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Bu M, Fan W, Li R, He B, Cui P. Lipid Metabolism and Improvement in Oilseed Crops: Recent Advances in Multi-Omics Studies. Metabolites 2023; 13:1170. [PMID: 38132852 PMCID: PMC10744971 DOI: 10.3390/metabo13121170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Oilseed crops are rich in plant lipids that not only provide essential fatty acids for the human diet but also play important roles as major sources of biofuels and indispensable raw materials for the chemical industry. The regulation of lipid metabolism genes is a major factor affecting oil production. In this review, we systematically summarize the metabolic pathways related to lipid production and storage in plants and highlight key research advances in characterizing the genes and regulatory factors influencing lipid anabolic metabolism. In addition, we integrate the latest results from multi-omics studies on lipid metabolism to provide a reference to better understand the molecular mechanisms underlying oil anabolism in oilseed crops.
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Affiliation(s)
- Mengjia Bu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Fan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ruonan Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bing He
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Peng Cui
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Cao P, Zhao Y, Wu F, Xin D, Liu C, Wu X, Lv J, Chen Q, Qi Z. Multi-Omics Techniques for Soybean Molecular Breeding. Int J Mol Sci 2022; 23:4994. [PMID: 35563386 PMCID: PMC9099442 DOI: 10.3390/ijms23094994] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Soybean is a major crop that provides essential protein and oil for food and feed. Since its origin in China over 5000 years ago, soybean has spread throughout the world, becoming the second most important vegetable oil crop and the primary source of plant protein for global consumption. From early domestication and artificial selection through hybridization and ultimately molecular breeding, the history of soybean breeding parallels major advances in plant science throughout the centuries. Now, rapid progress in plant omics is ushering in a new era of precision design breeding, exemplified by the engineering of elite soybean varieties with specific oil compositions to meet various end-use targets. The assembly of soybean reference genomes, made possible by the development of genome sequencing technology and bioinformatics over the past 20 years, was a great step forward in soybean research. It facilitated advances in soybean transcriptomics, proteomics, metabolomics, and phenomics, all of which paved the way for an integrated approach to molecular breeding in soybean. In this review, we summarize the latest progress in omics research, highlight novel findings made possible by omics techniques, note current drawbacks and areas for further research, and suggest that an efficient multi-omics approach may accelerate soybean breeding in the future. This review will be of interest not only to soybean breeders but also to researchers interested in the use of cutting-edge omics technologies for crop research and improvement.
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Affiliation(s)
- Pan Cao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Ying Zhao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Fengjiao Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Jian Lv
- Department of Innovation, Syngenta Biotechnology China, Beijing 102206, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
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Wang Y, Yang Z, Shi L, Yang R, Guo H, Zhang S, Geng G. Transcriptome analysis of Auricularia fibrillifera fruit-body responses to drought stress and rehydration. BMC Genomics 2022; 23:58. [PMID: 35033026 PMCID: PMC8760723 DOI: 10.1186/s12864-021-08284-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/28/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Drought stress severely restricts edible fungus production. The genus Auricularia has a rare drought tolerance, a rehydration capability, and is nutrient rich. RESULTS The key genes and metabolic pathways involved in drought-stress and rehydration were investigated using a transcriptome analysis to clarify the relevant molecular mechanisms. In total, 173.93 Mb clean reads, 26.09 Gb of data bulk, and 52,954 unigenes were obtained. Under drought-stress and rehydration conditions, 14,235 and 8539 differentially expressed genes, respectively, were detected. 'Tyrosine metabolic', 'caffeine metabolism', 'ribosome', 'phagosome', and 'proline and arginine metabolism', as well as 'peroxisome' and 'mitogen-activated protein kinase signaling' pathways, had major roles in A. fibrillifera responses to drought stress. 'Tyrosine' and 'caffeine metabolism' might reveal unknown mechanisms for the antioxidation of A. fibrillifera under drought-stress conditions. During the rehydration process, 'diterpenoid biosynthesis', 'butanoate metabolism', 'C5-branched dibasic acid', and 'aflatoxin biosynthesis' pathways were significantly enriched. Gibberellins and γ-aminobutyric acid were important in the recovery of A. fibrillifera growth after rehydration. Many genes related to antibiotics, vitamins, and other health-related ingredients were found in A. fibrillifera. CONCLUSION These findings suggested that the candidate genes and metabolites involved in crucial biological pathways might regulate the drought tolerance or rehydration of Auricularia, shedding light on the corresponding mechanisms and providing new potential targets for the breeding and cultivation of drought-tolerant fungi.
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Affiliation(s)
- Yiqin Wang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Zhifen Yang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Luxi Shi
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Rui Yang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Hao Guo
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Suqin Zhang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China.
| | - Guangdong Geng
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China.
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Shimamura M, Kumaki T, Hashimoto S, Saeki K, Ayabe SI, Higashitani A, Akashi T, Sato S, Aoki T. Phenolic Acids Induce Nod Factor Production in <i>Lotus japonicus</i>–<i>Mesorhizobium</i> Symbiosis. Microbes Environ 2022; 37. [PMID: 35283370 PMCID: PMC8958295 DOI: 10.1264/jsme2.me21094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In legume–rhizobia symbiosis, partner recognition and the initiation of symbiosis processes require the mutual exchange of chemical signals. Chemicals, generally (iso)flavonoids, in the root exudates of the host plant induce the expression of nod genes in rhizobia, and, thus, are called nod gene inducers. The expression of nod genes leads to the production of lipochitooligosaccharides (LCOs) called Nod factors. Natural nod gene inducer(s) in Lotus japonicus–Mesorhizobium symbiosis remain unknown. Therefore, we developed an LCO detection method based on ultra-high-performance liquid chromatography–tandem-quadrupole mass spectrometry (UPLC-TQMS) to identify these inducers and used it herein to screen 40 phenolic compounds and aldonic acids for their ability to induce LCOs in Mesorhizobium japonicum MAFF303099. We identified five phenolic acids with LCO-inducing activities, including p-coumaric, caffeic, and ferulic acids. The induced LCOs caused root hair deformation, and nodule numbers in L. japonicus inoculated with M. japonicum were increased by these phenolic acids. The three phenolic acids listed above induced the expression of the nodA, nodB, and ttsI genes in a strain harboring a multicopy plasmid encoding NodD1, but not that encoding NodD2. The presence of p-coumaric and ferulic acids in the root exudates of L. japonicus was confirmed by UPLC-TQMS, and the induction of ttsI::lacZ in the strain harboring the nodD1 plasmid was detected in the rhizosphere of L. japonicus. Based on these results, we propose that phenolic acids are a novel type of nod gene inducer in L. japonicus–Mesorhizobium symbiosis.
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Affiliation(s)
| | | | | | - Kazuhiko Saeki
- Department of Biological Sciences and Kyousei Science Center for Life and Nature, Nara Women’s University
| | | | | | | | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University
| | - Toshio Aoki
- Department of Applied Biological Sciences, Nihon University
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Peng L, Qian L, Wang M, Liu W, Song X, Cheng H, Yuan F, Zhao M. Comparative transcriptome analysis during seeds development between two soybean cultivars. PeerJ 2021; 9:e10772. [PMID: 33717671 PMCID: PMC7931715 DOI: 10.7717/peerj.10772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
Soybean is one of the important economic crops, which supplies a great deal of vegetable oil and proteins for human. The content of nutrients in different soybean seeds is different, which is related to the expression of multiple genes, but the mechanisms are complicated and still largely uncertain. In this study, to reveal the possible causes of the nutrients difference in soybeans A7 (containing low oil and high protein) and A35 (containing high oil and low protein), RNA-seq technology was performed to compare and identify the potential differential expressed genes (DEGs) at different seed developmental stages. The results showed that DEGs mainly presented at the early stages of seeds development and more DEGs were up-regulated at the early stage than the late stages. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEGs have diverged in A7 and A35. In A7, the DEGs were mainly involved in cell cycle and stresses, while in A35 were the fatty acids and sugar metabolism. Specifically, when the DEGs contributing to oil and protein metabolic pathways were analyzed, the differences between A7 and A35 mainly presented in fatty acids metabolism and seeds storage proteins (SSPs) synthesis. Furthermore, the enzymes, fatty acid dehydrogenase 2, 3-ketoacyl-CoA synthase and 9S-lipoxygenase, in the synthesis and elongation pathways of fatty acids, were revealed probably to be involved in the oil content difference between A7 and A35, the SSPs content might be due to the transcription factors: Leafy Cotyledon 2 and Abscisic acid-intensitive 3, while the sugar transporter, SWEET10a, might contribute to both oil and protein content differences. Finally, six DEGs were selected to analyze their expression using qRT-PCR, and the results were consistent with the RNA-seq results. Generally, the study provided a comprehensive and dynamic expression trends for the seed development processes, and uncovered the potential DEGs for the differences of oil in A7 and A35.
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Affiliation(s)
- Li Peng
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Linlin Qian
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Meinan Wang
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Wei Liu
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Xiangting Song
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Hao Cheng
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Fengjie Yuan
- Institute of Crop Science, Zhejiang Academy of Agricultural Sciences, Hang Zhou, China
| | - Man Zhao
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
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González G, Aguilera F, D'Afonseca V. Transcriptome profiling of raspberry ( Rubus idaeus Var. Amira) in response to infection by tomato ringspot virus (ToRSV). Heliyon 2020; 6:e04518. [PMID: 32817888 PMCID: PMC7424221 DOI: 10.1016/j.heliyon.2020.e04518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/28/2019] [Accepted: 07/17/2020] [Indexed: 11/01/2022] Open
Abstract
Raspberry (Rubus sp.) is a berries fruit with an ongoing agricultural and commercial interest due to its high contents of flavonoids and nutrients beneficial for human health. The growing demand for raspberries is facing great challenges associated mainly with the dispersal of diseases, which produces a decrease in productivity and fruit quality. A broad range of genomic resources is available for other Rosaceae species; however, genomic resources for species of the Rubus genus are still limited. Here, we characterize the transcriptome of the Rubus idaeus (Var. Amira) in order to 1) provide clues in the transcriptional changes of R. idaeus against tomato ringspot virus (ToRSV); and 2) generate genomic resources for this economically important species. We generate more than 200 million sequencing reads from two mRNA samples of raspberry, infected and not infected by ToRSV, using Illumina technology. After de novo assembly, we obtained 68,853 predicted protein-coding sequences of which 71.3% and 61.3% were annotated using Gene Ontology and Pfam databases, respectively. Moreover, we find 2,340 genes with differential expression between raspberries infected and not infected by ToRSV. Analysis of these genes shows functional enrichments of the oxidation-reduction process, cell wall biogenesis, terpene synthase activity, and lyase activity. These genes could be involved in the raspberry immune response through the interaction of different metabolic pathways; however, this statement needs further investigations. Up-regulation of genes encoding terpene synthases, multicopper oxidases, laccases, and beta-glucosidases might suggest that these enzymes appear to be the predominant transcriptome immune response of R. idaeus against ToRSV. Furthermore, we identify thousands of molecular markers (i.e., SSRs and SNPs), increasing considerably the genomic resources currently available for raspberries. This study is the first report on investigating the transcriptional changes of R. idaeus against ToRSV.
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Affiliation(s)
- Gloria González
- Center of Biotechnology for Natural Resources (CenBIO), Faculty of Agricultural Sciences and Forestry, Universidad Católica del Maule, Talca, Chile
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Vívian D'Afonseca
- Vice Rectory of Research and Post-Graduation (VRIP), Universidad Católica del Maule, Talca, Chile
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Lambert I, Paysant-Le Roux C, Colella S, Martin-Magniette ML. DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models. PLANT METHODS 2020; 16:68. [PMID: 32426025 PMCID: PMC7216733 DOI: 10.1186/s13007-020-00611-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/03/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND RNAseq is nowadays the method of choice for transcriptome analysis. In the last decades, a high number of statistical methods, and associated bioinformatics tools, for RNAseq analysis were developed. More recently, statistical studies realised neutral comparison studies using benchmark datasets, shedding light on the most appropriate approaches for RNAseq data analysis. RESULTS DiCoExpress is a script-based tool implemented in R that includes methods chosen based on their performance in neutral comparisons studies. DiCoExpress uses pre-existing R packages including FactoMineR, edgeR and coseq, to perform quality control, differential, and co-expression analysis of RNAseq data. Users can perform the full analysis, providing a mapped read expression data file and a file containing the information on the experimental design. Following the quality control step, the user can move on to the differential expression analysis performed using generalized linear models thanks to the automated contrast writing function. A co-expression analysis is implemented using the coseq package. Lists of differentially expressed genes and identified co-expression clusters are automatically analyzed for enrichment of annotations provided by the user. We used DiCoExpress to analyze a publicly available RNAseq dataset on the transcriptional response of Brassica napus L. to silicon treatment in plant roots and mature leaves. This dataset, including two biological factors and three replicates for each condition, allowed us to demonstrate in a tutorial all the features of DiCoExpress. CONCLUSIONS DiCoExpress is an R script-based tool allowing users to perform a full RNAseq analysis from quality controls to co-expression analysis through differential analysis based on contrasts inside generalized linear models. DiCoExpress focuses on the statistical modelling of gene expression according to the experimental design and facilitates the data analysis leading the biological interpretation of the results.
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Affiliation(s)
- Ilana Lambert
- LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, INRAE, SupAgro, Univ Montpellier, Montpellier, France
| | - Christine Paysant-Le Roux
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Bat. 630, 91405 Orsay, France
- Institute of Plant Sciences Paris Saclay (IPS2), Université de Paris, CNRS, INRAE, Bat. 630, 91405 Orsay, France
| | - Stefano Colella
- LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, INRAE, SupAgro, Univ Montpellier, Montpellier, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Bat. 630, 91405 Orsay, France
- Institute of Plant Sciences Paris Saclay (IPS2), Université de Paris, CNRS, INRAE, Bat. 630, 91405 Orsay, France
- UMR MIA-Paris, AgroParisTech, INRAE, Université Paris-Saclay, 75005 Paris, France
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Afzal M, Alghamdi SS, Migdadi HH, Khan MA, Nurmansyah, Mirza SB, El-Harty E. Legume genomics and transcriptomics: From classic breeding to modern technologies. Saudi J Biol Sci 2019; 27:543-555. [PMID: 31889880 PMCID: PMC6933173 DOI: 10.1016/j.sjbs.2019.11.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 02/06/2023] Open
Abstract
Legumes are essential and play a significant role in maintaining food standards and augmenting physiochemical soil properties through the biological nitrogen fixation process. Biotic and abiotic factors are the main factors limiting legume production. Classical breeding methodologies have been explored extensively about the problem of truncated yield in legumes but have not succeeded at the desired rate. Conventional breeding improved legume genotypes but with more resources and time. Recently, the invention of next-generation sequencing (NGS) and high-throughput methods for genotyping have opened new avenues for research and developments in legume studies. During the last decade, genome sequencing for many legume crops documented. Sequencing and re-sequencing of important legume species have made structural variation and functional genomics conceivable. NGS and other molecular techniques such as the development of markers; genotyping; high density genetic linkage maps; quantitative trait loci (QTLs) identification, expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs); and transcription factors incorporated into existing breeding technologies have made possible the accurate and accelerated delivery of information for researchers. The application of genome sequencing, RNA sequencing (transcriptome sequencing), and DNA sequencing (re-sequencing) provide considerable insights for legume development and improvement programs. Moreover, RNA-Seq helps to characterize genes, including differentially expressed genes, and can be applied for functional genomics studies, especially when there is limited information available for the studied genomes. Genome-based crop development studies and the availability of genomics data as well as decision-making gears look be specific for breeding programs. This review mainly presents an overview of the path from classical breeding to new emerging genomics tools, which will trigger and accelerate genomics-assisted breeding for recognition of novel genes for yield and quality characters for sustainable legume crop production.
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Affiliation(s)
- Muhammad Afzal
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salem S Alghamdi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hussein H Migdadi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Altaf Khan
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nurmansyah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Shaher Bano Mirza
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.,Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Chak Shahzad, Islamabad, Pakistan
| | - Ehab El-Harty
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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Sanderson LA, Caron CT, Tan R, Shen Y, Liu R, Bett KE. KnowPulse: A Web-Resource Focused on Diversity Data for Pulse Crop Improvement. FRONTIERS IN PLANT SCIENCE 2019; 10:965. [PMID: 31428111 PMCID: PMC6690010 DOI: 10.3389/fpls.2019.00965] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/10/2019] [Indexed: 05/25/2023]
Abstract
KnowPulse (https://knowpulse.usask.ca) is a breeder-focused web portal for pulse breeders and geneticists. With a focus on diversity data, KnowPulse provides information on genetic markers, sequence variants, phenotypic traits and germplasm for chickpea, common bean, field pea, faba bean, and lentil. Genotypic data is accessible through the genotype matrix tool, displayed as a marker-by-germplasm table of genotype calls specific to germplasm chosen by the researcher. It is also summarized on genetic marker and sequence variant pages. Phenotypic data is visualized in trait distribution plots: violin plots for quantitative data and histograms for qualitative data. These plots are accessible through trait, germplasm, and experiment pages, as well as through a single page search tool. KnowPulse is built using the open-source Tripal toolkit and utilizes open-source tools including, but not limited to, species-specific JBrowse instances, a BLAST interface, and whole-genome CViTjs visualizations. KnowPulse is constantly evolving with data and tools added as they become available. Full integration of genetic maps and quantitative trait loci is imminent, and development of tools exploring structural variation is being explored.
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Affiliation(s)
| | | | | | | | | | - Kirstin E. Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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Wu B, Ruan C, Han P, Ruan D, Xiong C, Ding J, Liu S. Comparative transcriptomic analysis of high- and low-oil Camellia oleifera reveals a coordinated mechanism for the regulation of upstream and downstream multigenes for high oleic acid accumulation. 3 Biotech 2019; 9:257. [PMID: 31192082 DOI: 10.1007/s13205-019-1792-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 06/03/2019] [Indexed: 01/08/2023] Open
Abstract
Tea oil camellia (Camellia oleifera) is an important woody oil tree in southern China. However, little is known regarding the molecular mechanisms that contribute to high oleic acid accumulation in tea oil camellia. Herein, we measured the oil content and fatty acid compositions of high- and low-oil tea oil camellia seeds and investigated the global gene expression profiles by RNA-seq. The results showed that at the early, second and third seed developmental stages, a total of 64, 253, and 124 genes, respectively, were significantly differentially expressed between the high- and low-oil cultivars. Gene ontology (GO) enrichment analysis of the identified differentially expressed transcription factors (TFs; ABI3, FUS3, LEC1, WRI1, TTG2 and DOF4.6) revealed some critical GO terms associated with oil biosynthesis and fatty acid accumulation, including glycolysis, zinc ion binding, positive regulation of fatty acid biosynthetic process, triglyceride biosynthetic process, seed coat development, abscisic acid-mediated signaling pathway and embryo development. Comprehensive comparisons of transcriptomic profiles and expression analysis of multigenes based on qRT-PCR showed that coordinated high expression of the upstream genes HAD, EAR and KASI directly increased the relative levels of C16:0-ACP, which provided enough precursor resources for oleic acid biosynthesis. Continuous high expression of the SAD gene accelerated oleic acid synthesis and accumulation, and coordinated low expression of the downstream genes FAD2, FAD3, FAD7, FAD8 and FAE1 decreased the consumption of oleic acid for conversion. The coordinated regulation of these multigenes ensures the high accumulation of oleic acid in the seeds of tea oil camellia. Our data represent a comprehensive transcriptomic study of high- and low-oil tea oil camellia, not only increasing the number of sequences associated with lipid biosynthesis and fatty acid accumulation in public resource databases but also providing a scientific basis for genetic improvement of the oleic acid content in woody oil trees.
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Nadeem M, Li J, Yahya M, Wang M, Ali A, Cheng A, Wang X, Ma C. Grain Legumes and Fear of Salt Stress: Focus on Mechanisms and Management Strategies. Int J Mol Sci 2019; 20:E799. [PMID: 30781763 PMCID: PMC6412900 DOI: 10.3390/ijms20040799] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 12/27/2022] Open
Abstract
Salinity is an ever-present major constraint and a major threat to legume crops, particularly in areas with irrigated agriculture. Legumes demonstrate high sensitivity, especially during vegetative and reproductive phases. This review gives an overview of legumes sensitivity to salt stress (SS) and mechanisms to cope with salinity stress under unfavorable conditions. It also focuses on the promising management approaches, i.e., agronomic practices, breeding approaches, and genome editing techniques to improve performance of legumes under SS. Now, the onus is on researchers to comprehend the plants physiological and molecular mechanisms, in addition to various responses as part of their stress tolerance strategy. Due to their ability to fix biological nitrogen, high protein contents, dietary fiber, and essential mineral contents, legumes have become a fascinating group of plants. There is an immense need to develop SS tolerant legume varieties to meet growing demand of protein worldwide. This review covering crucial areas ranging from effects, mechanisms, and management strategies, may elucidate further the ways to develop SS-tolerant varieties and to produce legume crops in unfavorable environments.
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Affiliation(s)
- Muhammad Nadeem
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Jiajia Li
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Muhammad Yahya
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Minghua Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Asif Ali
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Andong Cheng
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Xiaobo Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Chuanxi Ma
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
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Horgan FG, Almazan MLP, Vu Q, Ramal AF, Bernal CC, Yasui H, Fujita D. Unanticipated benefits and potential ecological costs associated with pyramiding leafhopper resistance loci in rice. CROP PROTECTION (GUILDFORD, SURREY) 2019; 115:47-58. [PMID: 30739972 PMCID: PMC6358143 DOI: 10.1016/j.cropro.2018.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 05/16/2023]
Abstract
We tested the hypotheses that increasing the number of anti-herbivore resistance loci in crop plants will increase resistance strength, increase the spectrum of resistance (the number of species affected), and increase resistance stability. We further examined the potential ecological costs of pyramiding resistance under benign environments. In our experiments, we used 14 near-isogenic rice lines with zero (T65: recurrent parent), one, two or three resistance loci introgressed through marker-assisted selection. Lines with two or more loci that were originally bred for resistance to the green rice leafhopper, Nephotettix cincticeps, significantly reduced egg-laying by the green leafhopper, N. virescens. Declines in egg-number and in nymph weight were correlated with the numbers of resistance loci in the rice lines. To test the spectrum of resistance, we challenged the lines with a range of phloem feeders including the zig-zag leafhopper, Recilia dorsalis, brown planthopper, Nilaparvata lugens, and whitebacked planthopper, Sogatella furcifera. There was an increase in the number of tested species showing significant declines in egg-laying and nymph survival on lines with increasing numbers of loci. In a screen house trial that varied rates of nitrogenous fertilizer, a line with three loci had stable resistance against the green leafhopper and the grain yields of infested plants were maintained or increased (overcompensation). Under benign conditions, plant growth and grain yields declined with increasing numbers of resistance loci. However, under field conditions with natural exposure to herbivores, there were no significant differences in final yields. Our results clearly indicate the benefits, including unanticipated benefits such as providing resistance against multiple herbivore species, of pyramiding anti-herbivore resistance genes/loci in crop plants. We discuss our results as part of a review of existing research on pyramided resistance against leafhoppers and planthoppers in rice. We suggest that potential ecological costs may be overcome by the careful selection of gene combinations for pyramiding, avoidance of high (potentially redundant) loci numbers, and introgression of loci into robust plant types such as hybrid rice varieties.
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Affiliation(s)
- Finbarr G. Horgan
- University of Technology Sydney, 15 Broadway, Ultimo, Sydney, NSW 2007, Australia
- Tropical Ecosystems Research Network, 30C Nirondha, Temple Road, Piliyandala, Sri Lanka
| | | | - Quynh Vu
- Cuulong Delta Rice Research Institute, Tan Thanh, Thoi Lai District, Can Tho, Viet Nam
- Helmholtz Centre for Environmental Research, Theodor-Leiser-Strasse, 06210, Halle, Germany
| | - Angelee Fame Ramal
- School of Environmental Science and Management, University of the Philippines, Los Baños, 4030 Laguna, Philippines
| | | | - Hideshi Yasui
- Plant Breeding Laboratory, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
| | - Daisuke Fujita
- Saga University, Faculty of Agriculture, 1 Honjo-machi, Saga, 840-8502, Japan
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Cheng Q, Bai S, Ge G, Li P, Liu L, Zhang C, Jia Y. Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-Seq. BMC Genomics 2018; 19:807. [PMID: 30404602 PMCID: PMC6223052 DOI: 10.1186/s12864-018-5180-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/17/2018] [Indexed: 01/15/2023] Open
Abstract
Background Alfalfa (Medicago sativa) is a widely cultivated, essential commercial forage crop. The protein content in its leaves is the critical factor in determining the quality of alfalfa. Thus far, the understanding of the molecular mechanism of alfalfa defoliation traits remains unclear. The transcriptome database created by RNA-Seq is used to identify critical genes related to defoliation traits. Results In this study, we sequenced the transcriptomes of the Zhungeer variety (with easy leaf abscission) and WL319HQ variety (without easy leaf abscission). Among the identified 66,734 unigenes, 706 differentially expressed genes (DEGs) upregulated, and 392 unigenes downregulated in the Zhungeer vs WL319HQ leaf. KEGG pathway annotations showed that 8,414 unigenes were annotated to 87 pathways and contained 281 DEGs. Six DEGs belonging to the “Carotenoid biosynthesis”, “Plant hormone signal transduction” and “Circadian rhythm-plant” pathways involved in defoliation traits were identified and validated by RT-qPCR analyses. Conclusions This study used RNA-Seq to discover genes associated with defoliation traits between two alfalfa varieties. Our transcriptome data dramatically enriches alfalfa functional genomic studies. In addition, these data provide theoretical guidance for field production practice and genetic breeding, as well as references for future study of defoliation traits in alfalfa. Electronic supplementary material The online version of this article (10.1186/s12864-018-5180-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiming Cheng
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Sciences, Chengdu, 611731, China
| | - Gentu Ge
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Ping Li
- Sichuan Academy of Grassland Sciences, Chengdu, 611731, China
| | - Liying Liu
- Inner Mongolia Academy of Forestry Science, Hohhot, 010010, China
| | - Chengdong Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Randwick, NSW, 2052, Australia.
| | - Yushan Jia
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China.
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14
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Kallala N, M'sehli W, Jelali K, Kais Z, Mhadhbi H. Inoculation with Efficient Nitrogen Fixing and Indoleacetic Acid Producing Bacterial Microsymbiont Enhance Tolerance of the Model Legume Medicago truncatula to Iron Deficiency. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9134716. [PMID: 30406145 PMCID: PMC6201330 DOI: 10.1155/2018/9134716] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/25/2018] [Indexed: 12/23/2022]
Abstract
The aim of this study was to assess the effect of symbiotic bacteria inoculation on the response of Medicago truncatula genotypes to iron deficiency. The present work was conducted on three Medicago truncatula genotypes: A17, TN8.20, and TN1.11. Three treatments were performed: control (C), direct Fe deficiency (DD), and induced Fe deficiency by bicarbonate (ID). Plants were nitrogen-fertilized (T) or inoculated with two bacterial strains: Sinorhizobium meliloti TII7 and Sinorhizobium medicae SII4. Biometric, physiological, and biochemical parameters were analyzed. Iron deficiency had a significant lowering effect on plant biomass and chlorophyll content in all Medicago truncatula genotypes. TN1.11 showed the highest lipid peroxidation and leakage of electrolyte under iron deficiency conditions, which suggest that TN1.11 was more affected than A17 and TN8.20 by Fe starvation. Iron deficiency affected symbiotic performance indices of all Medicago truncatula genotypes inoculated with both Sinorhizobium strains, mainly nodules number and biomass as well as nitrogen-fixing capacity. Nevertheless, inoculation with Sinorhizobium strains mitigates the negative effect of Fe deficiency on plant growth and oxidative stress compared to nitrogen-fertilized plants. The highest auxin producing strain, TII7, preserves relatively high growth and root biomass and length when inoculated to TN8.20 and A17. On the other hand, both TII7 and SII4 strains improve the performance of sensitive genotype TN1.11 through reduction of the negative effect of iron deficiency on chlorophyll and plant Fe content. The bacterial inoculation improved Fe-deficient plant response to oxidative stress via the induction of the activities of antioxidant enzymes.
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Affiliation(s)
- Nadia Kallala
- Laboratory of Legumes, Center of Biotechnology of Borj-Cedria (CBBC), Hammam-Lif, Tunisia
- Faculty of Science, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - Wissal M'sehli
- Laboratory of Legumes, Center of Biotechnology of Borj-Cedria (CBBC), Hammam-Lif, Tunisia
| | - Karima Jelali
- Laboratory of Legumes, Center of Biotechnology of Borj-Cedria (CBBC), Hammam-Lif, Tunisia
- Faculty of Science, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - Zribi Kais
- Laboratory of Legumes, Center of Biotechnology of Borj-Cedria (CBBC), Hammam-Lif, Tunisia
| | - Haythem Mhadhbi
- Laboratory of Legumes, Center of Biotechnology of Borj-Cedria (CBBC), Hammam-Lif, Tunisia
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15
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Abdelrahman M, Jogaiah S, Burritt DJ, Tran LSP. Legume genetic resources and transcriptome dynamics under abiotic stress conditions. PLANT, CELL & ENVIRONMENT 2018; 41:1972-1983. [PMID: 29314055 DOI: 10.1111/pce.13123] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/08/2017] [Accepted: 12/08/2017] [Indexed: 05/04/2023]
Abstract
Grain legumes are an important source of nutrition and income for billions of consumers and farmers around the world. However, the low productivity of new legume varieties, due to the limited genetic diversity available for legume breeding programmes and poor policymaker support, combined with an increasingly unpredictable global climate is resulting in a large gap between current yields and the increasing demand for legumes as food. Hence, there is a need for novel approaches to develop new high-yielding legume cultivars that are able to cope with a range of environmental stressors. Next-generation technologies are providing the tools that could enable the more rapid and cost-effective genomic and transcriptomic studies for most major crops, allowing the identification of key functional and regulatory genes involved in abiotic stress resistance. In this review, we provide an overview of the recent achievements regarding abiotic stress resistance in a wide range of legume crops and highlight the transcriptomic and miRNA approaches that have been used. In addition, we critically evaluate the availability and importance of legume genetic resources with desirable abiotic stress resistance traits.
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Affiliation(s)
- Mostafa Abdelrahman
- Laboratory of Genomic Reproductive Biology, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Botany Department, Faculty of Science, Aswan University, Aswan, 81528, Egypt
| | - Sudisha Jogaiah
- Plant Healthcare and Diagnostic Center, Department of Studies in Biotechnology and Microbiology, Karnatak University, Dharwad, 580 003, India
| | - David J Burritt
- Department of Botany, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Lam-Son Phan Tran
- Plant Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
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16
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Rai MK, Shekhawat JK, Kataria V, Shekhawat N. De novo assembly of leaf transcriptome, functional annotation and genomic resources development in Prosopis cineraria , a multipurpose tree of Indian Thar Desert. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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17
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Zargar SM, Mahajan R, Nazir M, Nagar P, Kim ST, Rai V, Masi A, Ahmad SM, Shah RA, Ganai NA, Agrawal GK, Rakwal R. Common bean proteomics: Present status and future strategies. J Proteomics 2017; 169:239-248. [DOI: 10.1016/j.jprot.2017.03.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 11/30/2022]
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18
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Farooq M, Gogoi N, Hussain M, Barthakur S, Paul S, Bharadwaj N, Migdadi HM, Alghamdi SS, Siddique KHM. Effects, tolerance mechanisms and management of salt stress in grain legumes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 118:199-217. [PMID: 28648997 DOI: 10.1016/j.plaphy.2017.06.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 05/23/2023]
Abstract
Salt stress is an ever-present threat to crop yields, especially in countries with irrigated agriculture. Efforts to improve salt tolerance in crop plants are vital for sustainable crop production on marginal lands to ensure future food supplies. Grain legumes are a fascinating group of plants due to their high grain protein contents and ability to fix biological nitrogen. However, the accumulation of excessive salts in soil and the use of saline groundwater are threatening legume production worldwide. Salt stress disturbs photosynthesis and hormonal regulation and causes nutritional imbalance, specific ion toxicity and osmotic effects in legumes to reduce grain yield and quality. Understanding the responses of grain legumes to salt stress and the associated tolerance mechanisms, as well as assessing management options, may help in the development of strategies to improve the performance of grain legumes under salt stress. In this manuscript, we discuss the effects, tolerance mechanisms and management of salt stress in grain legumes. The principal inferences of the review are: (i) salt stress reduces seed germination (by up to more than 50%) either by inhibiting water uptake and/or the toxic effect of ions in the embryo, (ii) salt stress reduces growth (by more than 70%), mineral uptake, and yield (by 12-100%) due to ion toxicity and reduced photosynthesis, (iii) apoplastic acidification is a good indicator of salt stress tolerance, (iv) tolerance to salt stress in grain legumes may develop through excretion and/or compartmentalization of toxic ions, increased antioxidant capacity, accumulation of compatible osmolytes, and/or hormonal regulation, (v) seed priming and nutrient management may improve salt tolerance in grain legumes, (vi) plant growth promoting rhizobacteria and arbuscular mycorrhizal fungi may help to improve salt tolerance due to better plant nutrient availability, and (vii) the integration of screening, innovative breeding, and the development of transgenics and crop management strategies may enhance salt tolerance and yield in grain legumes on salt-affected soils.
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Affiliation(s)
- Muhammad Farooq
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan; The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, Perth, WA 6001, Australia; College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Nirmali Gogoi
- Department of Environmental Science, Tezpur University, Tezpur 784028, Assam, India
| | - Mubshar Hussain
- Department of Agronomy, Bahauddin Zakariya University Multan, Pakistan
| | - Sharmistha Barthakur
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Sreyashi Paul
- Department of Environmental Science, Tezpur University, Tezpur 784028, Assam, India
| | - Nandita Bharadwaj
- Department of Environmental Science, Tezpur University, Tezpur 784028, Assam, India
| | - Hussein M Migdadi
- College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Salem S Alghamdi
- College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, Perth, WA 6001, Australia
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19
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Zadražnik T, Moen A, Egge-Jacobsen W, Meglič V, Šuštar-Vozlič J. Towards a better understanding of protein changes in common bean under drought: A case study of N-glycoproteins. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 118:400-412. [PMID: 28711789 DOI: 10.1016/j.plaphy.2017.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/19/2017] [Accepted: 07/04/2017] [Indexed: 06/07/2023]
Abstract
Drought is one of the major abiotic stress conditions limiting crop growth and productivity. Glycosylation of proteins is very important post-translational modification that is involved in many physiological functions and biological pathways. To understand the involvement of N-glycoproteins in the mechanism of drought response in leaves of common bean, a proteomic approach using lectin affinity chromatography, SDS-PAGE and LC-MS/MS was applied. Quantification of N-glycoproteins was performed using MaxQuant with a label free quantification approach. Thirty five glycoproteins were changed in abundance in leaves of common bean under drought. The majority of these proteins were classified into functional groups that include cell wall processes, defence/stress related proteins and proteins related to proteolysis. Beta-glucosidase showed the highest increase in abundance among proteins involved in cell wall metabolism, suggesting its role in cell wall modification under drought stress. These results fit with the general concept of the stress response in plants and suggest that drought stress might affect biochemical metabolism in the cell wall. The structures of N-glycans were determined manually from spectra, where structures of high mannose, complex and hybrid types of N-glycans were found. The present study provided an insight into the glycoproteins related to drought stress in common bean at the proteome level, which is important for further understanding of molecular mechanisms of drought response in this important legume.
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Affiliation(s)
- Tanja Zadražnik
- Agricultural Institute of Slovenia, 1000 Ljubljana, Slovenia.
| | - Anders Moen
- University of Oslo, Department of Molecular Biosciences, 0316 Oslo, Norway
| | | | - Vladimir Meglič
- Agricultural Institute of Slovenia, 1000 Ljubljana, Slovenia
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20
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Gupta M, Bhaskar PB, Sriram S, Wang PH. Integration of omics approaches to understand oil/protein content during seed development in oilseed crops. PLANT CELL REPORTS 2017; 36:637-652. [PMID: 27796489 DOI: 10.1007/s00299-016-2064-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/11/2016] [Indexed: 05/23/2023]
Abstract
Oilseed crops, especially soybean (Glycine max) and canola/rapeseed (Brassica napus), produce seeds that are rich in both proteins and oils and that are major sources of energy and nutrition worldwide. Most of the nutritional content in the seed is accumulated in the embryo during the seed filling stages of seed development. Understanding the metabolic pathways that are active during seed filling and how they are regulated are essential prerequisites to crop improvement. In this review, we summarize various omics studies of soybean and canola/rapeseed during seed filling, with emphasis on oil and protein traits, to gain a systems-level understanding of seed development. Currently, most (80-85%) of the soybean and rapeseed reference genomes have been sequenced (950 and 850 megabases, respectively). Parallel to these efforts, extensive omics datasets from different seed filling stages have become available. Transcriptome and proteome studies have detected preponderance of starch metabolism and glycolysis enzymes to be the possible cause of higher oil in B. napus compared to other crops. Small RNAome studies performed during the seed filling stages have revealed miRNA-mediated regulation of transcription factors, with the suggestion that this interaction could be responsible for transitioning the seeds from embryogenesis to maturation. In addition, progress made in dissecting the regulation of de novo fatty acid synthesis and protein storage pathways is described. Advances in high-throughput omics and comprehensive tissue-specific analyses make this an exciting time to attempt knowledge-driven investigation of complex regulatory pathways.
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Affiliation(s)
- Manju Gupta
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Pudota B Bhaskar
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | | | - Po-Hao Wang
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
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21
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Cooper JW, Wilson MH, Derks MFL, Smit S, Kunert KJ, Cullis C, Foyer CH. Enhancing faba bean (Vicia faba L.) genome resources. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1941-1953. [PMID: 28419381 PMCID: PMC5429004 DOI: 10.1093/jxb/erx117] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Grain legume improvement is currently impeded by a lack of genomic resources. The paucity of genome information for faba bean can be attributed to the intrinsic difficulties of assembling/annotating its giant (~13 Gb) genome. In order to address this challenge, RNA-sequencing analysis was performed on faba bean (cv. Wizard) leaves. Read alignment to the faba bean reference transcriptome identified 16 300 high quality unigenes. In addition, Illumina paired-end sequencing was used to establish a baseline for genomic information assembly. Genomic reads were assembled de novo into contigs with a size range of 50-5000 bp. Over 85% of sequences did not align to known genes, of which ~10% could be aligned to known repetitive genetic elements. Over 26 000 of the reference transcriptome unigenes could be aligned to DNA-sequencing (DNA-seq) reads with high confidence. Moreover, this comparison identified 56 668 potential splice points in all identified unigenes. Sequence length data were extended at 461 putative loci through alignment of DNA-seq contigs to full-length, publicly available linkage marker sequences. Reads also yielded coverages of 3466× and 650× for the chloroplast and mitochondrial genomes, respectively. Inter- and intraspecies organelle genome comparisons established core legume organelle gene sets, and revealed polymorphic regions of faba bean organelle genomes.
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Affiliation(s)
- James W Cooper
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Michael H Wilson
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Martijn F L Derks
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
- Animal Breeding and Genomics, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Karl J Kunert
- Forestry and Agricultural Biotechnology Institute, Department of Plant Science, University of Pretoria, Hillcrest, Pretoria 0002, South Africa
| | - Christopher Cullis
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106-7080, USA
| | - Christine H Foyer
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, Leeds LS2 9JT, UK
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22
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Padvitski TA, Galinousky DV, Anisimova NV, Baer GY, Pirko YV, Yemets AI, Khotyleva LV, Blume YB, Kilchevsky AV. Analysis of cellulose synthase gene expression strategies in higher plants using RNA-sequencing data. CYTOL GENET+ 2017. [DOI: 10.3103/s0095452717010121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Wang Z, Li P, Yang Y, Chi Y, Fan B, Chen Z. Expression and Functional Analysis of a Novel Group of Legume-specific WRKY and Exo70 Protein Variants from Soybean. Sci Rep 2016; 6:32090. [PMID: 27572297 PMCID: PMC5004194 DOI: 10.1038/srep32090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/02/2016] [Indexed: 12/22/2022] Open
Abstract
Legumes fix atmospheric nitrogen through symbiosis with microorganisms and contain special traits in nitrogen assimilation and associated processes. Recently, we have reported a novel WRKY-related protein (GmWRP1) and a new clade of Exo70 proteins (GmExo70J) from soybean with homologs found only in legumes. GmWRP1 and some of the GmExo70J proteins are localized to Golgi apparatus through a novel N-terminal transmembrane domain. Here, we report further analysis of expression and functions of the novel GmWRP1 and GmExo70J genes. Promoter-GUS analysis in Arabidopsis revealed distinct tissue-specific expression patterns of the GmExo70J genes not only in vegetative but also in reproductive organs including mature tissues, where expression of previously characterized Exo70 genes is usually absent. Furthermore, expression of some GmExo70J genes including GmExo70J1, GmExo70J6 and GmExo70J7 increases greatly in floral organ-supporting receptacles during the development and maturation of siliques, indicating a possible role in seed development. More importantly, suppression of GmWRP1, GmExo70J7, GmExo70J8 and GmExo70J9 expression in soybean using virus- or artificial microRNA-mediated gene silencing resulted in accelerated leaf senescence and reduced nodule formation. These results strongly suggest that legume-specific GmWRP1 and GmExo70J proteins play important roles not only in legume symbiosis but also in other processes critical for legume growth and development.
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Affiliation(s)
- Ze Wang
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Panfeng Li
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Yan Yang
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Yingjun Chi
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Baofang Fan
- Department of Botany and Plant Pathology, 915 W. State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Zhixiang Chen
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
- Department of Botany and Plant Pathology, 915 W. State Street, Purdue University, West Lafayette, IN 47907, USA
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24
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Carter AM, Tegeder M. Increasing Nitrogen Fixation and Seed Development in Soybean Requires Complex Adjustments of Nodule Nitrogen Metabolism and Partitioning Processes. Curr Biol 2016; 26:2044-2051. [PMID: 27451897 DOI: 10.1016/j.cub.2016.06.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/19/2016] [Accepted: 06/01/2016] [Indexed: 10/21/2022]
Abstract
Legumes are able to access atmospheric di-nitrogen (N2) through a symbiotic relationship with rhizobia that reside within root nodules. In soybean, following N2 fixation by the bacteroids, ammonia is finally reduced in uninfected cells to allantoin and allantoic acid [1]. These ureides present the primary long-distance transport forms of nitrogen (N), and are exported from nodules via the xylem for shoot N supply. Transport of allantoin and allantoic acid out of nodules requires the function of ureide permeases (UPS1) located in cells adjacent to the vasculature [2, 3]. We expressed a common bean UPS1 transporter in cortex and endodermis cells of soybean nodules and found that delivery of N from nodules to shoot, as well as seed set, was significantly increased. In addition, the number of transgenic nodules was increased and symbiotic N2 fixation per nodule was elevated, indicating that transporter function in nodule N export is a limiting step in bacterial N acquisition. Further, the transgenic nodules showed considerable increases in nodule N assimilation, ureide synthesis, and metabolite levels. This suggests complex adjustments of nodule N metabolism and partitioning processes in support of symbiotic N2 fixation. We propose that the transgenic UPS1 plants display metabolic and allocation plasticity to overcome N2 fixation and seed yield limitations. Overall, it is demonstrated that transporter function in N export from nodules is a key step for enhancing atmospheric N2 fixation and nodule function and for improving shoot N nutrition and seed development in legumes.
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Affiliation(s)
- Amanda M Carter
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.
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Zheng F, Wu H, Zhang R, Li S, He W, Wong FL, Li G, Zhao S, Lam HM. Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family. BMC Genomics 2016; 17:402. [PMID: 27229309 PMCID: PMC4881053 DOI: 10.1186/s12864-016-2736-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 05/12/2016] [Indexed: 02/06/2023] Open
Abstract
Background Legumes are the second-most important crop family in agriculture for its economic and nutritional values. Disease resistance (R-) genes play an important role in responding to pathogen infections in plants. To further increase the yield of legume crops, we need a comprehensive understanding of the evolution of R-genes in the legume family. Results In this study, we developed a robust pipeline and identified a total of 4,217 R-genes in the genomes of seven sequenced legume species. A dramatic diversity of R-genes with structural variances indicated a rapid birth-and-death rate during the R-gene evolution in legumes. The number of R-genes transiently expanded and then quickly contracted after whole-genome duplications, which meant that R-genes were sensitive to subsequent diploidization. R proteins with the Coiled-coil (CC) domain are more conserved than others in legumes. Meanwhile, other types of legume R proteins with only one or two typical domains were subjected to higher rates of loss during evolution. Although R-genes evolved quickly in legumes, they tended to undergo purifying selection instead of positive selection during evolution. In addition, domestication events in some legume species preferentially selected for the genes directly involved in the plant-pathogen interaction pathway while suppressing those R-genes with low occurrence rates. Conclusions Our results provide insights into the dynamic evolution of R-genes in the legume family, which will be valuable for facilitating genetic improvements in the disease resistance of legume cultivars. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2736-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fengya Zheng
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Haiyang Wu
- BGI-Shenzhen, Shenzhen, 518083, China.,HKU-BGI Bioinformatics Laboratory and Department of Computer Science, University of Hong Kong, Pofulam, Hong Kong
| | - Rongzhi Zhang
- Crop research institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | | | | | - Fuk-Ling Wong
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Genying Li
- Crop research institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Shancen Zhao
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong. .,BGI-Shenzhen, Shenzhen, 518083, China.
| | - Hon-Ming Lam
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong.
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26
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Garg R, Shankar R, Thakkar B, Kudapa H, Krishnamurthy L, Mantri N, Varshney RK, Bhatia S, Jain M. Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea. Sci Rep 2016; 6:19228. [PMID: 26759178 PMCID: PMC4725360 DOI: 10.1038/srep19228] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/09/2015] [Indexed: 01/31/2023] Open
Abstract
Drought and salinity are the major factors that limit chickpea production worldwide. We performed whole transcriptome analyses of chickpea genotypes to investigate the molecular basis of drought and salinity stress response/adaptation. Phenotypic analyses confirmed the contrasting responses of the chickpea genotypes to drought or salinity stress. RNA-seq of the roots of drought and salinity related genotypes was carried out under control and stress conditions at vegetative and/or reproductive stages. Comparative analysis of the transcriptomes revealed divergent gene expression in the chickpea genotypes at different developmental stages. We identified a total of 4954 and 5545 genes exclusively regulated in drought-tolerant and salinity-tolerant genotypes, respectively. A significant fraction (~47%) of the transcription factor encoding genes showed differential expression under stress. The key enzymes involved in metabolic pathways, such as carbohydrate metabolism, photosynthesis, lipid metabolism, generation of precursor metabolites/energy, protein modification, redox homeostasis and cell wall component biogenesis, were affected by drought and/or salinity stresses. Interestingly, transcript isoforms showed expression specificity across the chickpea genotypes and/or developmental stages as illustrated by the AP2-EREBP family members. Our findings provide insights into the transcriptome dynamics and components of regulatory network associated with drought and salinity stress responses in chickpea.
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Affiliation(s)
- Rohini Garg
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Rama Shankar
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Bijal Thakkar
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Lakshmanan Krishnamurthy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Nitin Mantri
- School of Applied Sciences, RMIT University, Victoria, Australia
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Sabhyata Bhatia
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Mukesh Jain
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.,School of Computational &Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Transcriptome analysis of secondary cell wall development in Medicago truncatula. BMC Genomics 2016; 17:23. [PMID: 26728635 PMCID: PMC4700669 DOI: 10.1186/s12864-015-2330-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 12/17/2015] [Indexed: 11/18/2022] Open
Abstract
Background Legumes are important to humans by providing food, feed and raw materials for industrial utilizations. Some legumes, such as alfalfa, are potential bioenergy crops due to their high biomass productivity. Global transcriptional profiling has been successfully used to identify genes and regulatory pathways in secondary cell wall thickening in Arabidopsis, but such transcriptome data is lacking in legumes. Results A systematic microarray assay and high through-put real time PCR analysis of secondary cell wall development were performed along stem maturation in Medicago truncatula. More than 11,000 genes were differentially expressed during stem maturation, and were categorized into 10 expression clusters. Among these, 279 transcription factor genes were correlated with lignin/cellulose biosynthesis, therefore representing putative regulators of secondary wall development. The b-ZIP, NAC, WRKY, C2H2 zinc finger (ZF), homeobox, and HSF gene families were over-represented. Gene co-expression network analysis was employed to identify transcription factors that may regulate the biosynthesis of lignin, cellulose and hemicellulose. As a complementary approach to microarray, real-time PCR analysis was used to characterize the expression of 1,045 transcription factors in the stem samples, and 64 of these were upregulated more than 5-fold during stem maturation. Reverse genetics characterization of a cellulose synthase gene in cluster 10 confirmed its function in xylem development. Conclusions This study provides a useful transcriptome and expression resource for understanding cell wall development, which is pivotal to enhance biomass production in legumes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2330-6) contains supplementary material, which is available to authorized users.
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Dash S, Campbell JD, Cannon EKS, Cleary AM, Huang W, Kalberer SR, Karingula V, Rice AG, Singh J, Umale PE, Weeks NT, Wilkey AP, Farmer AD, Cannon SB. Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. Nucleic Acids Res 2015; 44:D1181-8. [PMID: 26546515 PMCID: PMC4702835 DOI: 10.1093/nar/gkv1159] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/19/2015] [Indexed: 12/02/2022] Open
Abstract
Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working on particular species, and also numerous GDPs for these species. LIS has been redesigned in the last three years both to better integrate data sets across the crop and model legumes, and to better accommodate specialized GDPs that serve particular legume species. To integrate data sets, LIS provides genome and map viewers, holds synteny mappings among all sequenced legume species and provides a set of gene families to allow traversal among orthologous and paralogous sequences across the legumes. To better accommodate other specialized GDPs, LIS uses open-source GMOD components where possible, and advocates use of common data templates, formats, schemas and interfaces so that data collected by one legume research community are accessible across all legume GDPs, through similar interfaces and using common APIs. This federated model for the legumes is managed as part of the ‘Legume Federation’ project (accessible via http://legumefederation.org), which can be thought of as an umbrella project encompassing LIS and other legume GDPs.
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Affiliation(s)
- Sudhansu Dash
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | | | | | - Alan M Cleary
- National Center for Genome Resources, Santa Fe, NM 87505, USA Dept. of Computer Science, Montana State University, Bozeman, MT 59715, USA
| | - Wei Huang
- Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Scott R Kalberer
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011, USA
| | - Vijay Karingula
- Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Alex G Rice
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Jugpreet Singh
- ORISE Fellow, USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Pooja E Umale
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Nathan T Weeks
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011, USA
| | - Andrew P Wilkey
- Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Steven B Cannon
- Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011, USA
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Kunert KJ, van Wyk SG, Cullis CA, Vorster BJ, Foyer CH. Potential use of phytocystatins in crop improvement, with a particular focus on legumes. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3559-70. [PMID: 25944929 DOI: 10.1093/jxb/erv211] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Phytocystatins are a well-characterized class of naturally occurring protease inhibitors that function by preventing the catalysis of papain-like cysteine proteases. The action of cystatins in biotic stress resistance has been studied intensively, but relatively little is known about their functions in plant growth and defence responses to abiotic stresses, such as drought. Extreme weather events, such as drought and flooding, will have negative impacts on the yields of crop plants, particularly grain legumes. The concepts that changes in cellular protein content and composition are required for acclimation to different abiotic stresses, and that these adjustments are achieved through regulation of proteolysis, are widely accepted. However, the nature and regulation of the protein turnover machinery that underpins essential stress-induced cellular restructuring remain poorly characterized. Cysteine proteases are intrinsic to the genetic programmes that underpin plant development and senescence, but their functions in stress-induced senescence are not well defined. Transgenic plants including soybean that have been engineered to constitutively express phytocystatins show enhanced tolerance to a range of different abiotic stresses including drought, suggesting that manipulation of cysteine protease activities by altered phytocystatin expression in crop plants might be used to improve resilience and quality in the face of climate change.
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Affiliation(s)
- Karl J Kunert
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Stefan G van Wyk
- Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Christopher A Cullis
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Barend J Vorster
- Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Christine H Foyer
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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Gentzbittel L, Andersen SU, Ben C, Rickauer M, Stougaard J, Young ND. Naturally occurring diversity helps to reveal genes of adaptive importance in legumes. FRONTIERS IN PLANT SCIENCE 2015; 6:269. [PMID: 25954294 PMCID: PMC4404971 DOI: 10.3389/fpls.2015.00269] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/03/2015] [Indexed: 05/05/2023]
Abstract
Environmental changes challenge plants and drive adaptation to new conditions, suggesting that natural biodiversity may be a source of adaptive alleles acting through phenotypic plasticity and/or micro-evolution. Crosses between accessions differing for a given trait have been the most common way to disentangle genetic and environmental components. Interestingly, such man-made crosses may combine alleles that never meet in nature. Another way to discover adaptive alleles, inspired by evolution, is to survey large ecotype collections and to use association genetics to identify loci of interest. Both of these two genetic approaches are based on the use of biodiversity and may eventually help us in identifying the genes that plants use to respond to challenges such as short-term stresses or those due to global climate change. In legumes, two wild species, Medicago truncatula and Lotus japonicus, plus the cultivated soybean (Glycine max) have been adopted as models for genomic studies. In this review, we will discuss the resources, limitations and future plans for a systematic use of biodiversity resources in model legumes to pinpoint genes of adaptive importance in legumes, and their application in breeding.
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Affiliation(s)
- Laurent Gentzbittel
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus UniversityAarhus, Denmark
| | - Cécile Ben
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Martina Rickauer
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus UniversityAarhus, Denmark
| | - Nevin D. Young
- Department of Plant Pathology, University of MinnesotaSt. Paul, MN, USA
- Department of Plant Biology, University of MinnesotaSt. Paul, MN, USA
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Zargar SM, Nazir M, Rai V, Hajduch M, Agrawal GK, Rakwal R. Towards a common bean proteome atlas: looking at the current state of research and the need for a comprehensive proteome. FRONTIERS IN PLANT SCIENCE 2015; 6:201. [PMID: 25870607 PMCID: PMC4375978 DOI: 10.3389/fpls.2015.00201] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/13/2015] [Indexed: 05/27/2023]
Affiliation(s)
- Sajad M. Zargar
- School of Biotechnology, SK University of Agricultural Sciences and Technology of JammuJammu, India
| | - Muslima Nazir
- Department of Botany, Jamia Hamdard UniversityNew Delhi, India
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, Indian Agricultural Research InstituteNew Delhi, India
| | - Martin Hajduch
- Reproduction and Developmental Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of ScienceNitra, Slovakia
| | - Ganesh K. Agrawal
- Research Laboratory for Biotechnology and BiochemistryKathmandu, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and BiochemistryKathmandu, Nepal
- Organization for Educational Initiatives, University of TsukubaTsukuba, Japan
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Chaudhary J, Patil GB, Sonah H, Deshmukh RK, Vuong TD, Valliyodan B, Nguyen HT. Expanding Omics Resources for Improvement of Soybean Seed Composition Traits. FRONTIERS IN PLANT SCIENCE 2015; 6:1021. [PMID: 26635846 PMCID: PMC4657443 DOI: 10.3389/fpls.2015.01021] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/05/2015] [Indexed: 05/19/2023]
Abstract
Food resources of the modern world are strained due to the increasing population. There is an urgent need for innovative methods and approaches to augment food production. Legume seeds are major resources of human food and animal feed with their unique nutrient compositions including oil, protein, carbohydrates, and other beneficial nutrients. Recent advances in next-generation sequencing (NGS) together with "omics" technologies have considerably strengthened soybean research. The availability of well annotated soybean genome sequence along with hundreds of identified quantitative trait loci (QTL) associated with different seed traits can be used for gene discovery and molecular marker development for breeding applications. Despite the remarkable progress in these technologies, the analysis and mining of existing seed genomics data are still challenging due to the complexity of genetic inheritance, metabolic partitioning, and developmental regulations. Integration of "omics tools" is an effective strategy to discover key regulators of various seed traits. In this review, recent advances in "omics" approaches and their use in soybean seed trait investigations are presented along with the available databases and technological platforms and their applicability in the improvement of soybean. This article also highlights the use of modern breeding approaches, such as genome-wide association studies (GWAS), genomic selection (GS), and marker-assisted recurrent selection (MARS) for developing superior cultivars. A catalog of available important resources for major seed composition traits, such as seed oil, protein, carbohydrates, and yield traits are provided to improve the knowledge base and future utilization of this information in the soybean crop improvement programs.
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Hunt AG. A rapid, simple, and inexpensive method for the preparation of strand-specific RNA-Seq libraries. Methods Mol Biol 2015; 1255:195-207. [PMID: 25487215 DOI: 10.1007/978-1-4939-2175-1_17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
High-throughput sequencing of short cDNA tags, or RNA-Seq, has become a staple of genome-wide gene expression studies in plants. RNA-Seq libraries necessarily contain tags that correspond to the mRNA-poly(A) junction, or polyadenylation site, and thus may be mined for data that can help study alternative polyadenylation. This report presents a simple, rapid, and inexpensive method for preparing strand-specific RNA-Seq libraries from varying quantities of total RNA.
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Affiliation(s)
- Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, 301A Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA,
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