24 results on '"Haifen Li"'
Search Results
2. Single‐cell RNA‐seq describes the transcriptome landscape and identifies critical transcription factors in the leaf blade of the allotetraploid peanut ( Arachis hypogaea L.)
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Xuanqiang Liang, Xiaoping Chen, Liping Wang, Shaoxiong Li, Puxuan Du, Haifen Li, Dongxiu Hu, Qing Lu, Yanbin Hong, Hao Liu, Haiyan Liu, and Rajeev K. Varshney
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Cell type ,Arachis ,Cellular differentiation ,genetic processes ,Population ,peanut improvement ,Plant Science ,Palisade cell ,Transcriptome ,Arabidopsis ,natural sciences ,Primordium ,RNA-Seq ,scRNA‐seq ,education ,Research Articles ,leaf cell ,education.field_of_study ,biology ,Epidermis (botany) ,Gene Expression Profiling ,fungi ,plant single‐cell ,food and beverages ,biology.organism_classification ,Cell biology ,Plant Leaves ,Agronomy and Crop Science ,leaf development ,Research Article ,Transcription Factors ,Biotechnology - Abstract
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.
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- 2021
3. Global transcriptome analysis of subterranean pod and seed in peanut (Arachis hypogaea L.) unravels the complexity of fruit development under dark condition
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Xuanqiang Liang, Hao Liu, Haiyan Liu, Shaoxiong Li, Qing Lu, Haifen Li, Yanbin Hong, Xiaoping Chen, and Rajeev K. Varshney
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0106 biological sciences ,0301 basic medicine ,Cell division ,Arachis ,Fruit development ,Plant physiology ,lcsh:Medicine ,Biology ,01 natural sciences ,Article ,Transcriptome ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Botany ,RNA, Messenger ,Photosynthesis ,lcsh:Science ,Gene ,Illumina dye sequencing ,Multidisciplinary ,Gene Expression Profiling ,lcsh:R ,food and beverages ,Darkness ,Arachis hypogaea ,Up-Regulation ,030104 developmental biology ,Point of delivery ,Phenotype ,Fruit ,Seeds ,Photomorphogenesis ,lcsh:Q ,Plant sciences ,010606 plant biology & botany - Abstract
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.
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- 2020
4. Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement
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Shaoxiong Li, Xuanqiang Liang, Zhong-Jian Liu, Xingyu Li, Fanbo Meng, Andrew H. Paterson, Haofa Lan, Rajeev K. Varshney, Zhikang Zhang, Kadambot H. M. Siddique, Yanbin Hong, Jinpeng Wang, Shanlin Yu, Guo-Qiang Zhang, Shijie Wen, Manish K. Pandey, Jiaqing Yuan, Xiaoping Chen, Haifen Li, Qing Lu, Jigao Yu, Xiyin Wang, Guiyuan Zhou, Jianan Zhang, Hao Liu, and Haiyan Liu
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0106 biological sciences ,0301 basic medicine ,Genome evolution ,Arachis ,Plant Science ,01 natural sciences ,Genome ,Arachis duranensis ,03 medical and health sciences ,Arachis ipaensis ,Lipid biosynthesis ,Molecular Biology ,Phylogeny ,Comparative genomics ,Genetics ,Whole Genome Sequencing ,biology ,Hypogaea ,food and beverages ,Sequence Analysis, DNA ,Lipid Metabolism ,biology.organism_classification ,Arachis hypogaea ,030104 developmental biology ,Peanut Oil ,Transcriptome ,Genome, Plant ,010606 plant biology & botany - Abstract
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.
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- 2019
5. Consensus map integration and QTL meta-analysis narrowed a locus for yield traits to 0.7 cM and refined a region for late leaf spot resistance traits to 0.38 cM on linkage group A05 in peanut (Arachis hypogaea L.)
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Hao Liu, Xiaoping Chen, Xingyu Li, Xuanqiang Liang, Haiyan Liu, Qing Lu, Shaoxiong Li, Haifen Li, Yanbin Hong, Guiyuan Zhou, and Shijie Wen
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0106 biological sciences ,0301 basic medicine ,Candidate gene ,Yield ,Arachis ,Late leaf spot ,lcsh:QH426-470 ,Genetic Linkage ,lcsh:Biotechnology ,Quantitative Trait Loci ,Locus (genetics) ,Quantitative trait locus ,Plant disease resistance ,01 natural sciences ,03 medical and health sciences ,Centimorgan ,Quantitative Trait, Heritable ,lcsh:TP248.13-248.65 ,Consensus Sequence ,Genetics ,Leaf spot ,Peanut (Arachis hypogaea L.) ,Genetic Association Studies ,Disease Resistance ,Plant Diseases ,biology ,fungi ,Chromosome Mapping ,food and beverages ,biology.organism_classification ,Meta-analysis ,lcsh:Genetics ,030104 developmental biology ,Epistasis ,DNA microarray ,Research Article ,010606 plant biology & botany ,Biotechnology - Abstract
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.
- Published
- 2018
6. A proteomic analysis of peanut seed at different stages of underground development to understand the changes of seed proteins
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Baojin Zhou, Hong Wu, Haiyan Liu, Yanbin Hong, Qing Lu, Xuanqiang Liang, Hao Liu, Haifen Li, Ruo Zhou, Shaoxiong Li, and Xiaoping Chen
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0106 biological sciences ,Proteomics ,Arachis ,Protein Expression ,Protein metabolism ,Plant Science ,01 natural sciences ,Biochemistry ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Allergies ,Medicine and Health Sciences ,Electrophoresis, Gel, Two-Dimensional ,Protein Interaction Maps ,Protein Metabolism ,chemistry.chemical_classification ,Regulation of gene expression ,0303 health sciences ,Multidisciplinary ,biology ,Allergic Diseases ,Plant Anatomy ,Seed Storage Proteins ,Eukaryota ,Plants ,Legumes ,Amino acid ,RNA, Plant ,Seeds ,Medicine ,Carbohydrate Metabolism ,Research Article ,Nutrient and Storage Proteins ,Science ,Immunology ,Food Allergies ,Research and Analysis Methods ,Real-Time Polymerase Chain Reaction ,Arachis duranensis ,03 medical and health sciences ,Arachis ipaensis ,Gene Expression and Vector Techniques ,Molecular Biology Techniques ,Molecular Biology ,030304 developmental biology ,Molecular Biology Assays and Analysis Techniques ,Organisms ,Biology and Life Sciences ,Proteins ,Metabolism ,Allergens ,biology.organism_classification ,Metabolic pathway ,Peanut ,chemistry ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Clinical Immunology ,Clinical Medicine ,010606 plant biology & botany - Abstract
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.
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- 2020
7. Improving Gene Annotation of the Peanut Genome by Integrated Proteogenomics Workflow
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Yanbin Hong, Xiaoping Chen, Shaohang Xu, Xuanqiang Liang, Ruo Zhou, Baojin Zhou, Qing Lu, Haifen Li, and Hao Liu
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0301 basic medicine ,Proteomics ,030102 biochemistry & molecular biology ,Arachis ,RNA-Seq ,Molecular Sequence Annotation ,General Chemistry ,Computational biology ,Gene Annotation ,Biology ,Proteogenomics ,Biochemistry ,Genome ,Arachis hypogaea ,Workflow ,03 medical and health sciences ,030104 developmental biology ,Tandem Mass Spectrometry - Abstract
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...
- Published
- 2020
8. Integrated Analysis of Comparative Lipidomics and Proteomics Reveals the Dynamic Changes of Lipid Molecular Species in High-Oleic Acid Peanut Seed
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Xuanqiang Liang, Li Deng, Baojin Zhou, Haifen Li, Xiaoping Chen, Jianzhong Gu, Li Ren, Hao Liu, Qing Lu, and Yanbin Hong
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0106 biological sciences ,Fatty Acid Desaturases ,Proteomics ,Arachis ,Biology ,medicine.disease_cause ,01 natural sciences ,Lipidomics ,medicine ,Gene ,High oleic acid ,Plant Proteins ,chemistry.chemical_classification ,Mutation ,010401 analytical chemistry ,food and beverages ,General Chemistry ,Lipidome ,Lipid Metabolism ,Lipids ,0104 chemical sciences ,Fatty acid desaturase ,Enzyme ,Biochemistry ,chemistry ,Seeds ,biology.protein ,lipids (amino acids, peptides, and proteins) ,General Agricultural and Biological Sciences ,010606 plant biology & botany ,Oleic Acid - Abstract
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.
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- 2019
9. Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.)
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Guiyuan Zhou, Xingyu Li, Haiyan Liu, Xiaoping Chen, Haofa Lan, Qing Lu, Shaoxiong Li, Yanbin Hong, Rajeev K. Varshney, Xuanqiang Liang, Huifang Jiang, Haifen Li, Jianan Zhang, Shijie Wen, and Hao Liu
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lcsh:QH426-470 ,Arachis ,lcsh:Biotechnology ,Quantitative trait locus ,Biology ,Genome ,Simple sequence repeats ,lcsh:TP248.13-248.65 ,Genetics ,Computer Simulation ,Peanut (Arachis hypogaea L.) ,Whole genome sequencing ,Molecular breeding ,Hypogaea ,food and beverages ,Genomics ,biology.organism_classification ,Arachis hypogaea ,lcsh:Genetics ,Genome sequence ,Microsatellite ,Genome, Plant ,Biotechnology ,In silico PCR ,Research Article ,Microsatellite Repeats - Abstract
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.
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- 2019
10. TALEN-mediated targeted mutagenesis of fatty acid desaturase 2 (FAD2) in peanut (Arachis hypogaea L.) promotes the accumulation of oleic acid
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Xuanqiang Liang, Qing Lu, Haifen Li, Xingyu Li, Hao Liu, Yanbin Hong, Shijie Wen, and Xiaoping Chen
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Fatty Acid Desaturases ,0301 basic medicine ,food.ingredient ,Arachis ,Mutant ,Plant Science ,Biology ,Plant Roots ,Genome engineering ,03 medical and health sciences ,chemistry.chemical_compound ,food ,Genome editing ,Transcription Activator-Like Effector Nucleases ,Genetics ,Transcription activator-like effector nuclease ,food and beverages ,General Medicine ,Oleic acid ,030104 developmental biology ,Fatty acid desaturase ,Biochemistry ,chemistry ,Mutagenesis ,Seeds ,biology.protein ,Peanut oil ,Agronomy and Crop Science ,DNA ,Oleic Acid ,Protein Binding - Abstract
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.
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- 2018
11. Widely targeted metabolomics characterizes the dynamic changes of chemical profile in postharvest peanut sprouts grown under the dark and light conditions
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Qinjian Liu, Rajeev K. Varshney, Haifen Li, Xiaoping Chen, Hao Liu, Yanbin Hong, Qing Lu, and Yuan Xiao
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chemistry.chemical_classification ,Metabolic pathway analysis ,biology ,biology.organism_classification ,Amino acid ,stomatognathic diseases ,chemistry ,Phytochemical ,Germination ,Seedling ,Postharvest ,Food science ,KEGG ,Food Science ,Targeted metabolomics - Abstract
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.
- Published
- 2021
12. Transcriptomic Analysis Reveals the High-Oleic Acid Feedback Regulating the Homologous Gene Expression of Stearoyl-ACP Desaturase 2 (SAD2) in Peanuts
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Qing Lu, Li Ren, Xiaoping Chen, Xuanqiang Liang, Haifen Li, Hao Liu, Jianzhong Gu, Yanbin Hong, and Li Deng
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Fatty Acid Desaturases ,0106 biological sciences ,0301 basic medicine ,Arachis ,Mutant ,01 natural sciences ,Mixed Function Oxygenases ,Transcriptome ,lcsh:Chemistry ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Gene expression ,lcsh:QH301-705.5 ,Phylogeny ,Spectroscopy ,chemistry.chemical_classification ,fatty acid desaturase ,food and beverages ,General Medicine ,Computer Science Applications ,Acyl carrier protein ,Biochemistry ,Seeds ,FAD2 ,lipids (amino acids, peptides, and proteins) ,SAD2 ,Genome, Plant ,Linoleic acid ,Biology ,Models, Biological ,Article ,Catalysis ,Inorganic Chemistry ,03 medical and health sciences ,Amino Acid Sequence ,Physical and Theoretical Chemistry ,Molecular Biology ,Gene Expression Profiling ,Organic Chemistry ,Fatty acid ,Lipid Metabolism ,Oleic acid ,030104 developmental biology ,Fatty acid desaturase ,chemistry ,lcsh:Biology (General) ,lcsh:QD1-999 ,oleic acid ,biology.protein ,peanut ,transcriptome ,010606 plant biology & botany - Abstract
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.
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- 2019
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13. Draft genome of the peanut A-genome progenitor ( Arachis duranensis ) provides insights into geocarpy, oil biosynthesis, and allergens
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Xiaoping Chen, Hongjie Li, Manish K. Pandey, Qingli Yang, Xiyin Wang, Vanika Garg, Haifen Li, Xiaoyuan Chi, Dadakhalandar Doddamani, Yanbin Hong, Hari Upadhyaya, Hui Guo, Aamir W. Khan, Fanghe Zhu, Xiaoyan Zhang, Lijuan Pan, Gary J. Pierce, Guiyuan Zhou, Katta A. V. S. Krishnamohan, Mingna Chen, Ni Zhong, Gaurav Agarwal, Shuanzhu Li, Annapurna Chitikineni, Guo-Qiang Zhang, Shivali Sharma, Na Chen, Haiyan Liu, Pasupuleti Janila, Shaoxiong Li, Min Wang, Tong Wang, Jie Sun, Xingyu Li, Chunyan Li, Mian Wang, Lina Yu, Shijie Wen, Sube Singh, Zhen Yang, Jinming Zhao, Chushu Zhang, Yue Yu, Jie Bi, Xiaojun Zhang, Zhong-Jian Liu, Andrew H. Paterson, Shuping Wang, Xuanqiang Liang, Rajeev K. Varshney, and Shanlin Yu
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0301 basic medicine ,Arachis ,Geocarpy ,Genome ,Arachis duranensis ,03 medical and health sciences ,Arachis ipaensis ,Botany ,Humans ,Plant Oils ,Gene family ,Gene ,Plant Proteins ,Multidisciplinary ,biology ,fungi ,food and beverages ,Biological Sciences ,biology.organism_classification ,Arachis hypogaea ,Tetraploidy ,030104 developmental biology ,Multigene Family ,Peanut Oil ,Genome, Plant - Abstract
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.
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- 2016
14. Transcriptome-wide sequencing provides insights into geocarpy in peanut (Arachis hypogaeaL.)
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Rajeev K. Varshney, Hong Wu, Shijie Wen, Ni Zhong, Xiaoyuan Chi, Xuanqiang Liang, Chen Na, Xiaoping Chen, Lijuan Pan, Heying Li, Guiyuan Zhou, Haiyan Liu, Xingyu Li, Wang Tong, Fanghe Zhu, Yanbin Hong, Shanlin Yu, Haifen Li, Yang Zhen, Mingna Chen, Wei Zhu, Shaoxiong Li, Hong Liu, Erhua Zhang, Wang Mian, and Qingli Yang
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0301 basic medicine ,Geocarpy ,Arachis ,Gravitropism ,RNA-Seq ,Plant Science ,Biology ,Transcriptome ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Botany ,Transcriptional regulation ,Gynophore ,Plant Proteins ,Sequence Analysis, RNA ,food and beverages ,Gene Ontology ,030104 developmental biology ,Point of delivery ,Evolutionary biology ,Fruit ,Seeds ,Photomorphogenesis ,Agronomy and Crop Science ,Biotechnology - Abstract
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.
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- 2015
15. Corrigendum: Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis)
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Xingyu Li, Shaoxiong Li, Yanbin Hong, Guiyuan Zhou, Guo-Qiang Zhang, Rajeev K. Varshney, Xuanqiang Liang, Hao Liu, Haifen Li, Zhong-Jian Liu, Haiyan Liu, Xiaoping Chen, Qing Lu, and Shijie Wen
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0301 basic medicine ,Whole genome sequencing ,Genome evolution ,biology ,Computer science ,genome sequence ,DRYAD ,Correction ,Sequence assembly ,Arachis ipaensis ,Computational biology ,Plant Science ,genome evolution ,lcsh:Plant culture ,biology.organism_classification ,Genome ,DNA sequencing ,03 medical and health sciences ,Annotation ,030104 developmental biology ,polyploidizations ,lcsh:SB1-1110 ,whole genome duplication - Abstract
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.
- Published
- 2018
16. Identification of the Candidate Proteins Related to Oleic Acid Accumulation during Peanut (Arachis hypogaea L.) Seed Development through Comparative Proteome Analysis
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Qing Lu, Yanbin Hong, Xiaoping Chen, Xuanqiang Liang, Li Deng, Jianzhong Gu, Hao Liu, Haifen Li, and Li Ren
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0301 basic medicine ,food.ingredient ,Linoleic acid ,Biology ,Proteomics ,Catalysis ,Inorganic Chemistry ,03 medical and health sciences ,chemistry.chemical_compound ,food ,Biosynthesis ,Lipid oxidation ,Physical and Theoretical Chemistry ,Molecular Biology ,Spectroscopy ,Organic Chemistry ,food and beverages ,General Medicine ,Computer Science Applications ,Arachis hypogaea ,Oleic acid ,030104 developmental biology ,chemistry ,Biochemistry ,Proteome ,Peanut oil ,peanut ,proteome ,oleic acid ,FAB2 ,fatty acid pathway - Abstract
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.
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- 2018
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17. Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (
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Haifen Li, Rajeev K. Varshney, Xiaoping Chen, Qing Lu, Xingyu Li, Yanbin Hong, Haiyan Liu, Shaoxiong Li, Hao Liu, Guo-Qiang Zhang, Shijie Wen, Guiyuan Zhou, Xuanqiang Liang, and Zhong-Jian Liu
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0106 biological sciences ,0301 basic medicine ,Arachis ,Genome evolution ,genome sequence ,Plant Science ,lcsh:Plant culture ,genome evolution ,01 natural sciences ,Genome ,Arachis duranensis ,03 medical and health sciences ,Arachis ipaensis ,lcsh:SB1-1110 ,Gene ,Original Research ,Genetics ,Whole genome sequencing ,biology ,food and beverages ,biology.organism_classification ,Arachis hypogaea ,030104 developmental biology ,polyploidizations ,whole genome duplication ,010606 plant biology & botany - Abstract
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.
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- 2018
18. Proteomic identification of gravitropic response genes in peanut gynophores
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Hong Wu, Wei Zhu, Fanghe Zhu, Yanbin Hong, Haifen Li, Xuanqiang Liang, Haiyan Liu, Xiaoping Chen, and Heying Li
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Proteomics ,Arachis ,Protease ,medicine.medical_treatment ,Gravitropism ,Biophysics ,food and beverages ,Biology ,Trypsin ,biology.organism_classification ,Biochemistry ,Gene expression profiling ,Transcriptome ,Plant Growth Regulators ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Proteome ,medicine ,Plant Proteins ,medicine.drug - Abstract
Peanut (Arachis hypogaea L.) is one of the most important oil-bearing crops in the world. The gravitropic response of peanut gynophores plays an essential role in peanut reproductive development. In this study, we developed an in vitro culture system and applied it to the study of peanut gynophore gravitropism. By comparing the proteomes of gynophores grown in vitro with the tip pointing upward (gravity stimulation sample) and downward (natural growth control) at 6 h and 12 h, we observed 42 and 39 with significantly altered expression pattern at 6 and 12 h, respectively. Out of these proteins, 13 proteins showed same expression profiling at both 6 h and 12 h. They were identified by MALDI-TOF/TOF and further characterized with quantitative real time RT-PCR. Among the 13 identified proteins, two were identified as class III acidic endochitinases, two were identified as Kunitz trypsin protease inhibitors, and the remaining proteins were identified as pathogenesis-related class 10 protein, Ara h 8 allergen isoform 3, voltage-dependent anion channel, gamma carbonic anhydrase 1, germin-like protein subfamily 3 member 3 precursor, chloride channel, glycine-rich RNA-binding protein and gibberellin receptor GID1. Real time RT-PCR analysis revealed that transcriptional regulation is consistent with expression at the protein level for class III acidic endochitinase, Kunitz trypsin protease inhibitor, chloride channel and pathogenesis-related class 10 protein, while the expression of the other 7 proteins might be regulated at post-transcriptional levels. This study identified several potential gravitropic response proteins in peanut gynophores and helps to understand early gravitropic responses in peanut gynophores. Biological significance The gravitropic response of the peanut gynophores plays an essential role in peanut production. However, the molecular mechanism responsible for gravitropic responses in the peanut gynophores has not been explored yet. The result generated in this study may provide in vitro culture system for gravitropism study of plant gravitropic response and novel insights into the proteome-level response and give a more comprehensive understanding of early gravitropic response in peanut gynophores. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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- 2013
19. Comparative proteomics analysis of developing peanut aerial and subterranean pods identifies pod swelling related proteins
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Fanghe Zhu, Erhua Zhang, Yanbin Hong, Xuanqiang Liang, Wei Zhu, Boshou Liao, Xiaoping Chen, Haifen Li, and Shengyi Liu
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Proteomics ,Arachis ,Light ,Proteome ,Protein catabolic process ,Biophysics ,Biology ,Biochemistry ,Gene Expression Regulation, Plant ,Botany ,Cellular metabolic process ,RNA, Messenger ,Photosynthesis ,Ovule ,Gynophore ,Plant Proteins ,Gene Expression Profiling ,food and beverages ,Darkness ,Cell biology ,Oxidative Stress ,Point of delivery ,Proteasome ,Seeds - Abstract
The peanut plant produces flowers aerially, while develops the fruits and seeds underground. Pod swelling is a vital process of peanut pod and seed development only occurring after the gynophore carrying the ovule into the soil. The failure of gynophore penetration into the soil leads to suppression of pod swelling initiation. However, the molecular mechanism underlying the process remains unknown. A comparative proteome analysis between developing aerial and subterranean pods at various developmental stages was performed using 2-DE approach. 47 significantly differentially expressed spots were selected to further identification by MALDI-TOF–TOF MS. They were corresponded to 31 distinct proteins, suggesting that many identified spots were modified in post-translation. Functional annotation revealed their involvement in twelve important biological processes, such as photosynthesis, oxidative stress response, lignin synthesis, fatty acid biosynthesis, glycolysis, protein catabolic process, cellular metabolic process, regulation process, etc. Furthermore, 10 identified proteins were validated by real-time RT-PCR analysis. Several photosynthesis and oxidative stress proteins displayed elevated expression levels in aerial pods. Otherwise, enzymes in lignin synthesis and ubiquitin proteasome system were down-accumulation in subterranean pods. These enzymes might function as potential candidate proteins and play critical roles to regulate pods swelling and development. Biological significance Pod swelling plays a crucial role in peanut fruit and seed development. However, a large number of aerial pods can't form normal pods due to suppression of swelling initiation by the failure of penetration into the soil, thereby causing to seed yield loss. Limited knowledge is available underlying molecular mechanism regulating initiation of swelling in peg tips and pod development. The results generated in this study may provide evidence for some functional proteins as potential candidates to pod swelling and new molecular insights to improve our understanding of pod development under light and darkness conditions, which may contribute valuable information to high yield breeding in future.
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- 2013
20. Overexpression of ARAhPR10, a Member of the PR10 Family, Decreases Levels of Aspergillus flavus Infection in Peanut Seeds
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Chunzheng Xie, Haifen Li, Xiaoping Chen, Xuanqiang Liang, Haiyan Liu, Shijie Wen, and Yanbin Hong
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Aflatoxin ,Agrobacterium ,Transgene ,Wild type ,food and beverages ,Aspergillus flavus ,General Medicine ,Biology ,biology.organism_classification ,Microbiology ,Arachis hypogaea ,Genotype ,Botany ,heterocyclic compounds ,Gene - Abstract
Peanut (Arachis hypogaea L.) is one of the most susceptible host crops to Aspergillus flavus invasion and subsequent aflatoxin contamination. In this report, a new member of PR10 family putative resistant gene (designated as ARAhPR10, No. EU661964.1) encoding a PR10 protein was isolated and characterized. Analysis of qRT-PCR showed that the expression of ARAhPR10 was induced by pre-harvested A. flavus infection, but no significant difference was observed between resistant genotype “GT-C20” and susceptible genotype “Yueyou 7”. Seven transgenic peanut lines expressing the ARAhPR10 gene under the control of 35S promoter were obtained using the Agrobacterium tumefaciens-mediated method. Real time RT-PCR results showed that the expression level of the ARAhPR10 was significantly higher and the A. flavus infection and aflatoxin content were significantly lower in seeds of transgenic lines than that of the wild type. A significant negative correlation between ARAhPR10 expression at transcript level and seeds aflatoxin production was observed. Combining the previous results, it is suggested that ARAhPR10 expression play an important role in peanut host resistance to A. flavus infection and aflatoxin producing.
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- 2013
21. Comparative transcriptome analysis of aerial and subterranean pods development provides insights into seed abortion in peanut
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Haifen Li, Fanghe Zhu, Yanbin Hong, Xiaoping Chen, Xuanqiang Liang, Rajeev K. Varshney, and Wei Zhu
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Candidate gene ,Microarray ,Arachis ,Aerial pod ,Plant Science ,Biology ,Development ,Article ,Transcriptome ,Auxin ,Gene Expression Regulation, Plant ,Botany ,Genetics ,Cluster Analysis ,Gene ,Oligonucleotide Array Sequence Analysis ,Regulation of gene expression ,chemistry.chemical_classification ,fungi ,Plant physiology ,food and beverages ,General Medicine ,Plant Components, Aerial ,Point of delivery ,Peanut ,chemistry ,RNA, Plant ,Fruit ,Seeds ,Subterranean pod ,Agronomy and Crop Science ,Seed abortion - Abstract
The peanut is a special plant for its aerial flowering but subterranean fructification. The failure of peg penetration into the soil leads to form aerial pod and finally seed abortion. However, the mechanism of seed abortion during aerial pod development remains obscure. Here, a comparative transcriptome analysis between aerial and subterranean pods at different developmental stages was produced using a customized NimbleGen microarray representing 36,158 unigenes. By comparing 4 consecutive time-points, totally 6,203 differentially expressed genes, 4,732 stage-specific expressed genes and 2,401 specific expressed genes only in aerial or subterranean pods were identified in this study. Functional annotation showed their mainly involvement in biosynthesis, metabolism, transcription regulation, transporting, stress response, photosynthesis, signal transduction, cell division, apoptosis, embryonic development, hormone response and light signaling, etc. Emphasis was focused on hormone response, cell apoptosis, embryonic development and light signaling relative genes. These genes might function as potential candidates to provide insights into seed abortion during aerial pod development. Ten candidate genes were validated by Real-time RT-PCR. Additionally, consistent with up-regulation of auxin response relative genes in aerial pods, endogenous IAA content was also significantly increased by HPLC analysis. This study will further provide new molecular insight that auxin and auxin response genes potentially contribute to peanut seed and pod development. Electronic supplementary material The online version of this article (doi:10.1007/s11103-014-0193-x) contains supplementary material, which is available to authorized users.
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- 2013
22. Transcriptome profiling of peanut (Arachis hypogaea) gynophores in gravitropic response
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Xuanqiang Liang, Fanghe Zhu, Yanbin Hong, Haiyan Liu, Xiaoping Chen, and Haifen Li
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Microarray ,Gravitropism ,food and beverages ,Plant Science ,Biology ,Arachis hypogaea ,Cell biology ,Metabolomics ,Gene expression ,Botany ,Agronomy and Crop Science ,Developmental biology ,Gene ,Gynophore - Abstract
Peanut (Arachis hypogaea L.) produces flowers aerially, but the fruit develops underground. This process is mediated by the gynophore, which always grows vertically downwards. The genetic basis underlying gravitropic bending of gynophores is not well understood. To identify genes related to gynophore gravitropism, gene expression profiles of gynophores cultured in vitro with tip pointing upward (gravitropic stimulation sample) and downward (control) at both 6 and 12 h were compared through a high-density peanut microarray. After gravitropic stimulation, there were 174 differentially expressed genes, including 91 upregulated and 83 downregulated genes at 6 h, and 491 differentially expressed genes including 129 upregulated and 362 downregulated genes at 12 h. The differentially expressed genes identified were assigned to 24 functional categories. Twenty pathways including carbon fixation, aminoacyl-tRNA biosynthesis, pentose phosphate pathway, starch and sucrose metabolism were identified. The quantitative real-time PCR analysis was performed for validation of microarray results. Our study paves the way to better understand the molecular mechanisms underlying the peanut gynophore gravitropism.
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- 2013
23. Characterization of peanut germin-like proteins, AhGLPs in plant development and defense
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Xuanqiang Liang, Fanghe Zhu, Ling Li, Xiaoyuan Chi, Wang Tong, Qingli Yang, Haifen Li, Shanlin Yu, and Xiaoping Chen
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Salinity ,Arachis ,Arabidopsis Thaliana ,Gene Expression ,lcsh:Medicine ,Plant Science ,Plant Genetics ,Biochemistry ,Model Organisms ,Plant Growth Regulators ,Plant and Algal Models ,Gene Expression Regulation, Plant ,Stress, Physiological ,Arabidopsis ,Gene expression ,Botany ,Genetics ,Plant defense against herbivory ,Protein Isoforms ,Arabidopsis thaliana ,Gene family ,lcsh:Science ,Biology ,Glycoproteins ,Plant Diseases ,Plant Growth and Development ,Regulation of gene expression ,Multidisciplinary ,biology ,Plant Biochemistry ,Gene Expression Profiling ,lcsh:R ,Gene Expression Regulation, Developmental ,food and beverages ,Salt Tolerance ,biology.organism_classification ,Plant Leaves ,Gene expression profiling ,Protein Transport ,Host-Pathogen Interactions ,Mutation ,Plant Biotechnology ,lcsh:Q ,Plant hormone ,Gene Function ,Research Article ,Abscisic Acid ,Aspergillus flavus - Abstract
Background Germin-like superfamily members are ubiquitously expressed in various plant species and play important roles in plant development and defense. Although several GLPs have been identified in peanut (Arachis hypogaea L.), their roles in development and defense remain unknown. In this research, we study the spatiotemporal expression of AhGLPs in peanut and their functions in plant defense. Results We have identified three new AhGLP members (AhGLP3b, AhGLP5b and AhGLP7b) that have distinct but very closely related DNA sequences. The spatial and temporal expression profiles revealed that each peanut GLP gene has its distinct expression pattern in various tissues and developmental stages. This suggests that these genes all have their distinct roles in peanut development. Subcellular location analysis demonstrated that AhGLP2 and 5 undergo a protein transport process after synthesis. The expression of all AhGLPs increased in responding to Aspergillus flavus infection, suggesting AhGLPs' ubiquitous roles in defense to A. flavus. Each AhGLP gene had its unique response to various abiotic stresses (including salt, H2O2 stress and wound), biotic stresses (including leaf spot, mosaic and rust) and plant hormone stimulations (including SA and ABA treatments). These results indicate that AhGLPs have their distinct roles in plant defense. Moreover, in vivo study of AhGLP transgenic Arabidopsis showed that both AhGLP2 and 3 had salt tolerance, which made transgenic Arabidopsis grow well under 100 mM NaCl stress. Conclusions For the first time, our study analyzes the AhGLP gene expression profiles in peanut and reveals their roles under various stresses. These results provide an insight into the developmental and defensive roles of GLP gene family in peanut.
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- 2013
24. Transcriptome identification of the resistance-associated genes (RAGs) to Aspergillus flavus infection in pre-harvested peanut (Arachis hypogaea)
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Haifen Li, Qingli Yang, Yang Zhen, Xiaoping Chen, Haiyan Liu, Ling Li, Xiao-Yuan Chi, Xuanqiang Liang, Wang Tong, Yanbin Hong, and Shanlin Yu
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Genetics ,Aflatoxin ,Aspergillus ,biology ,food and beverages ,Aspergillus flavus ,Plant Science ,Oligopeptide transport ,biology.organism_classification ,Transcriptome ,Genotype ,KEGG ,Agronomy and Crop Science ,Gene - Abstract
Pre-harvest aflatoxin contamination caused by Aspergillus favus is a major concern in peanut. However, little is known about the resistance mechanism, so the incorporation of resistance into cultivars with commercially-acceptable genetic background has been slowed. To identify resistance-associated genes potentially underlying the resistance mechanism, we compared transcriptome profiles in resistant and susceptible peanut genotypes under three different treatments: well watered, drought stress and both A. flavus and drought stress using a customised NimbleGen microarray representing 36 158 unigenes. Results showed that the profile of differentially expressed genes (DEGs) displayed a similar pattern of distribution among the functional classes between resistant and susceptible peanuts in response to drought stress. Under A. flavus infection with drought stress, a total of 490 unigenes involved in 26 pathways were differentially expressed in the resistant genotype YJ1 uniquely responding to A. flavus infection, in which 96 DEGs were related to eight pathways: oxidation reduction, proteolysis metabolism, coenzyme A biosynthesis, defence response, signalling, oligopeptide transport, transmembrane transport and carbohydrate biosynthesis/metabolism. Pathway analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database showed that eight networks were significantly associated with resistance to A. flavus infection in resistant genotype YJ1 compared with susceptible Yueyou7. To validate microarray analysis, 15 genes were randomly selected for real-time RT–PCR analysis. The results provided in this study may enhance our understanding of the pre-harvest peanut–A. flavus interaction and facilitate to develop aflatoxin resistant peanut lines in future breeding programs.
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- 2013
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