturally occurring mutations in the gene encoding for one of the members of DOF proteins named DOF 4.2.

Methods: The expression of zinc finger domain of DOF 4.2 (DOF 4.2-ZF) was investigated by first synthesis of cDNA library using different parts of Arabidopsis thaliana plant. Then the coding sequence for zinc finger domain of DOF 4.2 protein was prepared using nested PCR experiment and cloned into pGEX-6P-1 expression vector. Finally, the prepared construct was used for protein expression. Furthermore, molecular dynamics (MD) simulation was carried out to predict DNA binding affinity of DOF 4.2-ZF using AMBER package.

Results: For the first time a new variant of DOF 4.2-ZF protein with three mutations was detected. One of the mutations is silent while the other two mutations lead to amino acid replacement (S18G) as well as introduction of a stop codon ultimately resulting in a truncated protein production. In order to investigate whether the truncated form is able to recognize DNA binding motif, MD simulations were carried out and the results showed that the chance of binding of DOF 4.2-ZF protein to cognate DNA in its truncated form is very low.

Conclusion: The findings demonstrated that the observed mutations adversely affect the DNA binding ability of the truncated form of DOF4.2 if it is expressed in the mutant variant of A. thaliana used in this study.

Engineering Properties of Sweet Potato Starch for Industrial Applications by Biotechnological Techniques including Genome Editing

Sweet potato (Ipomoea batatas) is one of the largest food crops in the world. Due to its abundance of starch, sweet potato is a valuable ingredient in food derivatives, dietary supplements, and industrial raw materials. In addition, due to its ability to adapt to a wide range of harsh climate and soil conditions, sweet potato is a crop that copes well with the environmental stresses caused by climate change. However, due to the complexity of the sweet potato genome and the long breeding cycle, our ability to modify sweet potato starch is limited. In this review, we cover the recent development in sweet potato breeding, understanding of starch properties, and the progress in sweet potato genomics. We describe the applicational values of sweet potato starch in food, industrial products, and biofuel, in addition to the effects of starch properties in different industrial applications. We also explore the possibility of manipulating starch properties through biotechnological means, such as the CRISPR/Cas-based genome editing. The ability to target the genome with precision provides new opportunities for reducing breeding time, increasing yield, and optimizing the starch properties of sweet potatoes.

Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are vital for plant growth and development, signal transduction, immunity, and play diverse roles in plant defense responses. However, the LRR-RLK genes have not been systematically studied in Vernicia fordii (tung tree), especially its response to Fusarium wilt. Here, we carried out an integrative analysis of LRR-RLKs among five Euphorbiaceae species: Hevea brasiliensis (rubber tree), Manihot esculenta (cassava), Jatropha curcas (physic nut), Ricinus communis (castor bean), and V. fordii, which contained 223, 311, 186, 138, and 167 LRR-RLKs, respectively. Maximum-likelihood tree was estimated using LRR-RLKs of Arabidopsis thaliana as a template, and they allowed us to divide Euphorbiaceae LRR-RLKs into 22 groups. There are 126 segmental and 30 tandem duplications in these Euphorbiaceae genomes by synteny analysis. The tissue-specific expression patterns revealed that V. fordii LRR-RLKs (VfLRR-RLKs) were differentially expressed in various tissues, and some of them exhibited specific expression in meristems tissues, which suggested their potential functions during organ formation and cell fate specification. Two VfLRR-RLK pairs (Vf01G2125 and Vf03G1740, Vf06G2687 and Vf10G1659), which generated by tandem duplication events, were associated with possible resistance to Fusarium wilt infection. The qRT-PCR confirmed these four VfLRR-RLKs contained opposite expression profiles during pathogen infection in V. fordii and V. montana. Taken together, our data systematically analyzed the LRR-RLK family in Euphorbiaceae genomes for the first time. We highlight the putative roles of VfLRR-RLKs in response to Fusarium wilt infection, and VfLRR-RLKs may be further applied in marker-assisted breeding to control Fusarium wilt in V. fordii.

Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants

C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.

The apple DNA-binding one zinc-finger protein MdDof54 promotes drought resistance

DNA-binding one zinc-finger (Dof) proteins constitute a family of transcription factors with a highly conserved Dof domain that contains a C2C2 zinc-finger motif. Although several studies have demonstrated that Dof proteins are involved in multiple plant processes, including development and stress resistance, the functions of these proteins in drought stress resistance are largely unknown. Here, we report the identification of the MdDof54 gene from apple and document its positive roles in apple drought resistance. After long-term drought stress, compared with nontransgenic plants, MdDof54 RNAi plants had significantly shorter heights and weaker root systems; the transgenic plants also had lower shoot and root hydraulic conductivity, as well as lower photosynthesis rates. By contrast, compared with nontransgenic plants, MdDof54-overexpressing plants had higher photosynthesis rates and shoot hydraulic conductivity under long-term drought stress. Moreover, compared with nontransgenic plants, MdDof54-overexpressing plants had higher survival percentages under short-term drought stress, whereas MdDof54 RNAi plants had lower survival percentages. MdDof54 RNAi plants showed significant downregulation of 99 genes and significant upregulation of 992 genes in response to drought, and 366 of these genes were responsive to drought. We used DAP-seq and ChIP-seq analyses to demonstrate that MdDof54 recognizes cis-elements that contain an AAAG motif. Taken together, our results provide new information on the functions of MdDof54 in plant drought stress resistance as well as resources for apple breeding aimed at the improvement of drought resistance.

Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato

The mechanisms of carotenoid accumulation in yellow-fleshed sweetpotato cultivars are unclear. In this study, we compared the transcriptome profiles of a yellow-fleshed cultivar, Beniharuka (BH) and two of its spontaneous white-fleshed mutants (WH2 and WH3) to reveal the genes involved in yellow flesh. As a result of RNA sequencing, a total of 185 differentially expressed genes (DEGs) were commonly detected in WH2 and WH3 compared to BH. Of these genes, 85 DEGs and 100 DEGs were commonly upregulated and downregulated in WH2 and WH3 compared to BH, respectively. g1103.t1, a paralog of zeaxanthin epoxidase (ZEP), was only DEG common to WH2 and WH3 among 38 genes considered to be involved in carotenoid biosynthesis in storage roots. The expression level of g1103.t1 was also considerably lower in five white-fleshed cultivars than in five yellow-fleshed cultivars. Analysis of carotenoid composition in the storage roots showed that the epoxidised carotenoids were drastically reduced in both WH2 and WH3. Therefore, we propose that the ZEP paralog, g1103.t1, may be involved in carotenoid accumulation through the epoxidation of β-carotene and β-cryptoxanthin in sweetpotato.

Functional Analysis of Starch Metabolism in Plants

In plants, starch is synthesized in leaves during the day-time from fixed carbon through photosynthesis and is mobilized at night to support continued respiration, sucrose export, and growth in the dark. The main crops where starch is biosynthesized and stored are corn, rice, wheat, and potatoes, and they are mainly used as food resources for humankind. There are many genes that are involved in starch biosynthesis from cytosol to storage organs in plants. ADP-glucose, UDP- glucose, and glucose-6-phosphate are synthesized catalyzed by UDP-invertase, AGPase, hexokinase, and P- hexose-isomerase in cytosol. Starch composed of amylopectin and amylose is synthesized by starch synthase, granule bound starch synthase, starch-branching enzyme, debranching enzyme, and pullulanase, which is primarily responsible for starch production in storage organs. Recently, it has been uncovered that structural genes are controlled by proteins derived from other genes such as transcription factors. To obtain more precise information on starch metabolism, the functions of genes and transcription factors need to be studied to understand their roles and functions in starch biosynthesis in plants. However, the roles of genes related to starch biosynthesis are not yet clearly understood. The papers of this special issue contain reviews and research articles on these topics and will be a useful resource for researchers involved in the quality improvement of starch storage crops.

DOF, MYB and TCP transcription factors: Their possible roles on barley germination and seedling establishment

Seed germination is a multi-staged complex process during seed plant life cycle, and it is tightly regulated through a coordinated expression of diverse genes in diverse tissues. As regulatory molecules of gene expression, determination of transcription factors is crucial to understanding molecular basis and regulatory network of germination process and seedling establishment. However, limited data on the contributions of these transcription factors to the germination of crop barley (Hordeum vulgare L.) are available. Here, we investigated the expression profiles of selected transcription factors from different families (DOF, MYB and TCP) with qRT-PCR analysis in various tissues including coleoptiles, leaves and roots following the germination. Analysis of MYB and DOF gene expression profiles indicated that there were differing expressions in different aged tissues, HvMYB5 and HvDOF2 being the most outstanding one in the oldest tissue, 15-day-old root. On the other hand, investigated TCP genes were lowly expressed compared to selected MYB and DOF genes, except HvTCP3, where the highest expression was observed in 15-day-old root tissue. The obtained expression profiles illustrate the importance of potential regulatory roles of transcription factors in early developmental stages of barley germination and seedling establishment.

Transcriptome co-expression network analysis identifies key genes and regulators of ripening kiwifruit ester biosynthesis

BACKGROUND

Aroma is an important organoleptic quality for fruit and has a large influence on consumer preference. Kiwifruit esters undergo rapid and substantial changes contributing to the flavor during fruit ripening. Part of enzymes and their coding genes have been indicated potential candidates for flavor-related esters synthesis. However, there still exist obvious gaps in the biosynthetic pathways of esters and the mechanisms regulating ester biosynthesis in kiwifruit remain unknown.

RESULTS

Using gas chromatography-mass spectrometry (GC-MS), volatile compounds of kiwifruit were quantified in response to ethylene (ETH, 100 μl/l, 24 h, 20 °C) and 1-methylcyclopropene (1-MCP, 1 μl/l, 24 h, 20 °C). The results indicated that esters showed the most substantial changes enhanced by ethylene and were inhibited by 1-MCP. Correlations between RNA-seq results and concentrations of esters, constructed using Weighted Gene Co-Expression Network Analysis (WGCNA) indicated that three structural genes (fatty acid desaturase, AdFAD1; aldehyde dehydrogenase, AdALDH2; alcohol acyltransferase, AdAT17) had similar expression patterns that paralled the changes in total ester content, and AdFAD1 transcripts exhibited the highest correlation. In order to search for potential regulators for ester biosynthesis, 14 previously reported ethylene-responsive transcription factors (TFs) were included in the correlation analysis with esters and their biosynthetic genes. Using dual-luciferase assay, the in vivo regulatory activities of TFs on ester biosynthetic gene promoters were investigated and the results indicated that AdNAC5 and AdDof4 (DNA binding with one finger) trans-activated and trans-suppressed the AdFAD1 promoter.

CONCLUSIONS

The present study advanced the molecular basis of ripening-related ester biosynthesis in kiwifruit by identifying three biosynthetic related genes AdFAD1, AdALDH2 and AdAT17 by transcriptome analysis, and highlighted the function of two TFs by transactivation studies.

Genome-Wide Identification, Structure Characterization, and Expression Profiling of Dof Transcription Factor Gene Family in Wheat (Triticum aestivum L.)

DNA binding with one finger (Dof) proteins are plant-specific transcription factors with crucial roles in plant growth and stress response. Even so, little is known about them in wheat. In this study, 108 wheat Dof (TaDof) genes across 21 chromosomes were detected. Although variable in sequence length, molecular weight, and isoelectric point, all TaDof proteins contained conserved zinc-finger structures and were phylogenetically divided into 7 sub-groups. Exon/intron and motif analyses suggested that TaDof structures and conserved motifs were similar within sub-groups but diverse among sub-groups. Many segmental duplications were identified and Ka/Ks and inter-species synthetic analyses indicated that polyploidization was main reason for increased number of TaDofs. Prediction and experimental confirmation revealed that TaDofs functioned as transcription factors in the nucleus. Expression pattern profiling showed that TaDofs specifically affected growth and development, and biotic and abiotic stress responses. Wheat miRNAs and cis-regulator were predicted as essential players in molding TaDofs expression patterns. qRT-PCR analysis revealed that TaDofs were induced by salt and drought stresses. Customized annotation revealed that TaDofs were widely involved in phytohormone response, defense, growth and development, and metabolism. Our study provided a comprehensive understanding to wheat TaDofs.

High expression of GUS activities in sweet potato storage roots by sucrose-inducible minimal promoter

We developed transgenic sweet potato with Spo^min (sucrose-inducible minimal promoter)-GUS gene-fused constructs. Induced GUS activities by Spo^min were higher than those by CaMV 35S promoter. We developed transgenic sweet potato (Ipomoea batatas L. Lam. cv. Kokei no. 14) plants with Spo^min (sucrose-inducible minimal promoter)-GUS gene-fused constructs with signal peptides for sorting to cytosol, apoplast and ER, and we analyzed the GUS expression pattern of cut tissue after sucrose treatment. Induced GUS activities by Spo^min were several hundred times higher than those by the CaMV 35S promoter. Also, GUS activities in storage roots induced with a Spo^min-cytosol-GUS construct were higher than those with either Spo^min-apoplast or -ER-GUS constructs. The induced GUS activities by Spo^min were higher in storage roots without sucrose treatment than those with sucrose treatment. Chilling (4 °C) storage roots with Spo^min constructs for 4 weeks produced higher GUS activities than in storage roots stored at 25 °C for 4 weeks. The calculated maximum GUS content in the storage roots was up to about 224.2 μg/g fresh weight. The chilling treatment increased the free sucrose content in the storage roots, and this increase in endogenous sugar levels induced increased GUS activities in the storage roots. Therefore, Spo^min appears to be a useful promoter to develop protein production systems using sweet potato variety Kokei no. 14 storage roots by postharvest treatment.

Exploring regulatory networks in plants: transcription factors of starch metabolism

Biological networks are complex (non-linear), redundant (cyclic) and compartmentalized at the subcellular level. Rational manipulation of plant metabolism may have failed due to inherent difficulties of a comprehensive understanding of regulatory loops. We first need to identify key factors controlling the regulatory loops of primary metabolism. The paradigms of plant networks are revised in order to highlight the differences between metabolic and transcriptional networks. Comparison between animal and plant transcription factors (TFs) reveal some important differences. Plant transcriptional networks function at a lower hierarchy compared to animal regulatory networks. Plant genomes contain more TFs than animal genomes, but plant proteins are smaller and have less domains as animal proteins which are often multifunctional. We briefly summarize mutant analysis and co-expression results pinpointing some TFs regulating starch enzymes in plants. Detailed information is provided about biochemical reactions, TFs and cis regulatory motifs involved in sucrose-starch metabolism, in both source and sink tissues. Examples about coordinated responses to hormones and environmental cues in different tissues and species are listed. Further advancements require combined data from single-cell transcriptomic and metabolomic approaches. Cell fractionation and subcellular inspection may provide valuable insights. We propose that shuffling of promoter elements might be a promising strategy to improve in the near future starch content, crop yield or food quality.

Multifaceted Role of PheDof12-1 in the Regulation of Flowering Time and Abiotic Stress Responses in Moso Bamboo (Phyllostachys edulis)

DNA binding with one finger (Dof) proteins, forming an important transcriptional factor family, are involved in gene transcriptional regulation, development, stress responses, and flowering responses in annual plants. However, knowledge of Dofs in perennial and erratically flowering moso bamboo is limited. In view of this, a Dof gene, PheDof12-1, was isolated from moso bamboo. PheDof12-1 is located in the nucleus and has the highest expression in palea and the lowest in bract. Moreover, PheDof12-1 expression is high in flowering leaves, then declines during flower development. The transcription level of PheDof12-1 is highly induced by cold, drought, salt, and gibberellin A3 (GA₃) stresses. The functional characteristics of PheDof are researched for the first time in Arabidopsis, and the results show that transgenic Arabidopsis overexpressing PheDof12-1 shows early flowering under long-day (LD) conditions but there is no effect on flowering time under short-day (SD) conditions; the transcription levels of FT, SOC1, and AGL24 are upregulated; and FLC and SVP are downregulated. PheDof12-1 exhibits a strong diurnal rhythm, inhibited by light treatment and induced in dark. Yeast one-hybrid (Y1H) assay shows that PheDof12-1 can bind to the promoter sequence of PheCOL4. Taken together, these results indicate that PheDof12-1 might be involved in abiotic stress and flowering time, which makes it an important candidate gene for studying the molecular regulation mechanisms of moso bamboo flowering.

A sucrose non-fermenting-1-related protein kinase-1 gene, IbSnRK1, improves starch content, composition, granule size, degree of crystallinity and gelatinization in transgenic sweet potato

Sucrose non-fermenting-1-related protein kinase-1 (SnRK1) is an essential energy-sensing regulator and plays a key role in the global control of carbohydrate metabolism. The SnRK1 gene has been found to increase starch accumulation in several plant species. However, its roles in improving starch quality have not been reported to date. In this study, we found that the IbSnRK1 gene was highly expressed in the storage roots of sweet potato and strongly induced by exogenous sucrose. Its expression followed the circandian rhythm. Its overexpression not only increased starch content, but also decreased proportion of amylose, enlarged granule size and improved degree of crystallinity and gelatinization in transgenic sweet potato, which revealed, for the first time, the important roles of SnRK1 in improving starch quality of plants. The genes involved in starch biosynthesis pathway were systematically up-regulated, and the content of ADP-glucose as an important precursor for starch biosynthesis and the activities of key enzymes were significantly increased in transgenic sweet potato. These findings indicate that IbSnRK1 improves starch content and quality through systematical up-regulation of the genes and the increase in key enzyme activities involved in starch biosynthesis pathway in transgenic sweet potato. This gene has the potential to improve starch content and quality in sweet potato and other plants.

Regional Heritability Mapping Provides Insights into Dry Matter Content in African White and Yellow Cassava Populations

The HarvestPlus program for cassava ( Crantz) fortifies cassava with β-carotene by breeding for carotene-rich tubers (yellow cassava). However, a negative correlation between yellowness and dry matter (DM) content has been identified. We investigated the genetic control of DM in white and yellow cassava. We used regional heritability mapping (RHM) to associate DM with genomic segments in both subpopulations. Significant segments were subjected to candidate gene analysis and candidates were validated with prediction accuracies. The RHM procedure was validated via a simulation approach and revealed significant hits for white cassava on chromosomes 1, 4, 5, 10, 17, and 18, whereas hits for the yellow were on chromosome 1. Candidate gene analysis revealed genes in the carbohydrate biosynthesis pathway including plant serine-threonine protein kinases (SnRKs), UDP (uridine diphosphate)-glycosyltransferases, UDP-sugar transporters, invertases, pectinases, and regulons. Validation using 1252 unique identifiers from the SnRK gene family genome-wide recovered 50% of the predictive accuracy of whole-genome single nucleotide polymorphisms for DM, whereas validation using 53 likely genes (extracted from the literature) from significant segments recovered 32%. Genes including an acid invertase, a neutral or alkaline invertase, and a glucose-6-phosphate isomerase were validated on the basis of an a priori list for the cassava starch pathway, and also a fructose-biphosphate aldolase from the Calvin cycle pathway. The power of the RHM procedure was estimated as 47% when the causal quantitative trait loci generated 10% of the phenotypic variance (sample size = 451). Cassava DM genetics are complex and RHM may be useful for complex traits.

Evolution analysis of Dof transcription factor family and their expression in response to multiple abiotic stresses in Malus domestica

As a family of transcription factors, DNA binding with one figure (Dof) proteins play important roles in various biological processes in plants. Here, a total of 60 putative apple (Malus domestica) Dof genes (MdDof) were identified and mapped to different chromosomes. Chromosomal distribution and synteny analysis indicated that the expansion of the MdDof genes came primarily from segmental and duplication events, and from whole genome duplication, which lead to more Dof members in apples than in other plants. All 60 MdDof genes were classified into thirteen groups, according to multiple sequence alignment and the phylogenetic tree constructed of Dof genes from apple, peach (Prunus persica), Arabidopsis and rice. Within each group, the members shared a similar exon/intron and motif compositions, although the sizes of the MdDof genes and encoding proteins were quite different. Several Dof genes from the apple and peach were identified to be homologues based on their close synteny relationship, which suggested that these genes bear similar functions. Half of the MdDof genes were randomly selected to determine their responses to different stresses. The majority of MdDof genes were quite sensitive to PEG, NaCl, cold and exogenous ABA treatment. Our results suggested that MdDof family members may play important roles in plant tolerance to abiotic stress.

Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)

Background

Starch is the principle constituent of potato tubers and is of considerable importance for food and non-food applications. Its metabolism has been subject of extensive research over the past decades. Despite its importance, a description of the complete inventory of genes involved in starch metabolism and their genome organization in potato plants is still missing. Moreover, mechanisms regulating the expression of starch genes in leaves and tubers remain elusive with regard to differences between transitory and storage starch metabolism, respectively. This study aimed at identifying and mapping the complete set of potato starch genes, and to study their expression pattern in leaves and tubers using different sets of transcriptome data. Moreover, we wanted to uncover transcription factors co-regulated with starch accumulation in tubers in order to get insight into the regulation of starch metabolism.

Results

We identified 77 genomic loci encoding enzymes involved in starch metabolism. Novel isoforms of many enzymes were found. Their analysis will help to elucidate mechanisms of starch biosynthesis and degradation. Expression analysis of starch genes led to the identification of tissue-specific isoenzymes suggesting differences in the transcriptional regulation of starch metabolism between potato leaf and tuber tissues. Selection of genes predominantly expressed in developing potato tubers and exhibiting an expression pattern indicative for a role in starch biosynthesis enabled the identification of possible transcriptional regulators of tuber starch biosynthesis by co-expression analysis.

Conclusions

This study provides the annotation of the complete set of starch metabolic genes in potato plants and their genomic localizations. Novel, so far undescribed, enzyme isoforms were revealed. Comparative transcriptome analysis enabled the identification of tuber- and leaf-specific isoforms of starch genes. This finding suggests distinct regulatory mechanisms in transitory and storage starch metabolism. Putative regulatory proteins of starch biosynthesis in potato tubers have been identified by co-expression and their expression was verified by quantitative RT-PCR.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3381-z) contains supplementary material, which is available to authorized users.

Improvement for agronomically important traits by gene engineering in sweetpotato

Sweetpotato is the seventh most important food crop in the world. It is mainly used for human food, animal feed, and for manufacturing starch and alcohol. This crop, a highly heterozygous, generally self-incompatible, outcrossing polyploidy, poses numerous challenges for the conventional breeding. Its productivity and quality are often limited by abiotic and biotic stresses. Gene engineering has been shown to have the great potential for improving the resistance to these stresses as well as the nutritional quality of sweetpotato. To date, an Agrobacterium tumefaciens-mediated transformation system has been developed for a wide range of sweetpotato genotypes. Several genes associated with salinity and drought tolerance, diseases and pests resistance, and starch, carotenoids and anthocyanins biosynthesis have been isolated and characterized from sweetpotato. Gene engineering has been used to improve abiotic and biotic stresses resistance and quality of this crop. This review summarizes major research advances made so far in improving agronomically important traits by gene engineering in sweetpotato and suggests future prospects for research in this field.

Comparative Transcriptome Analysis Reveals Critical Function of Sucrose Metabolism Related-Enzymes in Starch Accumulation in the Storage Root of Sweet Potato

The starch properties of the storage root (SR) affect the quality of sweet potato (Ipomoea batatas (L.) Lam.). Although numerous studies have analyzed the accumulation and properties of starch in sweet potato SRs, the transcriptomic variation associated with starch properties in SR has not been quantified. In this study, we measured the starch and sugar contents and analyzed the transcriptome profiles of SRs harvested from sweet potatoes with high, medium, and extremely low starch contents, at five developmental stages [65, 80, 95, 110, and 125 days after transplanting (DAP)]. We found that differences in both water content and starch accumulation in the dry matter affect the starch content of SRs in different sweet potato genotypes. Based on transcriptome sequencing data, we assembled 112336 unigenes, and identified several differentially expressed genes (DEGs) involved in starch and sucrose metabolism, and revealed the transcriptional regulatory network controlling starch and sucrose metabolism in sweet potato SRs. Correlation analysis between expression patterns and starch and sugar contents suggested that the sugar-starch conversion steps catalyzed by sucrose synthase (SuSy) and UDP-glucose pyrophosphorylase (UGPase) may be essential for starch accumulation in the dry matter of SRs, and IbβFRUCT2, a vacuolar acid invertase, might also be a key regulator of starch content in the SRs. Our results provide valuable resources for future investigations aimed at deciphering the molecular mechanisms determining the starch properties of sweet potato SRs.

Genome-wide analysis of the DNA-binding with one zinc finger (Dof) transcription factor family in bananas

DNA-binding with one finger (Dof) domain proteins are a multigene family of plant-specific transcription factors involved in numerous aspects of plant growth and development. In this study, we report a genome-wide search for Musa acuminata Dof (MaDof) genes and their expression profiles at different developmental stages and in response to various abiotic stresses. In addition, a complete overview of the Dof gene family in bananas is presented, including the gene structures, chromosomal locations, cis-regulatory elements, conserved protein domains, and phylogenetic inferences. Based on the genome-wide analysis, we identified 74 full-length protein-coding MaDof genes unevenly distributed on 11 chromosomes. Phylogenetic analysis with Dof members from diverse plant species showed that MaDof genes can be classified into four subgroups (StDof I, II, III, and IV). The detailed genomic information of the MaDof gene homologs in the present study provides opportunities for functional analyses to unravel the exact role of the genes in plant growth and development.

Genome-Wide Identification of the Transcription Factors Involved in Citrus Fruit Ripening from the Transcriptomes of a Late-Ripening Sweet Orange Mutant and Its Wild Type

Fruit ripening is a genetically programmed process. Transcription factors (TFs) play key roles in plant development and ripening by temporarily and spatially regulating the transcription of their target genes. In this study, a total of 159 TFs were identified from a spontaneous late-ripening mutant 'Fengwan' (C. sinensis L. Osbeck) sweet orange (MT) and its wild-type counterpart ('Fengjie 72–1', WT) along the ripening period via the Transcription Factor Prediction of PlantTFDB 3.0. Fifty-two differentially expressed TFs were identified between MT and WT; 92 and 120 differentially expressed TFs were identified in WT and MT, respectively. The Venn diagram analysis showed that 16 differentially expressed TFs were identified between MT and WT and during the ripening of WT and MT. These TFs were primarily assigned to the families of C2H2, Dof, bHLH, ERF, MYB, NAC and LBD. Particularly, the number of TFs of the ERF family was the greatest between MT and WT. According to the results of the WGCNA analysis, a weighted correlation network analysis tool, several important TFs correlated to abscisic acid (ABA), citric acid, fructose, glucose and sucrose were identified, such as RD26, NTT, GATA7 and MYB21/62/77. Hierarchical cluster analysis and the expression analysis conducted at five fruit ripening stages further validated the pivotal TFs that potentially function during orange fruit development and ripening.

Altered Phenylpropanoid Metabolism in the Maize Lc-Expressed Sweet Potato (Ipomoea batatas) Affects Storage Root Development

There is no direct evidence of the effect of lignin metabolism on early storage root development in sweet potato. In this study, we found that heterologous expression of the maize leaf color (Lc) gene in sweet potato increased anthocyanin pigment accumulation in the whole plant and resulted in reduced size with an increased length/width ratio, low yield and less starch content in the early storage roots. RT-PCR analysis revealed dramatic up-regulation of the genes involved in the lignin biosynthesis pathway in developing storage roots, leading to greater lignin content in the Lc transgenic lines, compared to the wild type. This was also evidenced by the enhanced lignification of vascular cells in the early storage roots. Furthermore, increased expression of the β-amylase gene in leaves and storage roots also accelerated starch degradation and increased the sugar use efficiency, providing more energy and carbohydrate sources for lignin biosynthesis in the Lc transgenic sweet potato. Lesser starch accumulation was observed in the developing storage roots at the initiation stage in the Lc plants. Our study provides experimental evidence of the basic carbohydrate metabolism underlying the development of storage roots, which is the transformation of lignin biosynthesis to starch biosynthesis.

Transcriptome-Wide Identification and Expression Profiling of the DOF Transcription Factor Gene Family in Chrysanthemum morifolium

The family of DNA binding with one finger (DOF) transcription factors is plant specific, and these proteins contain a highly conserved domain (DOF domain) of 50-52 amino acids that includes a C2C2-type zinc finger motif at the N-terminus that is known to function in a number of plant processes. Here, we characterized 20 DOF genes in the important ornamental species chrysanthemum (Chrysanthemum morifolium) based on transcriptomic sequences. Phylogenetic analysis identified one pair of putative orthologous proteins in Arabidopsis and chrysanthemum and six pairs of paralogous proteins in chrysanthemum. Conserved motifs in the DOF proteins shared by Arabidopsis and chrysanthemum were analyzed using MEME. Bioinformatics analysis revealed that 13 CmDOFs could be targeted by 16 miRNA families. Moreover, we used 5' RLM-RACE to map the cleavage sites in CmDOF3, 15, and 21. The expression of these 20 genes in response to phytohormone treatments and abiotic stresses was characterized, and the expression patterns of six pairs of paralogous CmDOF genes were found to completely differ from one another, except for CmDOF6 and CmDOF7. This work will promote our research of the various functions of DOF gene family members in plant hormone and stress responses.

Genome-wide analysis and expression profiling of DNA-binding with one zinc finger (Dof) transcription factor family in potato

DNA-binding with one finger (Dof) domain proteins are a multigene family of plant-specific transcription factors involved in numerous aspects of plant growth and development. Here, we report a genome-wide search for Solanum tuberosum Dof (StDof) genes and their expression profiles at various developmental stages and in response to various abiotic stresses. In addition, a complete overview of Dof gene family in potato is presented, including the gene structures, chromosomal locations, cis-regulatory elements, conserved protein domains, and phylogenetic inferences. Based on the genome-wide analysis, we identified 35 full-length protein-coding StDof genes, unevenly distributed on 10 chromosomes. Phylogenetic analysis with Dof members from diverse plant species showed that StDof genes can be classified into four subgroups (StDofI, II, III, and IV). qPCR expression analysis of StDof gene transcripts showed the distinct expression patterns of StDof genes in various potato organs, and tuber developmental stages analyzed. Many StDof genes were upregulated in response to drought, salinity, and ABA treatments. Overall, the StDof gene expression pattern and the number of over-represented cis-acting elements in the promoter regions of the StDof genes indicate that most of the StDof genes have redundant functions. The detailed genomic information and expression profiles of the StDof gene homologs in the present study provide opportunities for functional analyses to unravel the genes' exact role in plant growth and development as well as in abiotic stress tolerance.

Temporal patterns of gene expression associated with tuberous root formation and development in sweetpotato (Ipomoea batatas)

BACKGROUND

The tuberous root of sweetpotato is undisputedly an important organ from agronomic and biological perspectives. Little is known regarding the regulatory networks programming tuberous root formation and development.

RESULTS

Here, as a first step toward understanding these networks, we analyzed and characterized the genome-wide transcriptional profiling and dynamics of sweetpotato root in seven distinct developmental stages using a customized microarray containing 39,724 genes. Analysis of these genes identified temporal programs of gene expression, including hundreds of transcription factor (TF) genes. We found that most genes active in roots were shared across all developmental stages, although significant quantitative changes in gene abundance were observed for 5,368 (including 435 TFs) genes. Clustering analysis of these differentially expressed genes pointed out six distinct expression patterns during root development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that genes involved in different processes were enriched at specific stages of root development. In contrast with the large number of shared expressed genes in root development, each stage or period of root development has only a small number of specific genes. In total, 712 (including 27 TFs) and 1,840 (including 115 TFs) genes were identified as root-stage and root-period specific, respectively at the level of microarray. Several of the specific TF genes are known regulators of root development, including DA1-related protein, SHORT-ROOT and BEL1-like. The remaining TFs with unknown roles would also play critical regulatory roles during sweetpotato tuberous root formation and development.

CONCLUSIONS

The results generated in this study provided spatiotemporal patterns of root gene expression in support of future efforts for understanding the underlying molecular mechanism that control sweetpotato yield and quality.

Insights into structural and functional diversity of Dof (DNA binding with one finger) transcription factor

The structural, functional and in-silico studies of Dof transcription factor attempted so far reveals immense opportunity to analyze the plant genomes in terms of number of Dof genes and discuss in light of the evolution. The multiple functions of Dof genes needs to explored for crop improvement. Transcription factors play a very vital role in gene regulation at transcriptional level and are being extensively studied across phylas. In recent years, sequencing of plant genomes has led to genome-wide identification and characterizations of diverse types of plant-specific transcription factor gene family providing key insights into their structural and functional diversity. The DNA binding with one finger (Dof), a class belonging to C2H2-type zinc finger family proteins, is a plant-specific transcription factor having multiple roles such as seed maturation and germination, phytohormone and light-mediated regulation and plant responses to biotic and abiotic stresses. Dof proteins are present across plant lineage, from green algae to higher angiosperm, and represent a unique class of transcription factor having bifunctional binding activities, with both DNA and proteins, to regulate the complex transcriptional machinery in plant cells. The structural and functional diversity of the Dof transcription factor family along with the bioinformatics analysis highlighting the phylogeny of Dof families is reviewed in light of its importance in plant biotechnology for crop improvement.

The role of the DNA-binding One Zinc Finger (DOF) transcription factor family in plants

The DOF (DNA-binding One Zinc Finger) family of transcription factors is involved in many fundamental processes in higher plants, including responses to light and phytohormones as well as roles in seed maturation and germination. DOF transcription factor genes are restricted in their distribution to plants, where they are in many copies in both gymnosperms and angiosperms and also present in lower plants such as the moss Physcomitrella patens and in the alga Chlamydomonas reinhardtii which possesses a single DOF gene. DOF transcription factors bind to their promoter targets at the consensus sequence AAAG. This binding depends upon the presence of the highly conserved DOF domain in the protein. Depending on the target gene, DOF factor binding may activate or repress transcription. DOF factors are expressed in most if not all tissues of higher plants, but frequently appear to be functionally redundant. Recent next-generation sequencing data provide a more comprehensive survey of the distribution of DOF sequence classes among plant species and within tissue types, and clues as to the evolution of functions assumed by this transcription factor family. DOFs do not appear to be implicated in the initial differentiation of the plant body plan into organs via the resolution of meristematic zones, in contrast to MADS-box and homeobox transcription factors, which are found in other non-plant eukaryotes, and this may reflect a more recent evolutionary origin.

Transcriptome analysis reveals novel genes potentially involved in photoperiodic tuberization in potato

Potato microtuber produced in vitro provides a model system to investigate photoperiod-dependent tuberization. However, the genes associated with potato tuberization remain to be elucidated. The present research involved three potato clones with distinct tuberization response to changes of photoperiod. Digital Gene Expression (DGE) Tag Profiling analysis of the short-day-sensitive clone identified 2218 genes that were regulated by day length. Both GO and KEGG pathway analysis provided insights into predominant biological processes and pathways, and enabled the selection of 56 genes associated with circadian rhythmicity, signal transduction, and development. Quantitative transcriptional analysis in the selected clones revealed 5 genes potentially associated with photoperiodic tuberization, which were predicted to encode a DOF protein, a blue light receptor, a lectin, a syntaxin-like protein, and a protein with unknown function. Our results strongly suggest that potato tuberization may be largely controlled by the homologs of genes shown to regulate flowering time in other plants.

T-type Ca²⁺ channels regulate the exit of cardiac myocytes from the cell cycle after birth

T-type Ca(2+) channels (TTCCs) are expressed in the fetal heart and then disappear from ventricular myocytes after birth. The hypothesis examined in this study was the α1G TTCCs' influence in myocyte maturation and their rapid withdrawal from the cell cycle after birth.

METHODS

Cardiac myocytes were isolated from neonatal and adult wild type (WT), α1G-/- and α1G over expressing (α1GDT) mice. Bromodeoxyuridine (BrdU) uptake, myocyte nucleation, cell cycle analysis, and T-type Ca(2+) currents were measured.

RESULTS

All myocytes were mono-nucleated at birth and 35% of WT myocytes expressed functional TTCCs. Very few neonatal myocytes had functional TTCCs in α1G-/- hearts. By the end of the first week after birth no WT or α1G-/- had functional TTCCs. During the first week after birth about 25% of WT myocytes were BrdU+ and became bi-nucleated. Significantly fewer α1G-/- myocytes became bi-nucleated and fewer of these myocytes were BrdU+. Neonatal α1G-/- myocytes were also smaller than WT. Adult WT and α1G-/- hearts were similar in size, but α1G-/- myocytes were smaller and a greater % were mono-nucleated. α1G over expressing hearts were smaller than WT but their myocytes were larger.

CONCLUSIONS

The studies performed show that loss of functional TTCCs is associated with bi-nucleation and myocyte withdrawal from the cell cycle. Loss of α1G TTCCs slowed the transition from mono- to bi-nucleation and resulted in an adult heart with a greater number of small cardiac myocytes. These results suggest that TTCCs are involved in the regulation of myocyte size and the exit of myocytes from the cell cycle during the first week after birth.

Genome-wide analysis of plant-specific Dof transcription factor family in tomato

The Dof (DNA binding with One Finger) family encoding single zinc finger proteins has been known as a family of plant-specific transcription factors. These transcription factors are involved in a variety of functions of importance for different biological processes in plants. In the current study, we identified 34 Dof family genes in tomato, distributed on 11 chromosomes. A complete overview of SlDof genes in tomato is presented, including the gene structures, chromosome locations, phylogeny, protein motifs and evolution pattern. Phylogenetic analysis of 34 SlDof proteins resulted in four classes constituting six clusters. In addition, a comparative analysis between these genes in tomato, Arabidopsis and rice was also performed. The tomato Dof family expansion has been dated to recent duplication events, and segmental duplication is predominant for the SlDof genes. Furthermore, the SlDof genes displayed differential expression either in their transcript abundance or in their expression patterns under normal growth conditions. This is the first step towards genome-wide analyses of the Dof genes in tomato. Our study provides a very useful reference for cloning and functional analysis of the members of this gene family in tomato and other species.

Genome-wide identification, characterization and expression analysis of populus leucine-rich repeat receptor-like protein kinase genes

Background

Leucine-rich repeat receptor-like kinases (LRR-RLKs) comprise the largest group within the receptor-like kinase (RLK) superfamily in plants. This gene family plays critical and diverse roles in plant growth, development and stress response. Although the LRR-RLK families in Arabidopsis and rice have been previously analyzed, no comprehensive studies have been performed on this gene family in tree species.

Results

In this work, 379 LRR-RLK genes were retrieved from the Populus trichocarpa genome and further grouped into 14 subfamilies based on their structural and sequence similarities. Approximately 82% (312 out of 379) of the PtLRR-RLK genes are located in segmental duplication blocks indicating the role of duplication process in the expansion of this gene family. The conservation and variation in motif composition and intron/exon arrangement among PtLRR-RLK subfamilies were analyzed to provide additional support for their phylogenetic relationship and more importantly to indicate the potential divergence in their functions. Expression profiling of PtLRR-RLKs showed that they were differentially expressed in different organs and tissues and some PtLRR-RLKs were specifically expressed in meristem tissues, which indicated their potential involvement in tissue development and differentiation. For most AtLRR-RLKs with defined functions, Populus homologues exhibiting similar expression patterns could be identified, which might indicate the functional conservation during evolution. Among 12 types of environmental cues analyzed by the genome-wide microarray data, PtLRR-RLKs showed specific responses to shoot organogenesis, wounding, low ammonium feeding, hypoxia and seasonal dormancy, but not to drought, re-watering after drought, flooding, AlCl₃ treatment and bacteria or fungi treatments.

Conclusions

This study provides the first comprehensive genomic analysis of the Populus LRR-RLK gene family. Segmental duplication contributes significantly to the expansion of this gene family. Populus and Arabidopsis LRR-RLK homologues not only share similar genetic structures but also exhibit comparable expression patterns which point to the possible functional conservation of these LRR-RLKs in two model systems. Transcriptome profiling provides the first insight into the functional divergence among PtLRR-RLK gene subfamilies and suggests that they might take important roles in growth and adaptation of tree species.

The transcription factor AtDOF4.2 regulates shoot branching and seed coat formation in Arabidopsis

Plant-specific DOF (DNA-binding with one finger)-type transcription factors regulate various biological processes. In the present study we characterized a silique-abundant gene AtDOF (Arabidopsis thaliana DOF) 4.2 for its functions in Arabidopsis. AtDOF4.2 is localized in the nuclear region and has transcriptional activation activity in both yeast and plant protoplast assays. The T-M-D motif in AtDOF4.2 is essential for its activation. AtDOF4.2-overexpressing plants exhibit an increased branching phenotype and mutation of the T-M-D motif in AtDOF4.2 significantly reduces branching in transgenic plants. AtDOF4.2 may achieve this function through the up-regulation of three branching-related genes, AtSTM (A. thaliana SHOOT MERISTEMLESS), AtTFL1 (A. thaliana TERMINAL FLOWER1) and AtCYP83B1 (A. thaliana CYTOCHROME P450 83B1). The seeds of an AtDOF4.2-overexpressing plant show a collapse-like morphology in the epidermal cells of the seed coat. The mucilage contents and the concentration and composition of mucilage monosaccharides are significantly changed in the seed coat of transgenic plants. AtDOF4.2 may exert its effects on the seed epidermis through the direct binding and activation of the cell wall loosening-related gene AtEXPA9 (A. thaliana EXPANSIN-A9). The dof4.2 mutant did not exhibit changes in branching or its seed coat; however, the silique length and seed yield were increased. AtDOF4.4, which is a close homologue of AtDOF4.2, also promotes shoot branching and affects silique size and seed yield. Manipulation of these genes should have a practical use in the improvement of agronomic traits in important crops.

The plant-specific dof transcription factors family: new players involved in vascular system development and functioning in Arabidopsis

In higher plants phloem and xylem are responsible for long-distance transport of water, nutrients, and signals that act systemically at short or long-distance to coordinate developmental processes. The formation of the plant vascular system is a complex process that integrates signaling events and gene regulation at transcriptional and posttranscriptional levels. Thanks to transcriptomic and proteomic analysis we start to better understand the mechanisms underlying the formation and the functioning of the vascular system. The role of the DNA-binding with one finger (Dof TFs), a group of plant-specific transcription factors, recently emerged as part of the transcriptional regulatory networks acting on the formation and functioning of the vascular tissues. More than half of the members of this TF family are expressed in the vascular system. In addition some of them have been proposed to be mobile proteins, suggesting a possible role in the control of short- or long-distance signaling as well. This review summarizes the current knowledge on Dof TFs family in Arabidopsis with a special focus on their role in vascular development and functioning.