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Jin W, Xie K, Tang W, Yang Y, Zhang J, Yu X, Lu Y. Comparative metabolomics and transcriptomics provide new insights into florpyrauxifen-benzyl resistance in Echinochloa glabrescens. FRONTIERS IN PLANT SCIENCE 2024; 15:1392460. [PMID: 39022606 PMCID: PMC11253777 DOI: 10.3389/fpls.2024.1392460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024]
Abstract
Echinochloa glabrescens Munro ex Hook. f. is a weed of the genus Echinocloa (Echinocloa spp.) that occurs frequently in paddy fields, causing serious harm to rice production. Florpyrauxifen-benzyl (FPB) is a foliar-applied herbicide used to control Echinocloa spp. in paddy fields. However, in recent years, with the widespread use of FPB in rice production, FPB-resistant barnyard grasses have been reported. Here, we identified an FPB-resistant E. glabrescens population with a resistance index (RI) of 10.65 and conducted a comparative analysis using untargeted metabolomics and transcriptomics to investigate the differences between an FPB-resistant E. glabrescens population and a susceptible E. glabrescens population after treatment with the recommended field dose of FPB. Our results showed that the FPB-resistant E. glabrescens had 115 differentially accumulated metabolites (DAMs; 65 up-regulated and 50 down-regulated) and 6397 differentially expressed genes (DEGs; 65 up-regulated and 50 down-regulated) compared to the susceptible E. glabrescens. The analysis of DAMs and DEGs revealed that DAMs were significantly enriched in Glutathione metabolism, Arginine and proline metabolism, and Zeatin biosynthesis pathways, while DEGs were mainly enriched in carbon fixation in photosynthetic organisms, photosynthesis, cyanoamino acid metabolism and glutathione metabolism, etc. The glutathione metabolism pathway was found to be significantly enriched for both DEGs and DAMs. Within this pathway, the metabolites (spermine) and genes (GSTU8, GSTU18, GSTF1) may play a pivotal role in the resistance mechanism of FPB-resistant E. glabrescens. Furthermore, we demonstrated the presence of GST-mediated metabolic resistance in an FPB-resistant E. glabrescens population by using NBD-Cl. Overall, our study provides new insights into the underlying mechanisms of E. glabrescens resistance to FPB through a comparative analysis of untargeted metabolomics and transcriptomics. Additionally, we identified the GST-mediated metabolic resistance in an FPB-resistant E. glabrescens population, and screened for three candidate genes (GSTU8, GSTU18, GSTF1), which has significant implications for improving the weed management efficacy of FPB in rice production and guiding judicious herbicide usage.
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Affiliation(s)
| | | | | | | | | | - Xiaoyue Yu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, China
| | - Yongliang Lu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, China
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2
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Montgomery J, Morran S, MacGregor DR, McElroy JS, Neve P, Neto C, Vila-Aiub MM, Sandoval MV, Menéndez AI, Kreiner JM, Fan L, Caicedo AL, Maughan PJ, Martins BAB, Mika J, Collavo A, Merotto A, Subramanian NK, Bagavathiannan MV, Cutti L, Islam MM, Gill BS, Cicchillo R, Gast R, Soni N, Wright TR, Zastrow-Hayes G, May G, Malone JM, Sehgal D, Kaundun SS, Dale RP, Vorster BJ, Peters B, Lerchl J, Tranel PJ, Beffa R, Fournier-Level A, Jugulam M, Fengler K, Llaca V, Patterson EL, Gaines TA. Current status of community resources and priorities for weed genomics research. Genome Biol 2024; 25:139. [PMID: 38802856 PMCID: PMC11129445 DOI: 10.1186/s13059-024-03274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.
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Affiliation(s)
- Jacob Montgomery
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Sarah Morran
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Dana R MacGregor
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - J Scott McElroy
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Paul Neve
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Célia Neto
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Martin M Vila-Aiub
- IFEVA-Conicet-Department of Ecology, University of Buenos Aires, Buenos Aires, Argentina
| | | | - Analia I Menéndez
- Department of Ecology, Faculty of Agronomy, University of Buenos Aires, Buenos Aires, Argentina
| | - Julia M Kreiner
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Longjiang Fan
- Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Peter J Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | | | - Jagoda Mika
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Aldo Merotto
- Department of Crop Sciences, Federal University of Rio Grande Do Sul, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Nithya K Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | - Luan Cutti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | | | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Robert Cicchillo
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Roger Gast
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Neeta Soni
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Terry R Wright
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | | | - Gregory May
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Jenna M Malone
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Deepmala Sehgal
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Shiv Shankhar Kaundun
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Richard P Dale
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Barend Juan Vorster
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Bodo Peters
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Roland Beffa
- Senior Scientist Consultant, Herbicide Resistance Action Committee / CropLife International, Liederbach, Germany
| | | | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Kevin Fengler
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Victor Llaca
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Eric L Patterson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA.
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Wang H, Fang J, Li X, Sun P, Gao H, Ren Y, Liu Y, Feng Z, Dong L. Epigenetic Regulation of CYP72A385-Mediated Metabolic Resistance to Novel Auxin Herbicide Florpyrauxifen-benzyl in Echinochloa crus-galli (L.) P. Beauv. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38600742 DOI: 10.1021/acs.jafc.4c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Weed's metabolic resistance to herbicides has undermined the sustainability of herbicides and global food security. Notably, we identified an Echinochloa crus-galli (L.) P. Beauv population (R) that evolved resistance to the never-used florpyrauxifen-benzyl, in which florpyrauxifen-benzyl was metabolized faster than the susceptible E. crus-galli population (S). RNA-seq identified potential metabolism-related genes, EcCYP72A385 and EcCYP85A1, whose expression in yeast exhibited the capacity to degrade florpyrauxifen-benzyl. Region-2 in the EcCYP72A385 promoter showed significant demethylation after florpyrauxifen-benzyl treatment in the R population. DNA methyltransferase inhibitors induce EcCYP72A385 overexpression in the S population and endow it with tolerance to florpyrauxifen-benzyl. Moreover, methyltransferase-like 7A (EcMETTL7A) was overexpressed in the S population and specifically bound to the EcCYP72A385 promoter. Transgenic EcCYP72A385 in Arabidopsis and Oryza sativa L. exhibited resistance to florpyrauxifen-benzyl, whereas EcMETTL7A transgenic plants were sensitive. Overall, EcCYP72A385 is the principal functional gene for conferring resistance to florpyrauxifen-benzyl and is regulated by EcMETTL7A in E. crus-galli.
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Affiliation(s)
- Hao Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiapeng Fang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xiaoxu Li
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Penglei Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haitao Gao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanrong Ren
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Liu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhike Feng
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Liyao Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
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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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5
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Tan W, Zhou P, Huang X, Liao R, Wang X, Wu Y, Ni Z, Shi T, Yu X, Zhang H, Ma C, Gao F, Ma Y, Bai Y, Hayat F, Omondi OK, Coulibaly D, Gao Z. Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot. HORTICULTURE RESEARCH 2024; 11:uhae103. [PMID: 38689698 PMCID: PMC11059810 DOI: 10.1093/hr/uhae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 03/31/2024] [Indexed: 05/02/2024]
Abstract
Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.
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Affiliation(s)
- Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengyu Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruyu Liao
- Institute of Fruit, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Xiaoan Wang
- Institute of Fruit, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yaoyao Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaqing Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huiqin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chengdong Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufan Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Faisal Hayat
- Department of Pomology, College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Ouma Kenneth Omondi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Crops, Horticulture and Soils, Faculty of Agriculture, Egerton University, P.O. Box 536, Egerton 20115, Kenya
| | - Daouda Coulibaly
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Agricultural Sciences and Techniques-Horticulture, Rural Polytechnic Institute for Training and Applied Research (IPR/IFRA) of Katibougou, Koulikoro B.P.224, Mali
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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6
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Iwakami S, Ishizawa H, Sugiura K, Kashiwagi K, Oga T, Niwayama S, Uchino A. Syntenic analysis of ACCase loci and target-site-resistance mutations in cyhalofop-butyl resistant Echinochloa crus-galli var. crus-galli in Japan. PEST MANAGEMENT SCIENCE 2024; 80:627-636. [PMID: 37743410 DOI: 10.1002/ps.7789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/07/2023] [Accepted: 09/25/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Recently, suspected cyhalofop-butyl-resistant populations of allohexaploid weed Echinochloa crus-galli var. crus-galli were discovered in rice fields in Aichi Prefecture, Japan. Analyzing the target-site ACCase genes of cyhalofop-butyl helps understand the resistance mechanism. However, in E. crus-galli, the presence of multiple ACCase genes and the lack of detailed gene investigations have complicated the analysis of target-site genes. Therefore, in this study, we characterized the herbicide response of E. crus-galli lines and thoroughly characterized the ACCase genes, including the evaluation of gene mutations in the ACCase genes of each line. RESULT Four suspected resistant lines collected from Aichi Prefecture showed varying degrees of resistance to cyhalofop-butyl and other FOP-class ACCase inhibitors but were sensitive to herbicides with other modes of action. Through genomic analysis, six ACCase loci were identified in the E. crus-galli genome. We renamed each gene based on its syntenic relationship with other ACCase genes in the Poaceae species. RNA-sequencing analysis revealed that all ACCase genes, except the pseudogenized copy ACCase2A, were transcribed at a similar level in the shoots of E. crus-galli. Mutations known to confer resistance to FOP-class herbicides, that is W1999C, W2027C/S and I2041N, were found in all resistant lines in either ACCase1A, ACCase1B or ACCase2C. CONCLUSION In this study, we found that the E. crus-galli lines were resistant exclusively to ACCase-inhibiting herbicides, with a target-site resistance mutation in the ACCase gene. Characterization of ACCase loci in E. crus-galli provides a basis for further research on ACCase herbicide resistance in Echinochloa spp. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Satoshi Iwakami
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Kyoto, Japan
| | - Hinata Ishizawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Kyoto, Japan
| | - Kai Sugiura
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Kyoto, Japan
| | | | - Toshiya Oga
- Aichi Agricultural Research Center, Nagakute, Japan
| | | | - Akira Uchino
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsu, Japan
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Huang Y, Guo L, Xie L, Shang N, Wu D, Ye C, Rudell EC, Okada K, Zhu QH, Song BK, Cai D, Junior AM, Bai L, Fan L. A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes). Gigascience 2024; 13:giae006. [PMID: 38486346 PMCID: PMC10938897 DOI: 10.1093/gigascience/giae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/20/2023] [Accepted: 02/08/2024] [Indexed: 03/18/2024] Open
Abstract
Commelinales belongs to the commelinids clade, which also comprises Poales that includes the most important monocot species, such as rice, wheat, and maize. No reference genome of Commelinales is currently available. Water hyacinth (Pontederia crassipes or Eichhornia crassipes), a member of Commelinales, is one of the devastating aquatic weeds, although it is also grown as an ornamental and medical plant. Here, we present a chromosome-scale reference genome of the tetraploid water hyacinth with a total length of 1.22 Gb (over 95% of the estimated size) across 8 pseudochromosome pairs. With the representative genomes, we reconstructed a phylogeny of the commelinids, which supported Zingiberales and Commelinales being sister lineages of Arecales and shed lights on the controversial relationship of the orders. We also reconstructed ancestral karyotypes of the commelinids clade and confirmed the ancient commelinids genome having 8 chromosomes but not 5 as previously reported. Gene family analysis revealed contraction of disease-resistance genes during polyploidization of water hyacinth, likely a result of fitness requirement for its role as a weed. Genetic diversity analysis using 9 water hyacinth lines from 3 continents (South America, Asia, and Europe) revealed very closely related nuclear genomes and almost identical chloroplast genomes of the materials, as well as provided clues about the global dispersal of water hyacinth. The genomic resources of P. crassipes reported here contribute a crucial missing link of the commelinids species and offer novel insights into their phylogeny.
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Affiliation(s)
- Yujie Huang
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Zhongyuan Institute of Zhejiang University, Zhengzhou 450000, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Lingjuan Xie
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Nianmin Shang
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Dongya Wu
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chuyu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Eduardo Carlos Rudell
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS 68011, Brazil
| | - Kazunori Okada
- Agro-Biotechnology Research Center (AgTECH), University of Tokyo, Tokyo 113-8657, Japan
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, ACT 2601, Australia
| | - Beng-Kah Song
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor 46150, Malaysia
| | - Daguang Cai
- Department of Molecular Phytopathology and Biotechnology, Christian Albrechts University of Kiel, Kiel D-24118, Germany
| | - Aldo Merotto Junior
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS 68011, Brazil
| | - Lianyang Bai
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha 410125, China
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Zhongyuan Institute of Zhejiang University, Zhengzhou 450000, China
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8
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Gao H, Yu J, Chen J, Wang H, Liang S, Feng Z, Gu Y, Dong L. Target-Site and Metabolic Resistance Mechanisms to Penoxsulam in Late Watergrass ( Echinochloa phyllopogon) in China. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:17742-17751. [PMID: 37934576 DOI: 10.1021/acs.jafc.3c05921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Echinochloa phyllopogon, a malignant weed in Northeast China's paddy fields, is currently presenting escalating resistance concerns. Our study centered on the HJHL-715 E. phyllopogon population, which showed heightened resistance to penoxsulam, through a whole-plant bioassay. Pretreatment with a P450 inhibitor malathion significantly increased penoxsulam sensitivity in resistant plants. In order to determine the resistance mechanism of the resistant population, we purified the resistant population from individual plants and isolated target-site resistance (TSR) and nontarget-site resistance (NTSR) materials. Pro-197-Thr and Trp-574-Leu mutations in acetolactate synthase (ALS) 1 and ALS2 of the resistant population drove reduced sensitivity of penoxsulam to the target-site ALS, the primary resistance mechanisms. To fully understand the NTSR mechanism, NTSR materials were investigated by using RNA-sequencing (RNA-seq) combined with a reference genome. High-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis further supported the enhanced penoxsulam metabolism in NTSR materials. Gene expression data and quantitative reverse transcription polymerase chain reaction (qRT-PCR) validation confirmed 29 overexpressed genes under penoxsulam treatment, with 16 genes concurrently upregulated with quinclorac and metamifop treatment. Overall, our study confirmed coexisting TSR and NTSR mechanisms in E. phyllopogon's resistance to ALS inhibitors.
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Affiliation(s)
- Haitao Gao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Jiaxing Yu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Jinyi Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Hao Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Shaoqi Liang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Zhike Feng
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Yucheng Gu
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, U.K
| | - Liyao Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
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9
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Sun M, Yan H, Zhang A, Jin Y, Lin C, Luo L, Wu B, Fan Y, Tian S, Cao X, Wang Z, Luo J, Yang Y, Jia J, Zhou P, Tang Q, Jones CS, Varshney RK, Srivastava RK, He M, Xie Z, Wang X, Feng G, Nie G, Huang D, Zhang X, Zhu F, Huang L. Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2348-2357. [PMID: 37530223 PMCID: PMC10579705 DOI: 10.1111/pbi.14136] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/01/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023]
Abstract
Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., 'Gene mapping', 'Co-expression', 'KEGG/GO Enrichment' analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through 'GWAS', which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.
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Affiliation(s)
- Min Sun
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Haidong Yan
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
- School of Plant and Environmental SciencesVirginia TechBlacksburgVirginiaUSA
- Department of GeneticsUniversity of GeorgiaAthensGeorgiaUSA
| | - Aling Zhang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yarong Jin
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Chuang Lin
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Lin Luo
- College of Life SciencesFujian Agriculture and Forestry UniversityFujianChina
| | - Bingchao Wu
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yuhang Fan
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Shilin Tian
- Novogene Bioinformatics InstituteBeijingChina
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life SciencesWuhan UniversityWuhanChina
| | | | - Zan Wang
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Jinchan Luo
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yuchen Yang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Jiyuan Jia
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Puding Zhou
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Qianzi Tang
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Chris Stephen Jones
- Feed and Forage DevelopmentInternational Livestock Research InstituteNairobiKenya
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
- Murdoch's Centre for Crop and Food Innovation, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rakesh K. Srivastava
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduSichuanChina
| | - Zheni Xie
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
- College of Agro‐Grassland ScienceNanjing Agricultural UniversityNanjingChina
| | - Xiaoshan Wang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Guangyan Feng
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Gang Nie
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Dejun Huang
- Herbivorous Livestock Research InstituteChongqing Academy of Animal SciencesChongqingChina
| | - Xinquan Zhang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Fangjie Zhu
- College of Life SciencesFujian Agriculture and Forestry UniversityFujianChina
| | - Linkai Huang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduSichuanChina
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10
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Sato MP, Iwakami S, Fukunishi K, Sugiura K, Yasuda K, Isobe S, Shirasawa K. Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon. DNA Res 2023; 30:dsad023. [PMID: 37943179 PMCID: PMC10634394 DOI: 10.1093/dnares/dsad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/27/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023] Open
Abstract
Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genome with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32,337, and 30,889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence could be a milestone in understanding the molecular mechanisms of the pernicious traits and in developing effective weed control strategies to avoid yield loss in rice production.
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Affiliation(s)
- Mitsuhiko P Sato
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Satoshi Iwakami
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kanade Fukunishi
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kai Sugiura
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kentaro Yasuda
- Agri-Innovation Education and Research Center, Akita Prefectural University, Akita 010-0451, Japan
| | - Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan
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11
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Renganathan VG, Renuka R, Vanniarajan C, Raveendran M, Elangovan A. Selection and validation of reliable reference genes for quantitative real-time PCR in Barnyard millet (Echinochloa spp.) under varied abiotic stress conditions. Sci Rep 2023; 13:15573. [PMID: 37731036 PMCID: PMC10511452 DOI: 10.1038/s41598-023-40526-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 08/11/2023] [Indexed: 09/22/2023] Open
Abstract
Quantitative real-time polymerase chain reaction (RT-qPCR) using a stable reference gene is widely used for gene expression research. Barnyard millet (Echinochloa spp.) is an ancient crop in Asia and Africa that is widely cultivated for food and fodder. It thrives well under drought, salinity, cold, and heat environmental conditions, besides adapting to any soil type. To date, there are no gene expression studies performed to identify the potential candidate gene responsible for stress response in barnyard millet, due to lack of reference gene. Here, 10 candidate reference genes, Actin (ACT), α-tubulin (α-TUB), β-tubulin (β-TUB), RNA pol II (RP II), elongation factor-1 alpha (EF-1α), adenine phosphoribosyltransferase (APRT), TATA-binding protein-like factor (TLF), ubiquitin-conjugating enzyme 2 (UBC2), ubiquitin-conjugating enzyme E2L5 (UBC5) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were selected from mRNA sequences of E. crus-galli and E. colona var frumentacea. Five statistical algorithms (geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder) were applied to determine the expression stabilities of these genes in barnyard millet grown under four different abiotic stress (drought, salinity, cold and heat) exposed at different time points. The UBC5 and ɑ-TUB in drought, GAPDH in salinity, GAPDH and APRT in cold, and EF-1α and RP II in heat were the most stable reference genes, whereas ß-TUB was the least stable irrespective of stress conditions applied. Further Vn/Vn + 1 analysis revealed two reference genes were sufficient to normalize gene expression across all sample sets. The suitability of identified reference genes was validated with Cu-ZnSOD (SOD1) in the plants exposed to different abiotic stress conditions. The results revealed that the relative quantification of the SOD1 gene varied according to reference genes and the number of reference genes used, thus highlighting the importance of the choice of a reference gene in such experiments. This study provides a foundational framework for standardizing RT-qPCR analyses, enabling accurate gene expression profiling in barnyard millet.
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Affiliation(s)
- Vellaichamy Gandhimeyyan Renganathan
- Department of Biotechnology, Centre of Excellence for Innovations, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Raman Renuka
- Department of Biotechnology, Centre of Excellence for Innovations, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India.
| | - Chockalingam Vanniarajan
- Anbil Dharmalingam Agricultural College & Research Institute, Tamil Nadu Agricultural University, Tiruchirappalli, India
| | - Muthurajan Raveendran
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Allimuthu Elangovan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
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12
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Hu X, Liu R, Mao H, Xu Y, Chen B, Li Y, Yang X. Inter-Species Investigation of Biological Traits among Eight Echinochloa Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:3085. [PMID: 37687331 PMCID: PMC10489896 DOI: 10.3390/plants12173085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023]
Abstract
Due to the diversity of Echinochloa species and the limited understanding of their damage processes in rice fields, clarifying the biological properties of distinct species could help create a foundation for effective control techniques. Pot experiments and field competition trials were conducted using eight Echinochloa species to elucidate their biological differences and assess their varying levels of negative impact on rice. The survey outcomes showed that E. oryzoides had the highest 1000-grain weight (3.12 g) while E. colona had the lowest (0.90 g). The largest grain number per spikelet found in E. glabrescens (940) was 3.4 times greater than that in E. oryzoides (277). Different species responded variably to changes in temperature and photoperiod. Except for E. caudate, all Echinochloa species exhibited a shortened growth period with the delay of the sowing date. Under field competitive conditions, all Echinochloa species exhibited significantly greater net photosynthetic rates than rice, with E. crusgalli exhibiting the highest photosynthetic capacity. Moreover, in this resource-limited setting, barnyardgrass species had a decrease in tiller formation and panicle initiation but a significant increase in plant height. These findings contribute valuable insights into the biological characteristics of barnyardgrass populations and provide guidance for implementing effective control measures in rice fields.
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Affiliation(s)
- Xuli Hu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
- Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Runqiang Liu
- Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Honghao Mao
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Yong Xu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Bin Chen
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Yongfeng Li
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Xia Yang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
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13
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Wu D, Xie L, Sun Y, Huang Y, Jia L, Dong C, Shen E, Ye CY, Qian Q, Fan L. A syntelog-based pan-genome provides insights into rice domestication and de-domestication. Genome Biol 2023; 24:179. [PMID: 37537691 PMCID: PMC10401782 DOI: 10.1186/s13059-023-03017-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate. RESULTS Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice. CONCLUSIONS This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.
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Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang University, Sanya, 572025, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
- Center for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou, 310058, China
| | - Lingjuan Xie
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yanqing Sun
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yujie Huang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lei Jia
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Chenfeng Dong
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Enhui Shen
- Hainan Institute of Zhejiang University, Sanya, 572025, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Longjiang Fan
- Hainan Institute of Zhejiang University, Sanya, 572025, China.
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
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14
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Rigon CAG, Cutti L, Turra GM, Ferreira EZ, Menegaz C, Schaidhauer W, Dayan FE, Gaines TA, Merotto A. Recurrent Selection of Echinochloa crus-galli with a Herbicide Mixture Reduces Progeny Sensitivity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6871-6881. [PMID: 37104538 DOI: 10.1021/acs.jafc.3c00920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Herbicide mixtures are used to increase the spectrum of weed control and to manage weeds with target-site resistance to some herbicides. However, the effect of mixtures on the evolution of herbicide resistance caused by enhanced metabolism is unknown. This study evaluated the effect of a fenoxaprop-p-ethyl and imazethapyr mixture on the evolution of herbicide resistance in Echinochloa crus-galli using recurrent selection at sublethal doses. The progeny from second generations selected with the mixture had lower control than parental plants or the unselected progeny. GR50 increased 1.6- and 2.6-fold after two selection cycles with the mixture in susceptible (POP1-S) and imazethapyr-resistant (POP2-IR) biotypes, respectively. There was evidence that recurrent selection with this sublethal mixture had the potential to evolve cross-resistance to diclofop, cyhalofop, sethoxydim, and quinclorac. Mixture selection did not cause increased relative expression for a set of analyzed genes (CYP71AK2, CYP72A122, CYP72A258, CYP81A12, CYP81A14, CYP81A21, CYP81A22, and GST1). Fenoxaprop, rather than imazethapyr, is the main contributor to the decreased control in the progenies after recurrent selection with the mixture in low doses. This is the first study reporting the effect of a herbicide mixture at low doses on herbicide resistance evolution. The lack of control using the mixture may result in decreased herbicide sensitivity of the weed progenies. Using mixtures may select important detoxifying genes that have the potential to metabolize herbicides in patterns that cannot currently be predicted. The use of fully recommended herbicide rates in herbicide mixtures is recommended to reduce the risk of this type of resistance evolution.
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Affiliation(s)
- Carlos A G Rigon
- Department of Crop Science, Federal University of Rio Grande do Sul, Av. Bento Goncalves, Porto Alegre 91540-000, Brazil
| | - Luan Cutti
- Department of Crop Science, Federal University of Rio Grande do Sul, Av. Bento Goncalves, Porto Alegre 91540-000, Brazil
| | - Guilherme M Turra
- Department of Crop Science, Federal University of Rio Grande do Sul, Av. Bento Goncalves, Porto Alegre 91540-000, Brazil
| | - Enrico Z Ferreira
- Department of Crop Science, Federal University of Rio Grande do Sul, Av. Bento Goncalves, Porto Alegre 91540-000, Brazil
| | - Christian Menegaz
- Department of Crop Science, Federal University of Rio Grande do Sul, Av. Bento Goncalves, Porto Alegre 91540-000, Brazil
| | - Walker Schaidhauer
- Department of Crop Science, Federal University of Rio Grande do Sul, Av. Bento Goncalves, Porto Alegre 91540-000, Brazil
| | - Franck E Dayan
- Department of Agricultural Biology, Colorado State University, 300 W. Pitkin St., Fort Collins, Colorado 80523, United States
| | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University, 300 W. Pitkin St., Fort Collins, Colorado 80523, United States
| | - Aldo Merotto
- Department of Crop Science, Federal University of Rio Grande do Sul, Av. Bento Goncalves, Porto Alegre 91540-000, Brazil
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15
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Huang Y, Wu D, Huang Z, Li X, Merotto A, Bai L, Fan L. Weed genomics: yielding insights into the genetics of weedy traits for crop improvement. ABIOTECH 2023; 4:20-30. [PMID: 37220539 PMCID: PMC10199979 DOI: 10.1007/s42994-022-00090-5] [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: 10/27/2022] [Accepted: 12/06/2022] [Indexed: 05/25/2023]
Abstract
Weeds cause tremendous economic and ecological damage worldwide. The number of genomes established for weed species has sharply increased during the recent decade, with some 26 weed species having been sequenced and de novo genomes assembled. These genomes range from 270 Mb (Barbarea vulgaris) to almost 4.4 Gb (Aegilops tauschii). Importantly, chromosome-level assemblies are now available for 17 of these 26 species, and genomic investigations on weed populations have been conducted in at least 12 species. The resulting genomic data have greatly facilitated studies of weed management and biology, especially origin and evolution. Available weed genomes have indeed revealed valuable weed-derived genetic materials for crop improvement. In this review, we summarize the recent progress made in weed genomics and provide a perspective for further exploitation in this emerging field.
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Affiliation(s)
- Yujie Huang
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058 China
| | - Dongya Wu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058 China
| | - Zhaofeng Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xiangyu Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Aldo Merotto
- Department of Crop Sciences, Agricultural School Federal University of Rio Grande do Sul, Porto Alegre, 91540-000 Brazil
| | - Lianyang Bai
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Sciences, Changshang, 410125 China
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058 China
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16
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Li J, Wang T, Liu W, Yin D, Lai Z, Zhang G, Zhang K, Ji J, Yin S. A high-quality chromosome-level genome assembly of Pelteobagrus vachelli provides insights into its environmental adaptation and population history. Front Genet 2022; 13:1050192. [DOI: 10.3389/fgene.2022.1050192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Pelteobagrus vachelli is a freshwater fish with high economic value, but the lack of genome resources has severely restricted its industrial development and population conservation. Here, we constructed the first chromosome-level genome assembly of P. vachelli with a total length of approximately 662.13 Mb and a contig N50 was 14.02 Mb, and scaffolds covering 99.79% of the assembly were anchored to 26 chromosomes. Combining the comparative genome results and transcriptome data under environmental stress (high temperature, hypoxia and Edwardsiella. ictaluri infection), the MAPK signaling pathway, PI3K-Akt signaling pathway and apelin signaling pathway play an important role in environmental adaptation of P. vachelli, and these pathways were interconnected by the ErbB family and involved in cell proliferation, differentiation and apoptosis. Population evolution analysis showed that artificial interventions have affected wild populations of P. vachelli. This study provides a useful genomic information for the genetic breeding of P. vachelli, as well as references for further studies on fish biology and evolution.
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Gao Y, Shen G, Yuan G, Tian Z. Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields. Int J Mol Sci 2022; 23:ijms232213864. [PMID: 36430336 PMCID: PMC9698722 DOI: 10.3390/ijms232213864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/30/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022] Open
Abstract
Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens, morphologically similar at the seedling stage, are the most pernicious barnyard grass species in paddy fields worldwide. Chloroplast (cp) genomes could be conducive to their identification. In this study, we assembled the complete cp genome sequences of Echinochloa crus-galli var. crus-galli (139,856 bp), E. crus-galli var. zelayensis (139,874 bp), and E. glabrescens (139,874 bp), which exhibited a typical circular tetramerous structure, large and small single-copy regions, and a pair of inverted repeats. In Echinochloa crus-galli var. crus-galli, there were 136 simple sequence (SSRs) and 62 long (LRs) repeats, and in the other two species, 139 SSRs and 68 LRs. Each cp genome contains 92 protein-encoding genes. In Echinochloa crus-galli var. crus-galli and E. glabrescens, 321 and 1 single-nucleotide polymorphisms were detected compared to Echinochloa crus-galli var. zelayensis. IR expansion and contraction revealed small differences between the three species. The phylogenetic tree based on cp genomes demonstrated the phylogenetic relationship between ten barnyard grass species and other common Gramineae plants, showing new genetic relationships of the genus Echinochloa. This study provides valuable information on cp genomes, useful for identifying and classifying the genus Echinochloa and studying its phylogenetic relationships and evolution.
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Wu D, Hu Y, Akashi S, Nojiri H, Guo L, Ye C, Zhu Q, Okada K, Fan L. Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1354-1367. [PMID: 35781905 PMCID: PMC9544640 DOI: 10.1111/tpj.15893] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/22/2022] [Accepted: 06/29/2022] [Indexed: 05/31/2023]
Abstract
Momilactone A, an important plant labdane-related diterpenoid, functions as a phytoalexin against pathogens and an allelochemical against neighboring plants. The genes involved in the biosynthesis of momilactone A are found in clusters, i.e., momilactone A biosynthetic gene clusters (MABGCs), in the rice and barnyardgrass genomes. In addition, we know little about the origin and evolution of MABGCs. Here, we integrated results from comprehensive phylogeny and comparative genomic analyses of the core genes of MABGC-like clusters and MABGCs in 40 monocot plant genomes, providing convincing evidence for the birth and evolution of MABGCs in grass species. The MABGCs found in the PACMAD clade of the core grass lineage (including Panicoideae and Chloridoideae) originated from a MABGC-like cluster in Triticeae (BOP clade) via lateral gene transfer (LGT) and followed by recruitment of MAS1/2 and CYP76L1 genes. The MABGCs in Oryzoideae originated from PACMAD through another LGT event and lost CYP76L1 afterwards. The Oryza MABGC and another Oryza diterpenoid cluster c2BGC are two distinct clusters, with the latter originating from gene duplication and relocation within Oryzoideae. Further comparison of the expression patterns of the MABGC genes between rice and barnyardgrass in response to pathogen infection and allelopathy provides novel insights into the functional innovation of MABGCs in plants. Our results demonstrate LGT-mediated origination of MABGCs in grass and shed lights into the evolutionary innovation and optimization of plant biosynthetic pathways.
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Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang UniversityYonyou Industrial ParkSanya572025China
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Yiyu Hu
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Shota Akashi
- Biotechnology Research CenterUniversity of Tokyo113‐8657TokyoJapan
| | - Hideaki Nojiri
- Biotechnology Research CenterUniversity of Tokyo113‐8657TokyoJapan
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou310006China
| | - Chu‐Yu Ye
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Qian‐Hao Zhu
- CSIRO Agriculture and Food, Black Mountain LaboratoriesCanberraACT2601Australia
| | - Kazunori Okada
- Biotechnology Research CenterUniversity of Tokyo113‐8657TokyoJapan
| | - Longjiang Fan
- Hainan Institute of Zhejiang UniversityYonyou Industrial ParkSanya572025China
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
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Wu D, Jiang B, Ye CY, Timko MP, Fan L. Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants. PLANT COMMUNICATIONS 2022; 3:100320. [PMID: 35576160 PMCID: PMC9251436 DOI: 10.1016/j.xplc.2022.100320] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/07/2022] [Accepted: 03/23/2022] [Indexed: 05/11/2023]
Abstract
Benzoxazinoids are a class of protective and allelopathic plant secondary metabolites that have been identified in multiple grass species and are encoded by the Bx biosynthetic gene cluster (BGC) in maize. Data mining of 41 high-quality grass genomes identified complete Bx clusters (containing genes Bx1-Bx5 and Bx8) in three genera (Zea, Echinochloa, and Dichanthelium) of Panicoideae and partial clusters in Triticeae. The Bx cluster probably originated from gene duplication and chromosomal translocation of native homologs of Bx genes. An ancient Bx cluster that included additional Bx genes (e.g., Bx6) is presumed to have been present in ancestral Panicoideae. The ancient Bx cluster was putatively gained by the Triticeae ancestor via horizontal transfer (HT) from the ancestral Panicoideae and later separated into multiple segments on different chromosomes. Bx6 appears to have been under less constrained selection compared with the Bx cluster during the evolution of Panicoideae, as evidenced by the fact that it was translocated away from the Bx cluster in Zea mays, moved to other chromosomes in Echinochloa, and even lost in Dichanthelium. Further investigations indicate that purifying selection and polyploidization have shaped the evolutionary trajectory of Bx clusters in the grass family. This study provides the first candidate case of HT of a BGC between plants and sheds new light on the evolution of BGCs.
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Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Bowen Jiang
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Longjiang Fan
- Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
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