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Plant cell development is an asynchronous process that is governed by multiple layers of gene regulation. However, the correlation between transcriptome and chromatin regulatory events in an allotetraploid species at the single-cell resolution has not been widely studied. Herein, we employed fluorescence-activated nuclei sorting to isolate single nuclei and simultaneously investigate the transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same leaf single-cell of Arachis hypogaea. A total of 5,930 cells with 10,793 expressed genes were classified into 17 cell-clusters and 5,315 chromatin fragments were enriched to target 26,083 genes in the snATAC-seq landscape. The developmental trajectory revealed a conserved ethylene-AP2 module in leaf cell differentiation and provided novel insight for mesophyll and vascular cell development. Additionally, dual-omics described the epidermal progenitor cell development trajectory, primordium and palisade cells were able to convert into spongy cells, and bundle sheath cells developed earlier than other vascular-cells. Further cell-cycle analysis demonstrated that cytokinin biosynthesis promotes mesophyll cell genome replication and lipid pathway participates in guard cell development. snRNA-seq identified that the AT-hook transcription factor AhAHL11promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 displaying contrasting results by repressing leaf development via the jasmonic acid pathway in ectopically expressed Arabidopsis. Conclusively, our study demonstrates that snRNA-seq combined with snATAC-seq is an effective platform for exploring the association between chromatin regulatory events and transcriptional activity across diverse cell types in peanut leaves. The broad application of this approach will enable significant advances in the functional research of tissue growth and development in plant species. Plant cell development is an asynchronous process that is governed by multiple layers of gene regulation. However, the correlation between transcriptome and chromatin regulatory events in an allotetraploid species at the single-cell resolution has not been widely studied. Herein, we employed fluorescence-activated nuclei sorting to isolate single nuclei and simultaneously investigate the transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same leaf single-cell of peanut. Totally 5,930 cells with 10,793 expressed genes were classified into 17 cell-clusters and 5,315 chromatin fragments were enriched to target 26,083 genes in the snATAC-seq landscape. Developmental trajectory revealed a conserved ethylene-AP2 module in leaf cell differentiation and provided novel insights for mesophyll and vascular cells development. Further ell-cycle demonstrated that cytokinin promotes mesophyll-cell genome replication and lipid pathway participates in guard cell development. snRNA-seq identified AhAHL11 promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 repressing leaf development via jasmonic acid pathway. Conclusively, snRNA-seq combined with snATAC-seq is an effective platform for exploring the association between chromatin regulatory events and transcriptional activity across diverse cell-types. The broad application of this approach will enable significant advances in the functional research of tissue growth and development in plant species.

Summary Single‐cell RNA‐seq (scRNA‐seq) has been highlighted as a powerful tool for the description of human cell transcriptome, but the technology has not been broadly applied in plant cells. Herein, we describe the successful development of a robust protoplast cell isolation system in the peanut leaf. A total of 6,815 single cells were divided into eight cell clusters based on reported marker genes by applying scRNA‐seq. Further, a pseudo‐time analysis was used to describe the developmental trajectory and interaction network of transcription factors (TFs) of distinct cell types during leaf growth. The trajectory enabled re‐investigation of the primordium‐driven development processes of the mesophyll and epidermis. These results suggest that palisade cells likely differentiate into spongy cells, while the epidermal cells originated earlier than the primordium. Subsequently, the developed method integrated multiple technologies to efficiently validate the scRNA‐seq result in a homogenous cell population. The expression levels of several TFs were strongly correlated with epidermal ontogeny in accordance with obtained scRNA‐seq values. Additionally, peanut AHL23 (AT‐HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 23), which is localized in nucleus, promoted leaf growth when ectopically expressed in Arabidopsis by modulating the phytohormone pathway. Together, our study displays that application of scRNA‐seq can provide new hypotheses regarding cell differentiation in the leaf blade of Arachis hypogaea. We believe that this approach will enable significant advances in the functional study of leaf blade cells in the allotetraploid peanut and other plant species.

Plant cell proliferation associated with multiple layers of gene regulation, including modulation of transcriptome by changes in chromatin accessibility. However, cell proliferation is an asynchronous process precluding a temporal understanding of regulatory events leading to single-cell fate commitment. Here, a robust single nucleus RNA sequencing approach, where single nucleus employed for simultaneous investigation of transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same single-cell of Arachis hypogaea leaves. A total of 5,930 leaf cells with 10,793 expressed genes were used to construct development trajectory and characterized large-scale critical differentially expressed genes (DEGs). Additionally, uncovered extending insights of chromatin opening guided 5,315 DEGs expression involved biological pathway determines differentiation direction in distinct cell-types. But obtained members in each cell-clusters not exhibits obvious difference in distinct cell-cycling regulated genome duplication phases. Furthermore, snRNA-seq identified AT-hook transcription factor AhAHL11 promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 displays contrasting results to repress the leaf development by jasmonic acid pathway in ectopically expressed Arabidopsis. We concluded that, snRNA-seq combined with snATAC-seq is an extensible platform to explore association between the chromatin regulatory events and gene expression across diversity cell-types in peanut leaf, broadly application of this approach will enable significant advances in the functional research of tissues ontology in plant species.

Peanut pods develop underground, which is the most salient characteristic in peanut. However, its developmental transcriptome remains largely unknown. In the present study, we sequenced over one billion transcripts to explore the developmental transcriptome of peanut pod using Illumina sequencing. Moreover, we identified and quantified the abundances of 165,689 transcripts in seed and shell tissues along with a pod developmental gradient. The dynamic changes of differentially expressed transcripts (DETs) were described in seed and shell. Additionally, we found that photosynthetic genes were not only pronouncedly enriched in aerial pod, but also played roles in developing pod under dark condition. Genes functioning in photomorphogenesis showed distinct expression profiles along subterranean pod development. Clustering analysis unraveled a dynamic transcriptome, in which transcripts for DNA synthesis and cell division during pod expansion were transitioning to transcripts for cell expansion and storage activity during seed filling. Collectively, our study formed a transcriptional baseline for peanut fruit development under dark condition.

This paper proposes a robust control design based on a new switched robust integral sliding mode (SRISM) for switched systems with unmatched uncertainties. The SRISM is a sliding surface consisting of multiple sliding modes of subsystems and is robust with respect to the structural decomposed unmatched uncertainties. Each sliding mode of the subsystem can suppress the unmatched uncertainties. Their parameters are given by the conditions of linear matrix inequalities (LMIs), and their reachabilities are guaranteed by the sliding mode controllers. Finally, numerical and application simulation results for an inverted pendulum swing-up control are provided to illustrate the validity of the robust control design.

A new rate-dependent hysteresis model and a nonsmooth Kalman filtering are proposed for the state estimation of the rate-dependent hysteresis in piezoceramic actuators disturbed by stochastic noise. In the modeling scheme, a sandwich model with rate-dependent hysteresis consists of both input and output linear subsystem. Firstly, according to the properties of this complex nonlinear system, a non-smooth stochastic state-space model is introduced. Then, an auto-switcher filter is introduced to solve the state estimation of the rate-dependent hysteresis. The filter can be switched automatically according to the operating conditions. Moreover, the convergence of the proposed novel filter method is studied. Finally, the simulation result shows that the rate-dependent hysteresis model is used to describe the properties of piezoelectric actuators more accurate than the static hysteresis model when the frequency of input voltage is increasing, and the estimation errors of the non-smooth filter can converge close to zero quickly.

This paper investigates the problem of adaptive synchronization for discrete-time complex dynamical networks with random delays. In such complex systems, there occurs two kinds of nonidentical probability delays, i.e. self-feedback delays and coupling delays, and these delays are assumed to take values in a given finite sets with probability distributions. By means of the Lyapunov theory, discrete-time Jensen inequality and reciprocal convex combination approach, several delay-probability-distribution-dependent conditions are derived in the linear matrix inequality (LMI) format such that the discrete-time complex dynamical networks with random delays are globally synchronization in mean square. In addition, we use Watts–Strogatz (WS) random complex networks and regular Rulkov networks as two numerical examples to illustrate the effectiveness of our theoretical analysis.

Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.

High oleic acid (OA) peanut seeds (PS) can be beneficial for human health. However, chemical variations in high-OA PS after domestic cooking are not fully understood. In order to investigate the impact of different cooking methods on the chemical profile of high-OA PS, widely established metabolomics approach was employed to identify the relative contents of PS metabolites. Herein, 630 metabolites within 27 categories were characterized in PS, of which 141, 157, 402 differential metabolites were observed in each treatment group (boiling, baking, and frying) when compared to the raw seed. Accordingly, bioactive substances were maximally preserved in baked high-OA PS. Further conventional methods (HPLC-UV/GC-MS) quantified the absolute composition of amino and fatty acids, verifying the reliability of metabolomic analysis. Collectively, the understanding of the phytochemical substances in relation to the domestic cooking method established a foundation for future high-OA PS processing.

High oleic acid (OA) peanut seed (PS), contains a higher ratio of oleic acid (C18:1) compared to general PS, which is favored by consumers due to its health benefits. However, comprehensive lipid metabolite profiles of high-OA PS, once they have been processed via domestic cooking methods, have never been produced. To establish a scientific guide for the selection of the most appropriate processing method for high-OA PS, lipidomics was performed to identify 706 lipid metabolites in high-OA PS following boiling, baking and frying, between the three groups, 75, 175 and 242 lipid metabolites were differentially expressed respectively. Additionally, 46 glycerolipids with C18:1 molecular were observed in the lipid profiles of the treatment groups compared to the raw sample. Further evaluation of seven lipid peroxides and six antioxidant status of each testing group suggested that boiled PS retained the highest levels of lipids and antioxidant activity. Following these findings, boiling appears to be an appropriate processing method when attempting to conserve the beneficial substances found in the PS. Finally, the levels of major free fatty acids present in high-OA PS, were jointly quantified by conventional methods (GC-MS) and lipidomic analysis. FA/C16:0 levels were similar, FA/C18:0, FA/C18:1 displayed opposite results, FA/C18:2 levels increased following frying and FA/C18:3 levels were down regulated once the PS was boiled. This indicates that GC-MS is a potential method of validation for the results of lipidomic analysis. Conclusively, this in depth understanding of lipid content in relation to domestic cooking methods has provided a foundation for the processing of high-OA peanut products.

Background Many large-effect quantitative trait loci (QTLs) for yield and disease resistance related traits have been identified in different mapping populations of peanut (Arachis hypogaea L.) under multiple environments. However, only a limited number of QTLs have been used in marker-assisted selection (MAS) because of unfavorable epistatic interactions between QTLs in different genetic backgrounds. Thus, it is essential to identify consensus QTLs across different environments and genetic backgrounds for use in MAS. Here, we used QTL meta-analysis to identify a set of consensus QTLs for yield and disease resistance related traits in peanut. Results A new integrated consensus genetic map with 5874 loci was constructed. The map comprised 20 linkage groups (LGs) and was up to a total length of 2918.62 cM with average marker density of 2.01 loci per centimorgan (cM). A total of 292 initial QTLs were projected on the new consensus map, and 40 meta-QTLs (MQTLs) for yield and disease resistance related traits were detected on four LGs. The genetic intervals of these consensus MQTLs varied from 0.20 cM to 7.4 cM, which is narrower than the genetic intervals of the initial QTLs, meaning they may be suitable for use in MAS. Importantly, a region of the map that previously co-localized multiple major QTLs for pod traits was narrowed from 3.7 cM to 0.7 cM using an overlap region of four MQTLs for yield related traits on LG A05, which corresponds to a physical region of about 630.3 kb on the A05 pseudomolecule of peanut, including 38 annotated candidate genes (54 transcripts) related to catalytic activity and metabolic process. Additionally, one major MQTL for late leaf spot (LLS) was identified in a region of about 0.38 cM. BLAST searches identified 26 candidate genes (30 different transcripts) in this region, some of which were annotated as related to regulation of disease resistance in different plant species. Conclusions Combined with the high-density marker consensus map, all the detected MQTLs could be useful in MAS. The biological functions of the 64 candidate genes should be validated to unravel the molecular mechanisms of yield and disease resistance in peanut. Electronic supplementary material The online version of this article (10.1186/s12864-018-5288-3) contains supplementary material, which is available to authorized users.

In order to obtain more valuable insights into the protein dynamics and accumulation of allergens in seeds during underground development, we performed a proteomic study on developing peanut seeds at seven different stages. A total of 264 proteins with altered abundance and contained at least one unique peptide was detected by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS). All identified proteins were classified into five functional categories as level 1 and 20 secondary functional categories as level 2. Among them, 88 identified proteins (IPs) were related to carbohydrate/ amino acid/ lipid transport and metabolism, indicating that carbohydrate/amino acid/ lipid metabolism played a key role in the underground development of peanut seeds. Hierarchical cluster analysis showed that all IPs could be classified into eight cluster groups according to the abundance profiles, suggesting that the modulatory patterns of these identified proteins were complicated during seed development. The largest group contained 41 IPs, the expression of which decreased at R 2 and reached a maximum at R3 but gradually decreased from R4. A total of 14 IPs were identified as allergen-like proteins by BLAST with A genome (Arachis duranensis) or B genome (Arachis ipaensis) translated allergen sequences. Abundance profile analysis of 14 identified allergens showed that the expression of all allergen proteins was low or undetectable by 2-DE at the early stages (R1 to R4), and began to accumulate from the R5 stage and gradually increased. Network analysis showed that most of the significant proteins were involved in active metabolic pathways in early development. Real time RT-PCR analysis revealed that transcriptional regulation was approximately consistent with expression at the protein level for 8 selected identified proteins. In addition, some amino acid sequences that may be associated with new allergens were also discussed.

Peanut (Arachis hypogaea L.) is a staple crop in semiarid tropical and subtropical regions. Although the genome of peanut has been fully sequenced, the current gene annotations are still incomplete...

Modern peanut contains fatty acid desaturase 2 (FAD2) mutation, which is capable of producing high oleic acid for human health. However, the dynamic changes of the lipidome regarding fad2 remain elusive in peanut seed. In the present study, 547 lipid features were identified in high- and normal-oleic peanut seeds by utilizing the mass spectrometric approach. The fad2-induced differently expressed lipids (DELs) were polarly distributed at early and maturation stages during high-oleic acid (OA) seed development. Subsequently, integration of previously published proteomic data and lipidomic data revealed that 21 proteins and 149 DELs were annotated into the triacylglycerol assembly map, of which nine enzymes and 31 lipid species shared similar variation tendencies. Additionally, the variation tendencies of 17 acyl fatty acids were described in a hypothetical biosynthetic pathway. Collectively, the understanding of the lipid composition correlated with fad2 established a foundation for future high-OA peanut breeding based on lipidomic data.

Background Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely distributed across the entire plant genome and can be used to develop SSR markers, which can then be used to conduct genetic analyses and molecular breeding. Cultivated peanut (A. hypogaea L.), an important oil crop worldwide, is an allotetraploid (AABB, 2n = 4× = 40) plant species. Because of its complex genome, genomic marker development has been very challenging. However, sequencing of cultivated peanut genome allowed us to develop genomic markers and construct a high-density physical map. Results A total of 8,329,496 SSRs were identified, including 3,772,653, 4,414,961, and 141,882 SSRs that were distributed in subgenome A, B, and nine scaffolds, respectively. Based on the flanking sequences of the identified SSRs, a total of 973,984 newly developed SSR markers were developed in subgenome A (462,267), B (489,394), and nine scaffolds (22,323), with an average density of 392.45 markers per Mb. In silico PCR evaluation showed that an average of 88.32% of the SSR markers generated only one in silico-specific product in two tetraploid A. hypogaea varieties, Tifrunner and Shitouqi. A total of 39,599 common SSR markers were identified among the two A. hypogaea varieties and two progenitors, A. duranensis and A. ipaensis. Additionally, an amplification effectiveness of 44.15% was observed by real PCR validation. Moreover, a total of 1276 public SSR loci were integrated with the newly developed SSR markers. Finally, a previously known leaf spot quantitative trait locus (QTL), qLLS_T13_A05_7, was determined to be in a 1.448-Mb region on chromosome A05. In this region, a total of 819 newly developed SSR markers were located and 108 candidate genes were detected. Conclusions The availability of these newly developed and public SSR markers both provide a large number of molecular markers that could potentially be used to enhance the process of trait genetic analyses and improve molecular breeding strategies for cultivated peanut.

A first creation of high oleic acid peanut varieties by using transcription activator-like effecter nucleases (TALENs) mediated targeted mutagenesis of Fatty Acid Desaturase 2 (FAD2). Transcription activator like effector nucleases (TALENs), which allow the precise editing of DNA, have already been developed and applied for genome engineering in diverse organisms. However, they are scarcely used in higher plant study and crop improvement, especially in allopolyploid plants. In the present study, we aimed to create targeted mutagenesis by TALENs in peanut. Targeted mutations in the conserved coding sequence of Arachis hypogaea fatty acid desaturase 2 (AhFAD2) were created by TALENs. Genetic stability of AhFAD2 mutations was identified by DNA sequencing in up to 9.52 and 4.11% of the regeneration plants at two different targeted sites, respectively. Mutation frequencies among AhFAD2 mutant lines were significantly correlated to oleic acid accumulation. Genetically, stable individuals of positive mutant lines displayed a 0.5-2 fold increase in the oleic acid content compared with non-transgenic controls. This finding suggested that TALEN-mediated targeted mutagenesis could increase the oleic acid content in edible peanut oil. Furthermore, this was the first report on peanut genome editing event, and the obtained high oleic mutants could serve for peanut breeding project.

Peanut sprouts (PSs) are edible food with a high nutritional value. It is well known that different light treatments during seedling germination affect the nutritional elements of PSs. However, the comprehensive exploration of the chemical profile variation after light and dark treatments is not widely used in PSs due to the lack of high-throughout examination technology. In the present study, a widely targeted method based on UHPLC-QTRAP-MS/MS equipment was carried out to identify and screen differential metabolites. A total of 797 metabolites were identified from PSs, and 97 differential metabolites were screened between light and dark treatment groups. The majority of phytochemical compounds, such as flavonoids, alkaloids, nucleotides, amino acids, saccharides, and alcohols, were significantly up-regulated in PSs germinated under the dark conditions, which were positively related to the large-scale metabolic data of human diseases by KEGG metabolic pathway analysis. Collectively, our data suggest that the seeds should be protected from exposure to light during PS germination, which might improve the nutritional value of the final peanut product.

In this paper, a nonsmooth Kalman filtering method is proposed for noise suppression of micropositioning stages with piezoelectric actuators described by the so-called sandwich model with hysteresis. According to the characteristics of the system, a nonsmooth stochastic state-space equation is constructed. In this model, an autoswitcher is introduced to adapt the nonsmooth operation conditions. Then, the convergence of the novel Kalman filter is discussed. Subsequently, the comparison in simulation between the proposed filtering scheme with the unscented Kalman filter and particle filter is presented. Finally, the experimental results on a micropositioning stage with piezoelectric actuator are illustrated.

Peanuts with high oleic acid content are usually considered to be beneficial for human health and edible oil storage. In breeding practice, peanut lines with high monounsaturated fatty acids are selected using fatty acid desaturase 2 (FAD2), which is responsible for the conversion of oleic acid (C18:1) to linoleic acid (C18:2). Here, comparative transcriptomics were used to analyze the global gene expression profile of high- and normal-oleic peanut cultivars at six time points during seed development. First, the mutant type of FAD2 was determined in the high-oleic peanut (H176). The result suggested that early translation termination occurred simultaneously in the coding sequence of FAD2-A and FAD2-B, and the cultivar H176 is capable of utilizing a potential germplasm resource for future high-oleic peanut breeding. Furthermore, transcriptomic analysis identified 74 differentially expressed genes (DEGs) involved in lipid metabolism in high-oleic peanut seed, of which five DEGs encoded the fatty acid desaturase. Aradu.XM2MR belonged to the homologous gene of stearoyl-ACP (acyl carrier protein) desaturase 2 (SAD2) that converted the C18:0 into C18:1. Further subcellular localization studies indicated that FAD2 was located at the endoplasmic reticulum (ER), and Aradu.XM2MR was targeted to the plastid in Arabidopsis protoplast cells. To examine the dynamic mechanism of this finding, we focused on the peroxidase (POD)-mediated fatty acid (FA) degradation pathway. The fad2 mutant significantly increased the POD activity and H2O2 concentration at the early stage of seed development, implying that redox signaling likely acted as a messenger to connect the signaling transduction between the high-oleic content and Aradu.XM2MR transcription level. Taken together, transcriptome analysis revealed the feedback mechanism of SAD2 (Aradu.XM2MR) associated with FAD2 mutation during the seed developmental stage, which could provide a potential peanut breeding strategy based on identified candidate genes to improve the content of oleic acid.

Additional file 2: Figure S1. Chromosome-wide distribution of SSRs in A. hypogaea cv. Fuhuasheng genome. Figure S2. Number of SSR repeat motifs. Figure S3. Abundance of the top 30 different types of SSR motifs. Figure S4. Number (A) and percentage (B) of different types of SSR markers. Figure S5. Summary of SSR types of the developed SSR markers. Figure S6. Product size of 188 SSR markers tested by PCR amplification. Figure S7. Number of loci in the public SSR markers as determined by e-PCR remapping. Figure S8. Comparison of known QTLs in genetic and physical maps.

Smoothed Gehan rank estimation methods are widely used in accelerated failure time (AFT) models with/without clusters. However, most methods are sensitive to outliers in the covariates. In order to solve this problem, we propose robust approaches based on the smoothed Gehan rank estimation methods for the AFT model, allowing for clusters by employing two different weight functions. Simulation studies show that the proposed methods outperform existing smoothed rank estimation methods regarding their biases and standard deviations when there are outliers in the covariates. The proposed methods are also applied to a real data set from the “Major cardiovascular interventions" study.

Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45–56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis. For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.

A characteristic feature of peanut is the subterranean fructification, geocarpy, in which the gynophore ('peg'), a specialized organ that transitions from upward growth habit to downward outgrowth upon fertilization, drives the developing pod into the soil for subsequent development underground. As a step towards understanding this phenomenon, we explore the developmental dynamics of the peanut pod transcriptome at 11 successive stages. We identified 110 217 transcripts across developmental stages and quantified their abundance along a pod developmental gradient in pod wall. We found that the majority of transcripts were differentially expressed along the developmental gradient as well as identified temporal programs of gene expression, including hundreds of transcription factors. Thought to be an adaptation to particularly harsh subterranean environments, both up- and down-regulated gene sets in pod wall were enriched for response to a broad array of stimuli, like gravity, light and subterranean environmental factors. We also identified hundreds of transcripts associated with gravitropism and photomorphogenesis, which may be involved in the geocarpy. Collectively, this study forms a transcriptional baseline for geocarpy in peanut as well as provides a considerable body of evidence that transcriptional regulation in peanut aerial and subterranean fruits is complex.

In the original article, there was an error. The link of sequencing data was not attached in Supplementary Material section. A correction has been made to the Supplementary Material section: The genome assembly and annotation data were deposited in the DRYAD digital repository (https://datadryad.org/). All the data can be downloaded from DRYAD by searching for doi: 10.5061/dryad.hm5vs13 or by directly accessing the link: https://doi.org/10.5061/dryad.hm5vs13. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.

Peanuts (Arachis hypogaea L.) are an important oilseed crop, containing high contents of protein and fatty acids (FA). The major components of FA found in peanut oil are unsaturated FAs, including oleic acid (OA, C18:1) and linoleic acid (LOA, C18:2). Moreover, the high content of OA in peanut oil is beneficial for human health and long-term storage due to its antioxidant activity. However, the dynamic changes in proteomics related to OA accumulation during seed development still remain largely unexplored. In the present study, a comparative proteome analysis based on iTRAQ (isobaric Tags for Relative and Absolute Quantification) was performed to identify the critical candidate factors involved in OA formation. A total of 389 differentially expressed proteins (DEPs) were identified between high-oleate cultivar Kainong176 and low-oleate cultivar Kainong70. Among these DEPs, 201 and 188 proteins were upregulated and downregulated, respectively. In addition, these DEPs were categorized into biosynthesis pathways of unsaturated FAs at the early stage during the high-oleic peanut seed development, and several DEPs involved in lipid oxidation pathway were found at the stage of seed maturation. Meanwhile, 28 DEPs were sporadically distributed in distinct stages of seed formation, and their molecular functions were directly correlated to FA biosynthesis and degradation. Fortunately, the expression of FAB2 (stearoyl-acyl carrier protein desaturase), the rate-limiting enzyme in the upstream biosynthesis process of OA, was significantly increased in the early stage and then decreased in the late stage of seed development in the high-oleate cultivar Kainong176. Furthermore, real-time PCR verified the expression pattern of FAB2 at the mRNA level, which was consistent with its protein abundance. However, opposite results were found for the low-oleate cultivar Kainong70. Overall, the comparative proteome analysis provided valuable insight into the molecular dynamics of OA accumulation during peanut seed development.

Peanuts (Arachis hypogaea L.) are an important oilseed crop, containing high contents of protein and fatty acids (FA). The major components of FA found in peanut oil are unsaturated FAs, including oleic acid (OA, C18:1) and linoleic acid (LOA, C18:2). Moreover, the high content of OA in peanut oil is beneficial for human health and long-term storage due to its antioxidant activity. However, the dynamic changes in proteomics related to OA accumulation during seed development still remain largely unexplored. In the present study, a comparative proteome analysis based on iTRAQ (isobaric Tags for Relative and Absolute Quantification) was performed to identify the critical candidate factors involved in OA formation. A total of 389 differentially expressed proteins (DEPs) were identified between high-oleate cultivar Kainong176 and low-oleate cultivar Kainong70. Among these DEPs, 201 and 188 proteins were upregulated and downregulated, respectively. In addition, these DEPs were categorized into biosynthesis pathways of unsaturated FAs at the early stage during the high-oleic peanut seed development, and several DEPs involved in lipid oxidation pathway were found at the stage of seed maturation. Meanwhile, 28 DEPs were sporadically distributed in distinct stages of seed formation, and their molecular functions were directly correlated to FA biosynthesis and degradation. Fortunately, the expression of FAB2 (stearoyl-acyl carrier protein desaturase), the rate-limiting enzyme in the upstream biosynthesis process of OA, was significantly increased in the early stage and then decreased in the late stage of seed development in the high-oleate cultivar Kainong176. Furthermore, real-time PCR verified the expression pattern of FAB2 at the mRNA level, which was consistent with its protein abundance. However, opposite results were found for the low-oleate cultivar Kainong70. Overall, the comparative proteome analysis provided valuable insight into the molecular dynamics of OA accumulation during peanut seed development.

Peanut (Arachis hypogaea L.), an important leguminous crop, is widely cultivated in tropical and subtropical regions. Peanut is an allotetraploid, having A and B subgenomes that maybe have originated in its diploid progenitors Arachis duranensis (A-genome) and Arachis ipaensis (B-genome), respectively. We previously sequenced the former and here present the draft genome of the latter, expanding our knowledge of the unique biology of Arachis. The assembled genome of A. ipaensis is ~1.39 Gb with 39,704 predicted protein-encoding genes. A gene family analysis revealed that the FAR1 family may be involved in regulating peanut special fruit development. Genomic evolutionary analyses estimated that the two progenitors diverged ~3.3 million years ago and suggested that A. ipaensis experienced a whole-genome duplication event after the divergence of Glycine max. We identified a set of disease resistance-related genes and candidate genes for biological nitrogen fixation. In particular, two and four homologous genes that may be involved in the regulation of nodule development were obtained from A. ipaensis and A. duranensis, respectively. We outline a comprehensive network involved in drought adaptation. Additionally, we analyzed the metabolic pathways involved in oil biosynthesis and found genes related to fatty acid and triacylglycerol synthesis. Importantly, three new FAD2 homologous genes were identified from A. ipaensis and one was completely homologous at the amino acid level with FAD2 from A. hypogaea. The availability of the A. ipaensis and A. duranensis genomic assemblies will advance our knowledge of the peanut genome.

Figure S3. Enrichment analysis of gene ontology terms for the candidate genes for yield and late leaf spot. (DOCX 174â kb)

Figure S1. Distribution of all the initial QTLs on the linkage groups of the integrated consensus map. (DOCX 671â kb)

The insertion reactions of lithium silylquinolylamide dimers [{8-(2-R-C9H5N)N(Me3Si)}Li·OEt2]2 (R = H, 1a; R = Me, 1b) with dimethylcyanamide afforded dimeric lithium 8-quinolylguanidinates [{8-(2-R-C9H5N)NC(NMe2)N(SiMe3)}Li]2 (R = H, 2a; R = Me, 2b) with a cisoid arrangement of the ligands. Further reaction of 2b with MCl2 (M = Co or Fe) formed the eight-membered binuclear metallic 8-quinolylguanidinate complexes [{8-(2-CH3-C9H5N)NC(NMe2)N(SiMe3)}MCl]2 (M = Fe, 3; Co, 4). The reaction of 2a with (MeC5H4)TiCl3 afforded a centrosymmetric dimeric titanium(IV) complex [{8-(C9H6N)NC(NMe2)N}Ti(MeC5H4)Cl]2 (5) via a metathesis reaction and the elimination of SiMe3Cl. The guanidinate ligand 2b was hydrolyzed with an equimolar amount of water, and reacted with (MeC5H4)TiCl3 forming a monoligated half-titanocene compound {8-(2-CH3-C9H5N)N(H)C(NMe2)N}Ti(MeC5H4)Cl2 (6). Therefore lithium silylquinolylamide dimers provided various coordinative multi-dentate ligands and resulted in a family of metal complexes.