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Chen K, Yang H, Wu D, Peng Y, Lian L, Bai L, Wang L. Weed biology and management in the multi-omics era: Progress and perspectives. PLANT COMMUNICATIONS 2024; 5:100816. [PMID: 38219012 PMCID: PMC11009161 DOI: 10.1016/j.xplc.2024.100816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/20/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.
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Affiliation(s)
- Ke Chen
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Haona Yang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Di Wu
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yajun Peng
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lei Lian
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao 266000, China
| | - Lianyang Bai
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Lifeng Wang
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
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Cao X, Xiao L, Zhang L, Chen M, Bian P, Ma Q, Chen S, He Q, Ma X, Yao Z, Zhao S. Phenotypic and histological analyses on the resistance of melon to Phelipanche aegyptiaca. FRONTIERS IN PLANT SCIENCE 2023; 14:1070319. [PMID: 37035047 PMCID: PMC10079939 DOI: 10.3389/fpls.2023.1070319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/14/2023] [Indexed: 06/19/2023]
Abstract
Melon (Cucumis melo L.) is an economically important crop in Xinjiang, China, but its production is constrained by the parasitic plant Phelipanche aegyptiaca that attaches to the roots of many crops and causes severe stunting and loss of yield. Rhizotron, pot, and field experiments were employed to evaluate the resistance of 27 melon cultivars to P. aegyptiaca. Then, the resistant and susceptible cultivars were inoculated with P. aegyptiaca from six populations to assess their resistance stability and broad spectrum. Further microscopic and histological analyses were used to clarify the resistance phenotypes and histological structure. The results showed that Huangpi 9818 and KR1326 were more resistant to P. aegyptiaca compared to other cultivars in the rhizotron, pot, and field experiments. In addition, compared to the susceptible cultivar K1076, Huangpi 9818 and KR1326 showed broad-spectrum resistance to six P. aegyptiaca populations. These two resistant cultivars had lower P. aegyptiaca biomass and fewer and smaller P. aegyptiaca attachments on their roots compared to susceptible cultivar K1076. KR1326 (resistant) and K1076 (susceptible) were selected to further study resistance phenotypes and mechanisms. Germination-inducing activity of root exudates and microscopic analysis showed that the resistance in KR1326 was not related to low induction of P. aegyptiaca germination. The tubercles of parasite on KR1326 were observed slightly brown at 14 days after inoculation (DAI), the necrosis and arrest of parasite development occurred at 23 DAI. Histological analysis of necrosis tubercles showed that the endophyte of parasite had reached host central cylinder, connected with host xylem, and accumulation of secretions and callose were detected in neighbouring cells. We concluded that KR1326 is an important melon cultivar for P. aegyptiaca resistance that could be used to expand the genetic basis of cultivated muskmelon for resistance to the parasite.
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Affiliation(s)
- Xiaolei Cao
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Shihezi University, Shihezi, Xinjiang, China
| | - Lifeng Xiao
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang, China
| | - Lu Zhang
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang, China
| | - Meixiu Chen
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang, China
| | - Pengxuan Bian
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang, China
| | - Qianqian Ma
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang, China
| | - Siyu Chen
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang, China
| | - Quanlong He
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang, China
| | - Xinli Ma
- Hami Melon Research Center, Xinjiang Academy of Agricultural Science, Urumqi, Xinjiang, China
| | - Zhaoqun Yao
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang, China
| | - Sifeng Zhao
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang, China
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3
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Genomic and Epigenomic Mechanisms of the Interaction between Parasitic and Host Plants. Int J Mol Sci 2023; 24:ijms24032647. [PMID: 36768970 PMCID: PMC9917227 DOI: 10.3390/ijms24032647] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 02/01/2023] Open
Abstract
Parasitic plants extract nutrients from the other plants to finish their life cycle and reproduce. The control of parasitic weeds is notoriously difficult due to their tight physical association and their close biological relationship to their hosts. Parasitic plants differ in their susceptible host ranges, and the host species differ in their susceptibility to parasitic plants. Current data show that adaptations of parasitic plants to various hosts are largely genetically determined. However, multiple cases of rapid adaptation in genetically homogenous parasitic weed populations to new hosts strongly suggest the involvement of epigenetic mechanisms. Recent progress in genome-wide analyses of gene expression and epigenetic features revealed many new molecular details of the parasitic plants' interactions with their host plants. The experimental data obtained in the last several years show that multiple common features have independently evolved in different lines of the parasitic plants. In this review we discuss the most interesting new details in the interaction between parasitic and host plants.
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Jhu MY, Sinha NR. Parasitic Plants: An Overview of Mechanisms by Which Plants Perceive and Respond to Parasites. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:433-455. [PMID: 35363532 DOI: 10.1146/annurev-arplant-102820-100635] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In contrast to most autotrophic plants, which produce carbohydrates from carbon dioxide using photosynthesis, parasitic plants obtain water and nutrients by parasitizing host plants. Many important crop plants are infested by these heterotrophic plants, leading to severe agricultural loss and reduced food security. Understanding how host plants perceive and resist parasitic plants provides insight into underlying defense mechanisms and the potential for agricultural applications. In this review, we offer a comprehensive overview of the current understanding of host perception of parasitic plants and the pre-attachment and post-attachment defense responses mounted by the host. Since most current research overlooks the role of organ specificity in resistance responses, we also summarize the current understanding and cases of cross-organ parasitism, which indicates nonconventional haustorial connections on other host organs, for example, when stem parasitic plants form haustoria on their host roots. Understanding how different tissue types respond to parasitic plants could provide the potential for developing a universal resistance mechanism in crops against both root and stem parasitic plants.
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Affiliation(s)
- Min-Yao Jhu
- Department of Plant Biology, University of California, Davis, California, USA;
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, California, USA;
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Li J, Li X, Han P, Liu H, Gong J, Zhou W, Shi B, Liu A, Xu L. Genome-wide investigation of bHLH genes and expression analysis under different biotic and abiotic stresses in Helianthus annuus L. Int J Biol Macromol 2021; 189:72-83. [PMID: 34411617 DOI: 10.1016/j.ijbiomac.2021.08.072] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 10/20/2022]
Abstract
The basic helix-loop-helix (bHLH) transcription factors play important roles in many processes such as plant growth, metabolism and response to biotic/abiotic stresses. Sunflower (Helianthus annuus) is a major oil crop, cultivated throughout the world. However, no systematic characterization of bHLH gene members in sunflower (HabHLH) and their functions involved in drought, cadmium tolerance and Orobanche cumana resistance has been reported yet. In this study, 183 HabHLH genes were identified and named according to their chromosomal locations. We classified these proteins into 21 subfamilies by phylogenetic tree analysis. Subsequently, DNA-binding patterns, sequence analysis, duplication analysis and gene structures were analyzed. All of the HabHLH genes were randomly distributed on 17 chromosomes, and 10 pairs of tandem duplicated genes and one pair of segmental duplicated genes were detected in the HabHLH family. Among the duplicated gene pairs, eight pairs of HabHLH genes suffer from positive selection. Moreover, qRT-PCR results revealed significant up-regulated expression of HabHLH024 gene in response to both abiotic (cadmium, drought) and biotic (Orobanche cumana) stresses, suggesting its important functions in response to different stresses. Therefore, HabHLH024 would be the potential candidate gene for the sunflower tolerance breeding.
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Affiliation(s)
- Juanjuan Li
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Xin Li
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Peng Han
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Hui Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, WA 6009, Australia
| | - Jianchuan Gong
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Weijun Zhou
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Bixian Shi
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China.
| | - Ling Xu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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Biological and Transcriptomic Characterization of Pre-Haustorial Resistance to Sunflower Broomrape ( Orobanche cumana W.) in Sunflowers ( Helianthus annuus). PLANTS 2021; 10:plants10091810. [PMID: 34579343 PMCID: PMC8465872 DOI: 10.3390/plants10091810] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/01/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022]
Abstract
Infestations with sunflower broomrape (Orobanche cumana Wallr.), an obligatory root parasite, constitute a major limitation to sunflower production in many regions around the world. Breeding for resistance is the most effective approach to reduce sunflower broomrape infestation, yet resistance mechanisms are often broken by new races of the pathogen. Elucidating the mechanisms controlling resistance to broomrape at the molecular level is, thus, a desirable way to obtain long-lasting resistance. In this study, we investigated broomrape resistance in a confectionery sunflower cultivar with a robust and long-lasting resistance to sunflower broomrape. Visual screening and histological examination of sunflower roots revealed that penetration of the broomrape haustorium into the sunflower roots was blocked at the cortex, indicating a pre-haustorial mechanism of resistance. A comparative RNA sequencing between broomrape-resistant and -susceptible accessions allowed the identification of genes that were significantly differentially expressed upon broomrape infestation. Among these genes were β-1,3-endoglucanase, β-glucanase, and ethylene-responsive transcription factor 4 (ERF4). These genes were previously reported to be pathogenesis-related in other plant species. This transcriptomic investigation, together with the histological examinations, led us to conclude that the resistance mechanism involves the identification of the broomrape and the consequent formation of a physical barrier that prevents the establishment of the broomrape into the sunflower roots.
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Jocković M, Jocić S, Cvejić S, Marjanović-Jeromela A, Jocković J, Radanović A, Miladinović D. Genetic Improvement in Sunflower Breeding—Integrated Omics Approach. PLANTS 2021; 10:plants10061150. [PMID: 34200113 PMCID: PMC8228292 DOI: 10.3390/plants10061150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 01/23/2023]
Abstract
Foresight in climate change and the challenges ahead requires a systematic approach to sunflower breeding that will encompass all available technologies. There is a great scarcity of desirable genetic variation, which is in fact undiscovered because it has not been sufficiently researched as detection and designing favorable genetic variation largely depends on thorough genome sequencing through broad and deep resequencing. Basic exploration of genomes is insufficient to find insight about important physiological and molecular mechanisms unique to crops. That is why integrating information from genomics, epigenomics, transcriptomics, proteomics, metabolomics and phenomics enables a comprehensive understanding of the molecular mechanisms in the background of architecture of many important quantitative traits. Omics technologies offer novel possibilities for deciphering the complex pathways and molecular profiling through the level of systems biology and can provide important answers that can be utilized for more efficient breeding of sunflower. In this review, we present omics profiling approaches in order to address their possibilities and usefulness as a potential breeding tools in sunflower genetic improvement.
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Affiliation(s)
- Milan Jocković
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
- Correspondence:
| | - Siniša Jocić
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Sandra Cvejić
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Ana Marjanović-Jeromela
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Jelena Jocković
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Dositeja Obradovića 3, 21000 Novi Sad, Serbia;
| | - Aleksandra Radanović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
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Li J, Islam F, Huang Q, Wang J, Zhou W, Xu L, Yang C. Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses. PLoS One 2020; 15:e0241965. [PMID: 33270651 PMCID: PMC7714227 DOI: 10.1371/journal.pone.0241965] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/26/2020] [Indexed: 12/05/2022] Open
Abstract
WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. Sunflower (Helianthus annuus L.) is one of the important vegetable oil supplies in the world. However, the information about WRKY genes in sunflower is limited. In this study, ninety HaWRKY genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group. Besides, HaWRKY genes within the same group or subgroup generally showed similar exon-intron structures and motif compositions. The gene duplication analysis showed that five pairs of HaWRKY genes (HaWRKY8/9, HaWRKY53/54, HaWRKY65/66, HaWRKY66/67 and HaWRKY71/72) are tandem duplicated and four HaWRKY gene pairs (HaWRKY15/82, HaWRKY25/65, HaWRKY28/55 and HaWRKY50/53) are also identified as segmental duplication events, indicating that these duplication genes were contribute to the diversity and expansion of HaWRKY gene families. The dN/dS ratio of these duplicated gene pairs were also calculated to understand the evolutionary constraints. In addition, synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses, which provide a foundation for further functional analyses of these genes. Those functional genes related to stress tolerance and quality improvement could be applied in marker assisted breeding of the crop.
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Affiliation(s)
- Juanjuan Li
- Zhejiang Key Lab of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Faisal Islam
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Lab of Spectroscopy Sensing, Zhejiang University, Hangzhou, China
| | - Qian Huang
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Lab of Spectroscopy Sensing, Zhejiang University, Hangzhou, China
| | - Jian Wang
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Lab of Spectroscopy Sensing, Zhejiang University, Hangzhou, China
| | - Weijun Zhou
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Lab of Spectroscopy Sensing, Zhejiang University, Hangzhou, China
| | - Ling Xu
- Zhejiang Key Lab of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- * E-mail: (LX); (CY)
| | - Chong Yang
- Bioengineering Research Laboratory, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
- * E-mail: (LX); (CY)
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Lian D, Li L, Liu X, Zhong X, Wang H, Zhou S, Gu L. Time-scale dynamics of proteome predicts the central carbon metabolism involved in triterpenoid accumulation responsive to nitrogen limitation in Ganoderma lucidum. Fungal Biol 2020; 125:294-304. [PMID: 33766308 DOI: 10.1016/j.funbio.2020.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/18/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
Central carbon metabolism describes the integration of transport pathway of main carbon sources inside the cell. Nitrogen (N) limitation is a favorable approach to stimulate ganoderic triterpenoid (GT) accumulation in Ganoderma lucidum. In this study, the dynamic regulation of metabolism reassignment towards GT biosynthesis responsive to N limitation was investigated by iTRAQ-based proteome. Physiological data suggested that N limitation slightly affected cell growth but significantly enhanced GT contents in the initial 20 days. From day 10, the protein contents were halted by prolonged N limitation duration. Proteomics-based investigations revealed that the carbon skeletons integrated into GT precursors were regenerated by glycolysis and the tricarboxylic acid (TCA) cycle. Cells strategically reserved nitrogen by barely incorporating it into TCA cycle intermediates to form amino acids, and enzymes involved in protein degradation were up regulated. Furthermore, regulation of proteins in response to abiotic stress and oxidation- reduction processes played a critical role in maintaining cellular homeostasis. These findings indicated that the flux of carbon into GT following N deficiency was a consequence of the remodeling of intermediate metabolism in TCA cycle and glycolysis reactions. This study provides a rationale for genetic engineering of G. lucidum, which may enable synchronized biomass and GT synthesis.
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Affiliation(s)
- Danhong Lian
- Food and Health Engineering Research Center of State Education Ministry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Lian Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xin Liu
- Food and Health Engineering Research Center of State Education Ministry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xin Zhong
- Food and Health Engineering Research Center of State Education Ministry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Haizhen Wang
- Food and Health Engineering Research Center of State Education Ministry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Sha Zhou
- Food and Health Engineering Research Center of State Education Ministry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Gu
- Food and Health Engineering Research Center of State Education Ministry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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Hu L, Wang J, Yang C, Islam F, Bouwmeester HJ, Muños S, Zhou W. The Effect of Virulence and Resistance Mechanisms on the Interactions between Parasitic Plants and Their Hosts. Int J Mol Sci 2020; 21:E9013. [PMID: 33260931 PMCID: PMC7730841 DOI: 10.3390/ijms21239013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/26/2020] [Accepted: 10/31/2020] [Indexed: 01/06/2023] Open
Abstract
Parasitic plants have a unique heterotrophic lifestyle based on the extraction of water and nutrients from host plants. Some parasitic plant species, particularly those of the family Orobanchaceae, attack crops and cause substantial yield losses. The breeding of resistant crop varieties is an inexpensive way to control parasitic weeds, but often does not provide a long-lasting solution because the parasites rapidly evolve to overcome resistance. Understanding mechanisms underlying naturally occurring parasitic plant resistance is of great interest and could help to develop methods to control parasitic plants. In this review, we describe the virulence mechanisms of parasitic plants and resistance mechanisms in their hosts, focusing on obligate root parasites of the genera Orobanche and Striga. We noticed that the resistance (R) genes in the host genome often encode proteins with nucleotide-binding and leucine-rich repeat domains (NLR proteins), hence we proposed a mechanism by which host plants use NLR proteins to activate downstream resistance gene expression. We speculated how parasitic plants and their hosts co-evolved and discussed what drives the evolution of virulence effectors in parasitic plants by considering concepts from similar studies of plant-microbe interaction. Most previous studies have focused on the host rather than the parasite, so we also provided an updated summary of genomic resources for parasitic plants and parasitic genes for further research to test our hypotheses. Finally, we discussed new approaches such as CRISPR/Cas9-mediated genome editing and RNAi silencing that can provide deeper insight into the intriguing life cycle of parasitic plants and could potentially contribute to the development of novel strategies for controlling parasitic weeds, thereby enhancing crop productivity and food security globally.
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Affiliation(s)
- Luyang Hu
- Institute of Crop Science and Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China; (L.H.); (J.W.); (F.I.)
| | - Jiansu Wang
- Institute of Crop Science and Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China; (L.H.); (J.W.); (F.I.)
| | - Chong Yang
- Bioengineering Research Laboratory, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou 510316, China;
| | - Faisal Islam
- Institute of Crop Science and Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China; (L.H.); (J.W.); (F.I.)
| | - Harro J. Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1000 BE Amsterdam, The Netherlands;
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRAE, CNRS, 31326 Castanet-Tolosan, France;
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China; (L.H.); (J.W.); (F.I.)
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Zorrilla JG, Cala A, Rial C, R Mejías FJ, Molinillo JMG, Varela RM, Macías FA. Synthesis of Active Strigolactone Analogues Based on Eudesmane- and Guaiane-Type Sesquiterpene Lactones. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9636-9645. [PMID: 32794743 DOI: 10.1021/acs.jafc.0c02361] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Strigolactones are natural products that are exuded by plants and stimulate parasitic weed germination. Their use in herbicides is limited since they are produced in small quantities, but the synthesis of bioactive analogues provides an alternative source. In this work, eleven analogues have been synthesized. Among them, nine compounds belong to a novel family named eudesmanestrigolactones. The procedure is short (3-6 steps), the starting materials are isolated on a multigram scale, and global yields are up to 8%, which significantly enhance isolated yields. In bioassay, the compounds germinated high percentages of Phelipanche ramosa, Orobanche cumana, and Orobanche crenata seeds, even at nanogram doses (100 nM). Bioactivity was stereochemistry-dependent, and it was discussed in terms of the presence and geometry of the enol ether, orientation of the butenolide, and unsaturation of ring A. The reported compounds provide a set of readily obtained allelochemicals with potential applications as preventive herbicides.
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Affiliation(s)
- Jesús G Zorrilla
- Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus CEIA3, School of Science, University of Cadiz, C/Republica Saharaui, 7, 11510 Puerto Real, Cádiz, Spain
| | - Antonio Cala
- Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus CEIA3, School of Science, University of Cadiz, C/Republica Saharaui, 7, 11510 Puerto Real, Cádiz, Spain
| | - Carlos Rial
- Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus CEIA3, School of Science, University of Cadiz, C/Republica Saharaui, 7, 11510 Puerto Real, Cádiz, Spain
| | - Francisco J R Mejías
- Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus CEIA3, School of Science, University of Cadiz, C/Republica Saharaui, 7, 11510 Puerto Real, Cádiz, Spain
| | - José M G Molinillo
- Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus CEIA3, School of Science, University of Cadiz, C/Republica Saharaui, 7, 11510 Puerto Real, Cádiz, Spain
| | - Rosa M Varela
- Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus CEIA3, School of Science, University of Cadiz, C/Republica Saharaui, 7, 11510 Puerto Real, Cádiz, Spain
| | - Francisco A Macías
- Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus CEIA3, School of Science, University of Cadiz, C/Republica Saharaui, 7, 11510 Puerto Real, Cádiz, Spain
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12
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De novo Transcriptome Reveals Gene Changes in the Development of the Endosperm Chalazal Haustorium in Taxillus chinensis (DC.) Danser. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7871918. [PMID: 32149138 PMCID: PMC7053452 DOI: 10.1155/2020/7871918] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 12/26/2019] [Indexed: 01/25/2023]
Abstract
Loranthus (Taxillus chinensis) is a facultative, hemiparasite and stem parasitic plant that attacks other plants for living. Transcriptome sequencing and bioinformatics analysis were applied in this study to identify the gene expression profiles of fresh seeds (CK), baby (FB), and adult haustoria tissues (FD). We assembled 160,571 loranthus genes, of which 64,926, 35,417, and 47,249 were aligned to NR, GO, and KEGG pathway databases, respectively. We identified 14,295, 15,921, and 16,402 genes in CK, FB, and FD, respectively. We next identified 5,480 differentially expressed genes (DEGs) in the process, of which 258, 174, 81, and 94 were encoding ribosomal proteins (RP), transcription factors (TF), ubiquitin, and disease resistance proteins, respectively. Some DEGs were identified to be upregulated along with the haustoria development (e.g., 68 RP and 26 ubiquitin genes). Notably, 36 RP DEGs peak at FB; 10 ER, 5 WRKY, 6 bHLH, and 4 MYB TF genes upregulated only in FD. Further, we identified 4 out of 32 microRNA genes dysregulated in the loranthus haustoria development. This is the first haustoria transcriptome of loranthus, and our findings will improve our understanding of the molecular mechanism of haustoria.
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13
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Genetic and Genomic Tools in Sunflower Breeding for Broomrape Resistance. Genes (Basel) 2020; 11:genes11020152. [PMID: 32019223 PMCID: PMC7073512 DOI: 10.3390/genes11020152] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 01/24/2020] [Accepted: 01/25/2020] [Indexed: 11/16/2022] Open
Abstract
Broomrape is a root parasitic plant causing yield losses in sunflower production. Since sunflower is an important oil crop, the development of broomrape-resistant hybrids is the prime breeding objective. Using conventional plant breeding methods, breeders have identified resistant genes and developed a number of hybrids resistant to broomrape, adapted to different growing regions worldwide. However, the spread of broomrape into new countries and the development of new and more virulent races have been noted intensively. Recent advances in sunflower genomics provide additional tools for plant breeders to improve resistance and find durable solutions for broomrape spread and virulence. This review describes the structure and distribution of new, virulent physiological broomrape races, sources of resistance for introduction into susceptible cultivated sunflower, qualitative and quantitative resistance genes along with gene pyramiding and marker assisted selection (MAS) strategies applied in the process of increasing sunflower resistance. In addition, it presents an overview of underutilized biotechnological tools, such as phenotyping, -omics, and genome editing techniques, which need to be introduced in the study of sunflower resistance to broomrape in order to achieve durable resistance.
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14
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Peng W, Ming QL, Zhai X, Zhang Q, Rahman K, Wu SJ, Qin LP, Han T. Polysaccharide Fraction Extracted from Endophytic Fungus Trichoderma atroviride D16 Has an Influence on the Proteomics Profile of the Salvia miltiorrhiza Hairy Roots. Biomolecules 2019; 9:E415. [PMID: 31455038 PMCID: PMC6769542 DOI: 10.3390/biom9090415] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 01/30/2023] Open
Abstract
Trichoderma atroviride develops a symbiont relationship with Salvia miltiorrhiza and this association involves a number of signaling pathways and proteomic responses between both partners. In our previous study, we have reported that polysaccharide fraction (PSF) of T. atroviride could promote tanshinones accumulation in S.miltiorrhiza hairy roots. Consequently, the present data elucidates the broad proteomics changes under treatment of PSF. Furthermore, we reported several previously undescribed and unexpected responses, containing gene expression patterns consistent with biochemical stresses and metabolic patterns inside the host. In summary, the PSF-induced tanshinones accumulation in S.miltiorrhiza hairy roots may be closely related to Ca2+ triggering, peroxide reaction, protein phosphorylation, and jasmonic acid (JA) signal transduction, leading to an increase in leucine-rich repeat (LRR) protein synthesis. This results in the changes in basic metabolic flux of sugars, amino acids, and protein synthesis, along with signal defense reactions. The results reported here increase our understanding of the interaction between T.atroviride and S.miltiorrhiza and specifically confirm the proteomic responses underlying the activities of PSF.
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Affiliation(s)
- Wei Peng
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, No.1166 Liutai Avenue, Chengdu 611137, China
| | - Qian-Liang Ming
- Department of Pharmacognosy, School of Pharmacy, Army Medical University, 30 Gaotanyan Street, Chongqing 400038, China
| | - Xin Zhai
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Qing Zhang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, No.1166 Liutai Avenue, Chengdu 611137, China
| | - Khalid Rahman
- Faculty of Science, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Si-Jia Wu
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Lu-Ping Qin
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Ting Han
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China.
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15
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Niu L, Xu X, Liu H, Wu X, Wang W. On the Promising Role of Enzyme Activity Assay in Interpreting Comparative Proteomic Data in Plants. Proteomics 2018; 18:e1800234. [PMID: 30179302 DOI: 10.1002/pmic.201800234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/18/2018] [Indexed: 11/09/2022]
Abstract
Comparative proteomics is widely used to detect protein changes, especially differential abundance proteins (DAPs) that are involved in plant responses to development, disease, or environment. Once DAPs are identified, it is essential to validate any change in their abundance, and their role in the biological process under study. In addition to common confirmation by quantitative RT-PCR, immunoblot, and multiple reaction monitoring analysis, it has been proposed that enzyme activity assay (EAA) can be complementary to the standard proteomics results, especially regarding the elucidation of protein (enzyme) function and the mechanism of enzyme-associated biochemical or metabolic pathways. The enzymes discussed here are the DAPs identified in comparative plant proteomics. Despite the small number of enzymes in a proteome, they often make up a substantial proportion of the DAPs identified in comparative studies. Currently, only a few studies have performed EAA to complement the interpretation of proteomic data, especially activity-based protein profiling. This viewpoint aims to arouse the attention of proteomic researchers on the promising role of EAA in plant proteomics and highlights the need for high-throughput assays of enzyme activities in comparative plant proteomics.
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Affiliation(s)
- Liangjie Niu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiangru Xu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hui Liu
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaolin Wu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wei Wang
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China.,College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
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16
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Wang WQ, Jensen ON, Møller IM, Hebelstrup KH, Rogowska-Wrzesinska A. Evaluation of sample preparation methods for mass spectrometry-based proteomic analysis of barley leaves. PLANT METHODS 2018; 14:72. [PMID: 30159003 PMCID: PMC6109330 DOI: 10.1186/s13007-018-0341-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 08/16/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Sample preparation is a critical process for proteomic studies. Many efficient and reproducible sample preparation methods have been developed for mass spectrometry-based proteomic analysis of human and animal tissues or cells, but no attempt has been made to evaluate these protocols for plants. We here present an LC-MS/MS-based proteomics study of barley leaf aimed at optimization of methods to achieve efficient and unbiased trypsin digestion of proteins prior to LC-MS/MS based sequencing and quantification of peptides. We evaluated two spin filter-aided sample preparation protocols using either sodium dodecyl-sulphate or sodium deoxycholate (SDC), and three in-solution digestion (ISD) protocols using SDC or trichloroacetic acid/acetone precipitation. RESULTS The proteomics workflow identified and quantified up to 1800 barley proteins based on sequencing of up to 6900 peptides per sample. The two spin filter-based protocols provided a 12-38% higher efficiency than the ISD protocols, including more proteins of low abundance. Among the ISD protocols, a simple one-step reduction and S-alkylation method (OP-ISD) was the most efficient for barley leaf sample preparation; it identified and quantified 1500 proteins and displayed higher peptide-to-protein inference ratio and higher average amino acid sequence coverage of proteins. The two spin filter-aided sample preparation protocols are compatible with TMT labelling for quantitative proteomics studies. They exhibited complementary performance as about 30% of the proteins were identified by either one or the other protocol, but also demonstrated a positive bias for membrane proteins when using SDC as detergent. CONCLUSIONS We provide detailed protocols for efficient plant protein sample preparation for LC-MS/MS-based proteomics studies. Spin filter-based protocols are the most efficient for the preparation of leaf samples for MS-based proteomics. However, a simple protocol provides comparable results although with different peptide digestion profile.
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Affiliation(s)
- Wei-Qing Wang
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Ole Nørregaard Jensen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark
| | - Kim H. Hebelstrup
- Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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17
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Chen W, Wan S, Shen L, Zhou Y, Huang C, Chu P, Guan R. Histological, Physiological, and Comparative Proteomic Analyses Provide Insights into Leaf Rolling in Brassica napus. J Proteome Res 2018; 17:1761-1772. [PMID: 29693398 DOI: 10.1021/acs.jproteome.7b00744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Moderate leaf rolling is important in ideotype breeding, as it improves photosynthetic efficiency and therefore increases crop yields. To understand the regulatory network of leaf rolling in Brassica napus, a down-curved leaf mutant ( Bndcl1) has been investigated. Physiological analyses indicated that the chlorophyll contents and antioxidant enzyme activities were remarkably increased and the photosynthetic performance was significantly improved in Bndcl1. Consistent with these findings, 943 differentially accumulated proteins (DAPs) were identified in the Bndcl1 mutant and its wild-type plants using iTRAQ-based comparative proteomic analyses. Enrichment analysis of proteins with higher abundance in Bndcl1 revealed that the functional category "photosynthesis" was significantly overrepresented. Moreover, proteins associated with oxidative stress response and photosystem II repairing were also up-accumulated in Bndcl1, which might help the mutant to sustain the photosynthetic efficiency under unfavorable conditions. Histological observation showed that the mutant displayed defects in adaxial-abaxial patterning. Important DAPs associated with leaf polarity establishment were detected in Bndcl1, including ribosomal proteins, proteins involved in post-transcriptional gene silencing, and proteins related to brassinosteroid. Together, our findings may help clarify the mechanisms underlying leaf rolling and its physiological effects on plants and may facilitate ideotype breeding in Brassica napus.
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Affiliation(s)
- Wenjing Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
| | - Shubei Wan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
| | - Linkui Shen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
| | - Ying Zhou
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
| | - Chengwei Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
| | - Pu Chu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
| | - Rongzhan Guan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production , Nanjing Agricultural University , No. 1 Weigang , Nanjing , Jiangsu 210095 , PR China
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18
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Dimitrijevic A, Horn R. Sunflower Hybrid Breeding: From Markers to Genomic Selection. FRONTIERS IN PLANT SCIENCE 2018; 8:2238. [PMID: 29387071 PMCID: PMC5776114 DOI: 10.3389/fpls.2017.02238] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/20/2017] [Indexed: 05/03/2023]
Abstract
In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi, or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare. Integrative approaches combining omic technologies (genomics, transcriptomics, proteomics, metabolomics and phenomics) using bioinformatic tools will facilitate the identification of target genes and markers for complex traits and will give a better insight into the mechanisms behind the traits.
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Affiliation(s)
| | - Renate Horn
- Institut für Biowissenschaften, Abteilung Pflanzengenetik, Universität Rostock, Rostock, Germany
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19
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Wang J, Islam F, Li L, Long M, Yang C, Jin X, Ali B, Mao B, Zhou W. Complementary RNA-Sequencing Based Transcriptomics and iTRAQ Proteomics Reveal the Mechanism of the Alleviation of Quinclorac Stress by Salicylic Acid in Oryza sativa ssp. japonica. Int J Mol Sci 2017; 18:ijms18091975. [PMID: 28906478 PMCID: PMC5618624 DOI: 10.3390/ijms18091975] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 12/16/2022] Open
Abstract
To uncover the alleviation mechanism of quinclorac stress by salicylic acid (SA), leaf samples of Oryza sativa ssp. Japonica under quinclorac stress with and without SA pre-treatment were analyzed for transcriptional and proteomic profiling to determine the differentially expressed genes (DEGs) and proteins (DEPs), respectively. Results showed that quinclorac stress altered the expression of 2207 DEGs (1427 up-regulated, 780 down-regulated) and 147 DEPs (98 down-regulated, 49 up-regulated). These genes and proteins were enriched in glutathione (GSH) metabolism, porphyrin and chlorophyll metabolism, the biosynthesis of secondary metabolites, glyoxylate and dicarboxylate metabolism, and so on. It also influenced apetala2- ethylene-responsive element binding protein (AP2-EREBP) family, myeloblastosis (MYB) family and WRKY family transcription factors. After SA pre-treatment, 697 genes and 124 proteins were differentially expressed. Pathway analysis showed similar enrichments in GSH, glyoxylate and dicarboxylate metabolism. Transcription factors were distributed in basic helix-loop-helix (bHLH), MYB, Tify and WRKY families. Quantitative real-time PCR results revealed that quinclorac stress induced the expression of glutathion reductase (GR) genes (OsGR2, OsGR3), which was further pronounced by SA pre-treatment. Quinclorac stress further mediated the accumulation of acetaldehyde in rice, while SA enhanced the expression of OsALDH2B5 and OsALDH7 to accelerate the metabolism of herbicide quinclorac for the protection of rice. Correlation analysis between transcriptome and proteomics demonstrated that, under quinclorac stress, correlated proteins/genes were mainly involved in the inhibition of intermediate steps in the biosynthesis of chlorophyll. Other interesting proteins/genes and pathways regulated by herbicide quinclorac and modulated by SA pre-treatment were also discussed, based on the transcriptome and proteomics results.
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Affiliation(s)
- Jian Wang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Faisal Islam
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Lan Li
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Meijuan Long
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Chong Yang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Xiaoli Jin
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Basharat Ali
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
- Institute of Crop Science and Resource Conservation (INRES), Abiotic Stress Tolerance in Crops, University of Bonn, 53115 Bonn, Germany.
| | - Bizeng Mao
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
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