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Fuertes-Aguilar J, Matilla AJ. Transcriptional Control of Seed Life: New Insights into the Role of the NAC Family. Int J Mol Sci 2024; 25:5369. [PMID: 38791407 PMCID: PMC11121595 DOI: 10.3390/ijms25105369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific sequences on DNA through their DNA-binding domain (DBD), a universal process. This update conveys information about the diverse roles of TFs, focusing on the NACs (NAM-ATAF-CUC), in regulating target-gene expression and influencing various aspects of plant biology. NAC TFs appeared before the emergence of land plants. The NAC family constitutes a diverse group of plant-specific TFs found in mosses, conifers, monocots, and eudicots. This update discusses the evolutionary origins of plant NAC genes/proteins from green algae to their crucial roles in plant development and stress response across various plant species. From mosses and lycophytes to various angiosperms, the number of NAC proteins increases significantly, suggesting a gradual evolution from basal streptophytic green algae. NAC TFs play a critical role in enhancing abiotic stress tolerance, with their function conserved in angiosperms. Furthermore, the modular organization of NACs, their dimeric function, and their localization within cellular compartments contribute to their functional versatility and complexity. While most NAC TFs are nuclear-localized and active, a subset is found in other cellular compartments, indicating inactive forms until specific cues trigger their translocation to the nucleus. Additionally, it highlights their involvement in endoplasmic reticulum (ER) stress-induced programmed cell death (PCD) by activating the vacuolar processing enzyme (VPE) gene. Moreover, this update provides a comprehensive overview of the diverse roles of NAC TFs in plants, including their participation in ER stress responses, leaf senescence (LS), and growth and development. Notably, NACs exhibit correlations with various phytohormones (i.e., ABA, GAs, CK, IAA, JA, and SA), and several NAC genes are inducible by them, influencing a broad spectrum of biological processes. The study of the spatiotemporal expression patterns provides insights into when and where specific NAC genes are active, shedding light on their metabolic contributions. Likewise, this review emphasizes the significance of NAC TFs in transcriptional modules, seed reserve accumulation, and regulation of seed dormancy and germination. Overall, it effectively communicates the intricate and essential functions of NAC TFs in plant biology. Finally, from an evolutionary standpoint, a phylogenetic analysis suggests that it is highly probable that the WRKY family is evolutionarily older than the NAC family.
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Affiliation(s)
| | - Angel J. Matilla
- Departamento de Biología Funcional, Universidad de Santiago de Compostela, 14971 Santiago de Compostela, Spain
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Wang M, Huang L, Kou Y, Li D, Hu W, Fan D, Cheng S, Yang Y, Zhang Z. Differentiation of Morphological Traits and Genome-Wide Expression Patterns between Rice Subspecies Indica and Japonica. Genes (Basel) 2023; 14:1971. [PMID: 37895320 PMCID: PMC10606143 DOI: 10.3390/genes14101971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Changes in gene expression patterns can lead to the variation of morphological traits. This phenomenon is particularly evident in recent evolution events such as crop domestication and responses to environmental stress, where alterations in expression levels can efficiently give rise to domesticated syndromes and adaptive phenotypes. Rice (Oryza sativa L.), one of the world's most crucial cereal crops, comprises two morphologically distinct subspecies, Indica and Japonica. To investigate the morphological divergence between these two rice subspecies, this study planted a total of 315 landrace individuals of both Indica and Japonica under identical cultivation conditions. Out of the 16 quantitative traits measured in this study, 12 exhibited significant differences between the subspecies. To determine the genetic divergence between Indica and Japonica at the whole-genome sequence level, we constructed a phylogenetic tree using a resequencing dataset encompassing 95 rice landrace accessions. The samples formed two major groups that neatly corresponded to the two subspecies, Indica and Japonica. Furthermore, neighbor-joining (NJ) trees based on the expression quantity of effectively expressed genes (EEGs) across five different tissues categorized 12 representative samples into two major clades aligning with the two subspecies. These results imply that divergence in genome-wide expression levels undergoes stabilizing selection under non-stressful conditions, with evolutionary trends in expression levels mirroring sequence variation levels. This study further supports the pivotal role of changes in genome-wide expression regulation in the divergence of the two rice subspecies, Indica and Japonica.
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Affiliation(s)
- Meixia Wang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang 330045, China; (Y.K.); (D.L.); (W.H.); (D.F.); (S.C.); (Y.Y.)
| | - Lei Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China;
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang 330045, China; (Y.K.); (D.L.); (W.H.); (D.F.); (S.C.); (Y.Y.)
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541004, China
| | - Danqi Li
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang 330045, China; (Y.K.); (D.L.); (W.H.); (D.F.); (S.C.); (Y.Y.)
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332900, China
| | - Wan Hu
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang 330045, China; (Y.K.); (D.L.); (W.H.); (D.F.); (S.C.); (Y.Y.)
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332900, China
| | - Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang 330045, China; (Y.K.); (D.L.); (W.H.); (D.F.); (S.C.); (Y.Y.)
| | - Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang 330045, China; (Y.K.); (D.L.); (W.H.); (D.F.); (S.C.); (Y.Y.)
| | - Yi Yang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang 330045, China; (Y.K.); (D.L.); (W.H.); (D.F.); (S.C.); (Y.Y.)
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang 330045, China; (Y.K.); (D.L.); (W.H.); (D.F.); (S.C.); (Y.Y.)
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541004, China
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Wang F, Zhou Z, Zhu L, Gu Y, Guo B, Lv C, Zhu J, Xu R. Genome-wide analysis of the MADS-box gene family involved in salt and waterlogging tolerance in barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1178065. [PMID: 37229117 PMCID: PMC10203460 DOI: 10.3389/fpls.2023.1178065] [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: 03/02/2023] [Accepted: 04/07/2023] [Indexed: 05/27/2023]
Abstract
MADS-box transcription factors are crucial members of regulatory networks underlying multiple developmental pathways and abiotic stress regulatory networks in plants. Studies on stress resistance-related functions of MADS-box genes are very limited in barley. To gain insight into this gene family and elucidate their roles in salt and waterlogging stress resistance, we performed genome-wide identification, characterization and expression analysis of MADS-box genes in barley. A whole-genome survey of barley revealed 83 MADS-box genes, which were categorized into type I (Mα, Mβ and Mγ) and type II (AP1, SEP1, AGL12, STK, AGL16, SVP and MIKC*) lineages based on phylogeny, protein motif structure. Twenty conserved motifs were determined and each HvMADS contained one to six motifs. We also found tandem repeat duplication was the driven force for HvMADS gene family expansion. Additionally, the co-expression regulatory network of 10 and 14 HvMADS genes was predicted in response to salt and waterlogging stress, and we proposed HvMADS11,13 and 35 as candidate genes for further exploration of the functions in abiotic stress. The extensive annotations and transcriptome profiling reported in this study ultimately provides the basis for MADS functional characterization in genetic engineering of barley and other gramineous crops.
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Ropars J, Giraud T. Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration. Curr Opin Microbiol 2022; 70:102236. [PMID: 36368125 DOI: 10.1016/j.mib.2022.102236] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/29/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022]
Abstract
Humans have domesticated genetically distant fungi for similar uses, the fermentation of lipid-rich and sugar-rich food to generate attractive aspects, odor and aroma, and to improve shelf life and product safety. Multiple independent domestication events also occurred within species. We review recent evidence of phenotypic convergence during the domestication of fungi for making cheese (Saccharomyces cerevisiae, Penicillium roqueforti, P. camemberti, and Geotrichum candidum) and for dry-cured meat making (P. nalgiovense and P. salamii). Convergence following adaptation to similar ecological niches involved colony aspect (fluffiness and color), lipolysis, proteolysis, volatile compound production, and competitive ability against food spoilers. We review evidence for convergence in genetic diversity loss in domesticated populations and in the degeneration of unused traits, such as toxin production and sexual reproduction. Phenotypic convergence sometimes occurred by similar mechanisms of genomic adaptation, in particular horizontal gene transfers and loss of genes.
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Affiliation(s)
- Jeanne Ropars
- Ecologie Systématique Evolution, IDEEV, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, IDEEV, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France.
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Yang Q, Li B, Rizwan HM, Sun K, Zeng J, Shi M, Guo T, Chen F. Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis. FRONTIERS IN PLANT SCIENCE 2022; 13:972734. [PMID: 36092439 PMCID: PMC9453495 DOI: 10.3389/fpls.2022.972734] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/27/2022] [Indexed: 05/07/2023]
Abstract
The NAC gene family is one of the largest plant transcription factors (TFs) families and plays important roles in plant growth, development, metabolism, and biotic and abiotic stresses. However, NAC gene family has not been reported in passion fruit (Passiflora edulis). In this study, a total of 105 NAC genes were identified in the passion fruit genome and were unevenly distributed across all nine-passion fruit chromomere, with a maximum of 48 PeNAC genes on chromosome one. The physicochemical features of all 105 PeNAC genes varied including 120 to 3,052 amino acids, 3 to 8 conserved motifs, and 1 to 3 introns. The PeNAC genes were named (PeNAC001-PeNAC105) according to their chromosomal locations and phylogenetically grouped into 15 clades (NAC-a to NAC-o). Most PeNAC proteins were predicted to be localized in the nucleus. The cis-element analysis indicated the possible roles of PeNAC genes in plant growth, development, light, hormones, and stress responsiveness. Moreover, the PeNAC gene duplications including tandem (11 gene pairs) and segmental (12 gene pairs) were identified and subjected to purifying selection. All PeNAC proteins exhibited similar 3D structures, and a protein-protein interaction network analysis with known Arabidopsis proteins was predicted. Furthermore, 17 putative ped-miRNAs were identified to target 25 PeNAC genes. Potential TFs including ERF, BBR-BPC, Dof, and bZIP were identified in promoter region of all 105 PeNAC genes and visualized in a TF regulatory network. GO and KEGG annotation analysis exposed that PeNAC genes were related to different biological, molecular, and cellular terms. The qRT-PCR expression analysis discovered that most of the PeNAC genes including PeNAC001, PeNAC003, PeNAC008, PeNAC028, PeNAC033, PeNAC058, PeNAC063, and PeNAC077 were significantly upregulated under Fusarium kyushuense and drought stress conditions compared to controls. In conclusion, these findings lay the foundation for further functional studies of PeNAC genes to facilitate the genetic improvement of plants to stress resistance.
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Affiliation(s)
| | | | | | | | | | | | | | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
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Cheng H, Xie X, Ren M, Yang S, Zhao X, Mahna N, Liu Y, Xu Y, Xiang Y, Chai H, Zheng L, Ge H, Jia R. Characterization of Three SEPALLATA-Like MADS-Box Genes Associated With Floral Development in Paphiopedilum henryanum (Orchidaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:916081. [PMID: 35693163 PMCID: PMC9178235 DOI: 10.3389/fpls.2022.916081] [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: 04/08/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Paphiopedilum (Orchidaceae) is one of the world's most popular orchids that is found in tropical and subtropical forests and has an enormous ornamental value. SEPALLATA-like (SEP-like) MADS-box genes are responsible for floral organ specification. In this study, three SEP-like MADS-box genes, PhSEP1, PhSEP2, and PhSEP3, were identified in Paphiopedilum henryanum. These genes were 732-916 bp, with conserved SEPI and SEPII motifs. Phylogenetic analysis revealed that PhSEP genes were evolutionarily closer to the core eudicot SEP3 lineage, whereas none of them belonged to core eudicot SEP1/2/4 clades. PhSEP genes displayed non-ubiquitous expression, which was detectable across all floral organs at all developmental stages of the flower buds. Furthermore, subcellular localization experiments revealed the localization of PhSEP proteins in the nucleus. Yeast two-hybrid assays revealed no self-activation of PhSEPs. The protein-protein interactions revealed that PhSEPs possibly interact with B-class DEFICIENS-like and E-class MADS-box proteins. Our study suggests that the three SEP-like genes may play key roles in flower development in P. henryanum, which will improve our understanding of the roles of the SEP-like MADS-box gene family and provide crucial insights into the mechanisms underlying floral development in orchids.
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Affiliation(s)
- Hao Cheng
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Xiulan Xie
- National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Maozhi Ren
- National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Shuhua Yang
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Zhao
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nasser Mahna
- Department of Horticultural Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Yi Liu
- National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Yufeng Xu
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yukai Xiang
- Department of High-Performance Computing, National Supercomputing Center in Chengdu, Chengdu, China
| | - Hua Chai
- Department of High-Performance Computing, National Supercomputing Center in Chengdu, Chengdu, China
| | - Liang Zheng
- Department of High-Performance Computing, National Supercomputing Center in Chengdu, Chengdu, China
| | - Hong Ge
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruidong Jia
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Zhou E, Zhang Y, Wang H, Jia Z, Wang X, Wen J, Shen J, Fu T, Yi B. Identification and Characterization of the MIKC-Type MADS-Box Gene Family in Brassica napus and Its Role in Floral Transition. Int J Mol Sci 2022; 23:ijms23084289. [PMID: 35457106 PMCID: PMC9026197 DOI: 10.3390/ijms23084289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 01/03/2023] Open
Abstract
Increasing rapeseed yield has always been a primary goal of rapeseed research and breeding. However, flowering time is a prerequisite for stable rapeseed yield and determines its adaptability to ecological regions. MIKC-type MADS-box (MICK) genes are a class of transcription factors that are involved in various physiological and developmental processes in plants. To understand their role in floral transition-related pathways, a genome-wide screening was conducted with Brassica napus (B. napus), which revealed 172 members. Using previous data from a genome-wide association analysis of flowering traits, BnaSVP and BnaSEP1 were identified as candidate flowering genes. Therefore, we used the CRISPR/Cas9 system to verify the function of BnaSVP and BnaSEP1 in B. napus. T0 plants were edited efficiently at the BnaSVP and BnaSEP1 target sites to generate homozygous and heterozygous mutants with most mutations stably inherited by the next generation. Notably, the mutant only showed the early flowering phenotype when all homologous copies of BnaSVP were edited, indicating functional redundancy between homologous copies. However, no changes in flowering were observed in the BnaSEP1 mutant. Quantitative analysis of the pathway-related genes in the BnaSVP mutant revealed the upregulation of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and FLOWERING LOCUS T (FT) genes, which promoted early flowering in the mutant. In summary, our study created early flowering mutants, which provided valuable resources for early maturing breeding, and provided a new method for improving polyploid crops.
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Affiliation(s)
- Enqiang Zhou
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong 226001, China; (Y.Z.); (X.W.)
| | - Yin Zhang
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong 226001, China; (Y.Z.); (X.W.)
| | - Huadong Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
| | - Xuejun Wang
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong 226001, China; (Y.Z.); (X.W.)
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (E.Z.); (H.W.); (Z.J.); (J.W.); (J.S.); (T.F.)
- Correspondence: ; Tel.: +86-27-8728-1676; Fax: +86-27-8728-0009
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Trubanová N, Shi J, Schilling S. Firming up your tomato: a natural promoter variation in a MADS-box gene is causing all-flesh tomatoes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1-4. [PMID: 34986230 PMCID: PMC8730695 DOI: 10.1093/jxb/erab442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This article comments on: Liu L, Zhang K, Bai JR, Lu J, Lu X, Hu J, Pan C, He S, Yuan J, Zhang Y, Zhang M, Guo Y, Wang X, Huang Z, Du Y, Cheng F, Li J. 2022. All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter. Journal of Experimental Botany 73, 123–138.
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Affiliation(s)
- Nina Trubanová
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Ireland
| | - Jiaqi Shi
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Ireland
| | - Susanne Schilling
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Ireland
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Burban E, Tenaillon MI, Le Rouzic A. Gene network simulations provide testable predictions for the molecular domestication syndrome. Genetics 2021; 220:6440055. [PMID: 34849852 DOI: 10.1093/genetics/iyab214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/15/2021] [Indexed: 11/14/2022] Open
Abstract
The domestication of plant species lead to repeatable morphological evolution, often referred to as the phenotypic domestication syndrome. Domestication is also associated with important genomic changes, such as the loss of genetic diversity compared to adequately large wild populations, and modifications of gene expression patterns. Here, we explored theoretically the effect of a domestication-like scenario on the evolution of gene regulatory networks. We ran population genetics simulations in which individuals were featured by their genotype (an interaction matrix encoding a gene regulatory network) and their gene expressions, representing the phenotypic level. Our domestication scenario included a population bottleneck and a selection switch mimicking human-mediated directional and canalizing selection, i.e., change in the optimal gene expression level and selection towards more stable expression across environments. We showed that domestication profoundly alters genetic architectures. Based on four examples of plant domestication scenarios, our simulations predict (i) a drop in neutral allelic diversity, (ii) a change in gene expression variance that depends upon the domestication scenario, (iii) transient maladaptive plasticity, (iv) a deep rewiring of the gene regulatory networks, with a trend towards gain of regulatory interactions, and (v) a global increase in the genetic correlations among gene expressions, with a loss of modularity in the resulting coexpression patterns and in the underlying networks. We provide empirically testable predictions on the differences of genetic architectures between wild and domesticated forms. The characterization of such systematic evolutionary changes in the genetic architecture of traits contributes to define a molecular domestication syndrome.
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Affiliation(s)
- Ewen Burban
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France.,CNRS, Univ. Rennes, ECOBIO-UMR 6553, F-35000 Rennes, France
| | - Maud I Tenaillon
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190, Gif-sur-Yvette, France
| | - Arnaud Le Rouzic
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
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Groppi A, Liu S, Cornille A, Decroocq S, Bui QT, Tricon D, Cruaud C, Arribat S, Belser C, Marande W, Salse J, Huneau C, Rodde N, Rhalloussi W, Cauet S, Istace B, Denis E, Carrère S, Audergon JM, Roch G, Lambert P, Zhebentyayeva T, Liu WS, Bouchez O, Lopez-Roques C, Serre RF, Debuchy R, Tran J, Wincker P, Chen X, Pétriacq P, Barre A, Nikolski M, Aury JM, Abbott AG, Giraud T, Decroocq V. Population genomics of apricots unravels domestication history and adaptive events. Nat Commun 2021; 12:3956. [PMID: 34172741 PMCID: PMC8233370 DOI: 10.1038/s41467-021-24283-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/08/2021] [Indexed: 01/27/2023] Open
Abstract
Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.
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Affiliation(s)
- Alexis Groppi
- Univ. Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB), Bordeaux, 33076, France
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, 33077, France
| | - Shuo Liu
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue, Bayuquan District, Yingkou City, 115009, Liaoning, China
| | - Amandine Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, Gif-sur-Yvette, 91190, France
| | - Stéphane Decroocq
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
| | - Quynh Trang Bui
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
| | - David Tricon
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Sandrine Arribat
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Caroline Belser
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - William Marande
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Jérôme Salse
- INRAE/UBP UMR 1095 GDEC Genetique, Diversite et Ecophysiologie des Cereales, Laboratory PaleoEVO Paleogenomics & Evolution, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Cécile Huneau
- INRAE/UBP UMR 1095 GDEC Genetique, Diversite et Ecophysiologie des Cereales, Laboratory PaleoEVO Paleogenomics & Evolution, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Nathalie Rodde
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Wassim Rhalloussi
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Stéphane Cauet
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Benjamin Istace
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Erwan Denis
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Sébastien Carrère
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jean-Marc Audergon
- INRAE UR1052 GAFL, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Guillaume Roch
- INRAE UR1052 GAFL, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
- CEP INNOVATION, 23 Rue Jean Baldassini, Lyon, 69364, Cedex 07, France
| | - Patrick Lambert
- INRAE UR1052 GAFL, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Tetyana Zhebentyayeva
- The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, 16802, PA, USA
| | - Wei-Sheng Liu
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue, Bayuquan District, Yingkou City, 115009, Liaoning, China
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, 31326, France
| | | | - Rémy-Félix Serre
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, 31326, France
| | - Robert Debuchy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Joseph Tran
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, Villenave d'Ornon, 33882, France
| | - Patrick Wincker
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Xilong Chen
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, Gif-sur-Yvette, 91190, France
| | - Pierre Pétriacq
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
| | - Aurélien Barre
- Univ. Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB), Bordeaux, 33076, France
| | - Macha Nikolski
- Univ. Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB), Bordeaux, 33076, France
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, 33077, France
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Albert Glenn Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, USA
| | - Tatiana Giraud
- Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay AgroParisTech, Orsay, 91400, France.
| | - Véronique Decroocq
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France.
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11
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Dutra-Silva L, Pereira GE, Batista LR, Matteoli FP. Fungal diversity and occurrence of mycotoxin producing fungi in tropical vineyards. World J Microbiol Biotechnol 2021; 37:112. [PMID: 34081209 DOI: 10.1007/s11274-021-03081-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 05/29/2021] [Indexed: 11/28/2022]
Abstract
Grapevine cultivars are distributed worldwide, nevertheless the fermentation of its grape berries renders distinct wine products that are highly associated to the local fungal community. Despite the symbiotic association between wine and the fungal metabolism, impacting both the terroir and mycotoxin production, few studies have explored the vineyard ecosystem fungal community using both molecular marker sequencing and mycotoxin production assessment. In this study, we investigated the fungal community of three grapevine cultivars (Vitis vinifera L.) in two tropical vineyards. Illumina MiSeq sequencing was performed on two biocompartments: grape berries (GB) and grapevine soil (GS); yielding a total of 578,495 fungal internal transcribed spacer 1 reads, which were used for taxonomic classification. GB and GS fungal communities were mainly constituted by Ascomycota phylum. GS harbors a significant richer and more diverse fungal community than GB. Among GB samples, Syrah grape berries exclusively shared fungal community included wine-associated yeasts (e.g. Saccharomycopsis vini) that may play key roles in wine terroir. Mycotoxin production assessment revealed the high potential of Aspergillus section Flavi and Penicillium section Citrina isolates to produce aflatoxin B1-B2 and citrinin, respectively. This is the first study to employ next-generation sequencing to investigate vineyard associated fungal community in Brazil. Our findings provide valuable insights on the available tools for fungal ecology assessment applied to food products emphasizing the coexistence between classical and molecular tools.
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Affiliation(s)
- Lorena Dutra-Silva
- Department of Food Sciences, Federal University of Lavras, Lavras, MG, Brazil
| | - Giuliano E Pereira
- Brazilian Agricultural Research Corporation/Embrapa Grape & Wine, Bento Gonçalves, RS, Brazil
| | | | - Filipe P Matteoli
- Department of Soil Science, Luiz de Queiroz College of Agriculture, Piracicaba, SP, Brazil.
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12
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Alseekh S, Scossa F, Wen W, Luo J, Yan J, Beleggia R, Klee HJ, Huang S, Papa R, Fernie AR. Domestication of Crop Metabolomes: Desired and Unintended Consequences. TRENDS IN PLANT SCIENCE 2021; 26:650-661. [PMID: 33653662 DOI: 10.1016/j.tplants.2021.02.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 05/02/2023]
Abstract
The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178 Rome, Italy
| | - Weiwei Wen
- Key laboratory of Horticultural Plant Biology (MOE),College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Hubei, Wuhan 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China; College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-, CI), 71122 Foggia, Italy
| | - Harry J Klee
- Horticultural Sciences, University of Florida, Gainesville, FL, USA
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture - Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
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13
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Kan J, Gao G, He Q, Gao Q, Jiang C, Ahmar S, Liu J, Zhang J, Yang P. Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley. Int J Mol Sci 2021; 22:5354. [PMID: 34069581 PMCID: PMC8160967 DOI: 10.3390/ijms22105354] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 12/19/2022] Open
Abstract
The WRKY transcription factors (WRKYs) are known for their crucial roles in biotic and abiotic stress responses, and developmental and physiological processes. In barley, early studies revealed their importance, whereas their diversity at the population scale remains hardly estimated. In this study, 98 HsWRKYs and 103 HvWRKYs have been identified from the reference genome of wild and cultivated barley, respectively. The tandem duplication and segmental duplication events from the cultivated barley were observed. By taking advantage of early released exome-captured sequencing datasets in 90 wild barley accessions and 137 landraces, the diversity analysis uncovered synonymous and non-synonymous variants instead of loss-of-function mutations that had occurred at all WRKYs. For majority of WRKYs, the haplotype and nucleotide diversity both decreased in cultivated barley relative to the wild population. Five WRKYs were detected to have undergone selection, among which haplotypes of WRKY9 were enriched, correlating with the geographic collection sites. Collectively, profiting from the state-of-the-art barley genomic resources, this work represented the characterization and diversity of barley WRKY transcription factors, shedding light on future deciphering of their roles in barley domestication and adaptation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (J.K.); (G.G.); (Q.H.); (Q.G.); (C.J.); (S.A.); (J.L.); (J.Z.)
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14
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Chen Q, Li W, Tan L, Tian F. Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding. MOLECULAR PLANT 2021; 14:9-26. [PMID: 33316465 DOI: 10.1016/j.molp.2020.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 05/11/2023]
Abstract
Crop domestication has fundamentally altered the course of human history, causing a shift from hunter-gatherer to agricultural societies and stimulating the rise of modern civilization. A greater understanding of crop domestication would provide a theoretical basis for how we could improve current crops and develop new crops to deal with environmental challenges in a sustainable manner. Here, we provide a comprehensive summary of the similarities and differences in the domestication processes of maize and rice, two major staple food crops that feed the world. We propose that maize and rice might have evolved distinct genetic solutions toward domestication. Maize and rice domestication appears to be associated with distinct regulatory and evolutionary mechanisms. Rice domestication tended to select de novo, loss-of-function, coding variation, while maize domestication more frequently favored standing, gain-of-function, regulatory variation. At the gene network level, distinct genetic paths were used to acquire convergent phenotypes in maize and rice domestication, during which different central genes were utilized, orthologous genes played different evolutionary roles, and unique genes or regulatory modules were acquired for establishing new traits. Finally, we discuss how the knowledge gained from past domestication processes, together with emerging technologies, could be exploited to improve modern crop breeding and domesticate new crops to meet increasing human demands.
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Affiliation(s)
- Qiuyue Chen
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Weiya Li
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lubin Tan
- State Key Laboratory of Agrobiotechnology, National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China.
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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15
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Donkey genomes provide new insights into domestication and selection for coat color. Nat Commun 2020; 11:6014. [PMID: 33293529 PMCID: PMC7723042 DOI: 10.1038/s41467-020-19813-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/29/2020] [Indexed: 11/08/2022] Open
Abstract
Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition. A new donkey reference genome and comparisons with wild asses yields insights into the evolutionary history of donkey domestication and identifies a genetic variant that results in the non-Dun coat colours of domestic donkeys.
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16
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Tesfamicael KG, Gebre E, March TJ, Sznajder B, Mather DE, Rodríguez López CM. Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset. HORTICULTURE RESEARCH 2020; 7:185. [PMID: 33328450 PMCID: PMC7603512 DOI: 10.1038/s41438-020-00409-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/29/2020] [Accepted: 09/10/2020] [Indexed: 06/12/2023]
Abstract
Enset (Ensete ventricosum (Welw.) Cheesman) is a drought tolerant, vegetatively propagated crop that was domesticated in Ethiopia. It is a staple food for more than 20 million people in Ethiopia. Despite its current importance and immense potential, enset is among the most genetically understudied and underexploited food crops. We collected 230 enset wild and cultivated accessions across the main enset producing regions in Ethiopia and applied amplified fragment length polymorphism (AFLP) and genotype by sequencing (GBS) analyses to these accessions. Wild and cultivated accessions were clearly separated from each other, with 89 genes found to harbour SNPs that separated wild from cultivated accessions. Among these, 17 genes are thought to be involved in flower initiation and seed development. Among cultivated accessions, differentiation was mostly associated with geographical location and with proximity to wild populations. Our results indicate that vegetative propagation of elite clones has favoured capacity for vegetative growth at the expense of capacity for sexual reproduction. This is consistent with previous reports that cultivated enset tends to produce non-viable seeds and flowers less frequently than wild enset.
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Affiliation(s)
- Kiflu Gebramicael Tesfamicael
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Endale Gebre
- Policy Study Institute, P.O. Box: 2479, Addis Ababa, Ethiopia
| | - Timothy J March
- School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA, Australia
| | - Beata Sznajder
- School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA, Australia
| | - Diane E Mather
- School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA, Australia
| | - Carlos Marcelino Rodríguez López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA.
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17
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Domestication of the Emblematic White Cheese-Making Fungus Penicillium camemberti and Its Diversification into Two Varieties. Curr Biol 2020; 30:4441-4453.e4. [PMID: 32976806 DOI: 10.1016/j.cub.2020.08.082] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/02/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022]
Abstract
Domestication involves recent adaptation under strong human selection and rapid diversification and therefore constitutes a good model for studies of these processes. We studied the domestication of the emblematic white mold Penicillium camemberti, used for the maturation of soft cheeses, such as Camembert and Brie, about which surprisingly little was known, despite its economic and cultural importance. Whole-genome-based analyses of genetic relationships and diversity revealed that an ancient domestication event led to the emergence of the gray-green P. biforme mold used in cheese making, by divergence from the blue-green wild P. fuscoglaucum fungus. Another much more recent domestication event led to the generation of the P. camemberti clonal lineage as a sister group to P. biforme. Penicillium biforme displayed signs of phenotypic adaptation to cheese making relative to P. fuscoglaucum, in terms of whiter color, faster growth on cheese medium under cave conditions, lower amounts of toxin production, and greater ability to prevent the growth of other fungi. The P. camemberti lineage displayed even stronger signs of domestication for all these phenotypic features. We also identified two differentiated P. camemberti varieties, apparently associated with different kinds of cheeses and with contrasted phenotypic features in terms of color, growth, toxin production, and competitive ability. We have thus identified footprints of domestication in these fungi, with genetic differentiation between cheese and wild populations, bottlenecks, and specific phenotypic traits beneficial for cheese making. This study has not only fundamental implications for our understanding of domestication but can also have important effects on cheese making.
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18
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Abstract
Domestication is a co-evolutionary process that occurs when wild plants are brought into cultivation by humans, leading to origin of new species and/or differentiated populations that are critical for human survival. Darwin used domesticated species as early models for evolution, highlighting their variation and the key role of selection in species differentiation. Over the last two decades, a growing synthesis of plant genetics, genomics, and archaeobotany has led to challenges to old orthodoxies and the advent of fresh perspectives on how crop domestication and diversification proceed. I discuss four new insights into plant domestication - that in general domestication is a protracted process, that unconscious (natural) selection plays a prominent role, that interspecific hybridization may be an important mechanism for crop species diversification and range expansion, and that similar genes across multiple species underlies parallel/convergent phenotypic evolution between domesticated taxa. Insights into the evolutionary origin and diversification of crop species can help us in developing new varieties (and possibly even new species) to deal with current and future environmental challenges in a sustainable manner.
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Affiliation(s)
- Michael D Purugganan
- Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place New York University, New York, NY, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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19
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Denham T, Barton H, Castillo C, Crowther A, Dotte-Sarout E, Florin SA, Pritchard J, Barron A, Zhang Y, Fuller DQ. The domestication syndrome in vegetatively propagated field crops. ANNALS OF BOTANY 2020; 125:581-597. [PMID: 31903489 PMCID: PMC7102979 DOI: 10.1093/aob/mcz212] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/02/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Vegetatively propagated crops are globally significant in terms of current agricultural production, as well as for understanding the long-term history of early agriculture and plant domestication. Today, significant field crops include sugarcane (Saccharum officinarum), potato (Solanum tuberosum), manioc (Manihot esculenta), bananas and plantains (Musa cvs), sweet potato (Ipomoea batatas), yams (Dioscorea spp.) and taro (Colocasia esculenta). In comparison with sexually reproduced crops, especially cereals and legumes, the domestication syndrome in vegetatively propagated field crops is poorly defined. AIMS AND SCOPE Here, a range of phenotypic traits potentially comprising a syndrome associated with early domestication of vegetatively propagated field crops is proposed, including: mode of reproduction, yield of edible portion, ease of harvesting, defensive adaptations, timing of production and plant architecture. The archaeobotanical visibility of these syndrome traits is considered with a view to the reconstruction of the geographical and historical pathways of domestication for vegetatively propagated field crops in the past. CONCLUSIONS Although convergent phenotypic traits are identified, none of them are ubiquitous and some are divergent. In contrast to cereals and legumes, several traits seem to represent varying degrees of plastic response to growth environment and practices of cultivation, as opposed to solely morphogenetic 'fixation'.
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Affiliation(s)
- Tim Denham
- School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra ACT 0200, Australia
- For correspondence. E-mail
| | - Huw Barton
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester, UK
| | - Cristina Castillo
- University College London, Institute of Archaeology, 31–34 Gordon Square, London, UK
| | - Alison Crowther
- School of Social Science, University of Queensland, Brisbane, Australia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Emilie Dotte-Sarout
- School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra ACT 0200, Australia
- School of Social Sciences, Faculty of Arts, Business, Law & Education, University of Western Australia, Perth, Australia
| | - S Anna Florin
- School of Social Science, University of Queensland, Brisbane, Australia
| | - Jenifer Pritchard
- School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra ACT 0200, Australia
| | - Aleese Barron
- School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra ACT 0200, Australia
| | - Yekun Zhang
- School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra ACT 0200, Australia
| | - Dorian Q Fuller
- University College London, Institute of Archaeology, 31–34 Gordon Square, London, UK
- School of Archaeology and Museology, Northwest University, Xian, Shaanxi, China
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20
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Parker TA, Berny Mier Y Teran JC, Palkovic A, Jernstedt J, Gepts P. Pod indehiscence is a domestication and aridity resilience trait in common bean. THE NEW PHYTOLOGIST 2020; 225:558-570. [PMID: 31486530 DOI: 10.1111/nph.16164] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 08/14/2019] [Indexed: 05/05/2023]
Abstract
Plant domestication has strongly modified crop morphology and development. Nevertheless, many crops continue to display atavistic characteristics that were advantageous to their wild ancestors but are deleterious under cultivation, such as pod dehiscence (PD). Here, we provide the first comprehensive assessment of the inheritance of PD in the common bean (Phaseolus vulgaris), a major domesticated grain legume. Using three methods to evaluate the PD phenotype, we identified multiple, unlinked genetic regions controlling PD in a biparental population and two diversity panels. Subsequently, we assessed patterns of orthology among these loci and those controlling the trait in other species. Our results show that different genes were selected in each domestication and ecogeographic race. A chromosome Pv03 dirigent-like gene, involved in lignin biosynthesis, showed a base-pair substitution that is associated with decreased PD. This haplotype may underlie the expansion of Mesoamerican domesticates into northern Mexico, where arid conditions promote PD. The rise in frequency of the decreased-PD haplotype may be a consequence of the markedly different fitness landscape imposed by domestication. Environmental dependency and genetic redundancy can explain the maintenance of atavistic traits under domestication.
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Affiliation(s)
- Travis A Parker
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Jorge C Berny Mier Y Teran
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Antonia Palkovic
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Judy Jernstedt
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Paul Gepts
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
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Schilling S, Kennedy A, Pan S, Jermiin LS, Melzer R. Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization. THE NEW PHYTOLOGIST 2020; 225:511-529. [PMID: 31418861 DOI: 10.1111/nph.16122] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/06/2019] [Indexed: 05/21/2023]
Abstract
Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine-tuning important traits is of great importance. MADS-box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC-type MADS-box genes. Homoeolog retention is significantly above the average genome-wide retention rate for wheat genes, indicating that many MIKC-type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily-specific expression pattern, indicating broad conservation of function of MIKC-type genes during wheat evolution. We also found extensive expansion of some MIKC-type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC-type genes show novel expression patterns and respond, for example, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC-type genes may have played an important role in the adaptation of wheat to a diversity of conditions, hence contributing to the importance of wheat as a global staple food.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Alice Kennedy
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Sirui Pan
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Lars S Jermiin
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
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Abstract
Maize is an excellent model for the study of plant adaptation. Indeed, post domestication maize quickly adapted to a host of new environments across the globe. And work over the last decade has begun to highlight the role of the wild relatives of maize-the teosintes Zea mays ssp. parviglumis and ssp. mexicana-as excellent models for dissecting long-term local adaptation.Although human-driven selection associated with maize domestication has been extensively studied, the genetic basis of natural variation is still poorly understood. Here we review studies on the genetic basis of adaptation and plasticity in maize and its wild relatives. We highlight a range of different processes that contribute to adaptation and discuss evidence from natural, cultivated, and experimental populations. From an applied perspective, understanding the genetic bases of adaptation and the contribution of plasticity will provide us with new tools to both better understand and mitigate the effect of climate changes on natural and cultivated populations.
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Gros‐Balthazard M, Besnard G, Sarah G, Holtz Y, Leclercq J, Santoni S, Wegmann D, Glémin S, Khadari B. Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:143-157. [PMID: 31192486 PMCID: PMC6851578 DOI: 10.1111/tpj.14435] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/11/2023]
Abstract
The olive (Olea europaea L. subsp. europaea) is one of the oldest and most socio-economically important cultivated perennial crop in the Mediterranean region. Yet, its origins are still under debate and the genetic bases of the phenotypic changes associated with its domestication are unknown. We generated RNA-sequencing data for 68 wild and cultivated olive trees to study the genetic diversity and structure both at the transcription and sequence levels. To localize putative genes or expression pathways targeted by artificial selection during domestication, we employed a two-step approach in which we identified differentially expressed genes and screened the transcriptome for signatures of selection. Our analyses support a major domestication event in the eastern part of the Mediterranean basin followed by dispersion towards the West and subsequent admixture with western wild olives. While we found large changes in gene expression when comparing cultivated and wild olives, we found no major signature of selection on coding variants and weak signals primarily affected transcription factors. Our results indicated that the domestication of olives resulted in only moderate genomic consequences and that the domestication syndrome is mainly related to changes in gene expression, consistent with its evolutionary history and life history traits.
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Affiliation(s)
- Muriel Gros‐Balthazard
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
- Present address:
New York University Abu Dhabi (NYUAD), Center for Genomics and Systems BiologySaadiyat IslandAbu DhabiUnited Arab Emirates
| | | | - Gautier Sarah
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Yan Holtz
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Julie Leclercq
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Sylvain Santoni
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Daniel Wegmann
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
| | - Sylvain Glémin
- CNRSUniversité de RennesECOBIO (Ecosystèmes, biodiversité, évolution) − UMR 6553F‐35000RennesFrance
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Bouchaib Khadari
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
- Conservatoire Botanique National MéditerranéenUMR AGAPMontpellierFrance
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Hufford MB, Berny Mier Y Teran JC, Gepts P. Crop Biodiversity: An Unfinished Magnum Opus of Nature. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:727-751. [PMID: 31035827 DOI: 10.1146/annurev-arplant-042817-040240] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Crop biodiversity is one of the major inventions of humanity through the process of domestication. It is also an essential resource for crop improvement to adapt agriculture to ever-changing conditions like global climate change and consumer preferences. Domestication and the subsequent evolution under cultivation have profoundly shaped the genetic architecture of this biodiversity. In this review, we highlight recent advances in our understanding of crop biodiversity. Topics include the reduction of genetic diversity during domestication and counteracting factors, a discussion of the relationship between parallel phenotypic and genotypic evolution, the role of plasticity in genotype × environment interactions, and the important role subsistence farmers play in actively maintaining crop biodiversity and in participatory breeding. Linking genotype and phenotype remains the holy grail of crop biodiversity studies.
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Affiliation(s)
- Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011-1020, USA;
| | | | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, California 95616-8780, USA; ,
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Abstract
Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These “selective sweeps” can allow mildly deleterious alleles to come to fixation and may create a genetic load in the cultivated gene pool. Although the population-wide genomic consequences of domestication offer several predictions for levels of the genetic diversity in crops, our understanding of how this diversity corresponds to nutritional aspects of crops is not well understood. Many studies have found that modern cultivars have lower levels of key micronutrients and vitamins. We suspect that selection for palatability and increased yield at domestication and during postdomestication divergence exacerbated the low nutrient levels of many crops, although relatively little work has examined this question. Lack of diversity in modern germplasm may further limit our capacity to breed for higher nutrient levels, although little effort has gone into this beyond a handful of staple crops. This is an area where an understanding of domestication across many crop taxa may provide the necessary insight for breeding more nutritious crops in a rapidly changing world.
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Omari S, Kamenir Y, Benichou JIC, Pariente S, Sela H, Perl-Treves R. Landraces of snake melon, an ancient Middle Eastern crop, reveal extensive morphological and DNA diversity for potential genetic improvement. BMC Genet 2018; 19:34. [PMID: 29792158 PMCID: PMC5966880 DOI: 10.1186/s12863-018-0619-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 04/30/2018] [Indexed: 12/05/2022] Open
Abstract
Background Snake melon (Cucumis melo var. flexuosus, “Faqqous”) is a traditional and ancient vegetable in the Mediterranean area. A collection of landraces from 42 grower fields in Israel and Palestinian territories was grown and characterized in a “Common Garden” rain-fed experiment, at the morphological-horticultural and molecular level using seq-DArT markers. Results The different landraces (“populations”) showed extensive variation in morphology and quantitative traits such as yield and femaleness, and clustered into four horticultural varieties. Yield was assessed by five harvests along the season, with middle harvests producing the highest yields. Yield correlated with early vigor, and with femaleness, but not with late vigor. At the molecular level, 2784 SNP were produced and > 90% were mapped to the melon genome. Populations were very polymorphic (46–72% of the markers biallelic in a 4 individuals sample), and observed heterozygosity was higher than the expected, suggesting gene flow among populations and extensive cross pollination among individuals in the field. Genetic distances between landraces were significantly correlated with the geographical distance between collecting sites, and with long term March precipitation average; variation in yield correlated with April temperature maxima. Conclusions The extensive variation suggests that selection of local snake melon could result in yield improvement. Correlations between traits and climatic variables could suggest local adaptation of landraces to the diverse environment in which they evolved. This study stresses the importance of preserving this germplasm, and its potential for breeding better snake melons as an heirloom crop in our region. Electronic supplementary material The online version of this article (10.1186/s12863-018-0619-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samer Omari
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Yuri Kamenir
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Jennifer I C Benichou
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Sarah Pariente
- Department of Geography and Environment, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Hanan Sela
- Cereal Crop Improvement Institute, Faculty of Life Sciences, Tel-Aviv University, 6997801, Tel Aviv, Israel
| | - Rafael Perl-Treves
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel.
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27
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Pickersgill B. Parallel vs. Convergent Evolution in Domestication and Diversification of Crops in the Americas. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00056] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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28
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Schilling S, Pan S, Kennedy A, Melzer R. MADS-box genes and crop domestication: the jack of all traits. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1447-1469. [PMID: 29474735 DOI: 10.1093/jxb/erx479] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/10/2018] [Indexed: 05/25/2023]
Abstract
MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement. Numerous examples from a diversity of crop plants show that various developmental processes have been shaped by allelic variations in MADS-box genes. We propose that new genomic and genome editing resources provide an excellent starting point for further harnessing the potential of MADS-box genes to improve a variety of reproductive traits in crops. We also suggest that the biophysics of MADS-domain protein-protein and protein-DNA interactions, which is becoming increasingly well characterized, makes them especially suited to exploit coding sequence variations for targeted breeding approaches.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Sirui Pan
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Alice Kennedy
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Irel
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29
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Chávez-Pesqueira M, Núñez-Farfán J. Domestication and Genetics of Papaya: A Review. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00155] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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30
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Huang SSC, Ecker JR. Piecing together cis-regulatory networks: insights from epigenomics studies in plants. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 10:e1411. [PMID: 29194997 DOI: 10.1002/wsbm.1411] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022]
Abstract
5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. Epigenetic inheritance of phenotypes mediated by DNA methylation is well established in plants. Most of the known mechanisms of establishing, maintaining and modifying DNA methylation have been worked out in the reference plant Arabidopsis thaliana. Major functions of DNA methylation in plants include regulation of gene expression and silencing of transposable elements (TEs) and repetitive sequences, both of which have parallels in mammalian biology, involve interaction with the transcriptional machinery, and may have profound effects on the regulatory networks in the cell. Methylome and transcriptome dynamics have been investigated in development and environmental responses in Arabidopsis and agriculturally and ecologically important plants, revealing the interdependent relationship among genomic context, methylation patterns, and expression of TE and protein coding genes. Analyses of methylome variation among plant natural populations and species have begun to quantify the extent of genetic control of methylome variation vs. true epimutation, and model the evolutionary forces driving methylome evolution in both short and long time scales. The ability of DNA methylation to positively or negatively modulate binding affinity of transcription factors (TFs) provides a natural link from genome sequence and methylation changes to transcription. Technologies that allow systematic determination of methylation sensitivities of TFs, in native genomic and methylation context without confounding factors such as histone modifications, will provide baseline datasets for building cell-type- and individual-specific regulatory networks that underlie the establishment and inheritance of complex traits. This article is categorized under: Laboratory Methods and Technologies > Genetic/Genomic Methods Biological Mechanisms > Regulatory Biology.
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Affiliation(s)
- Shao-Shan C Huang
- Genomic Analysis Laboratory and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
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31
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Chacón-Fuentes M, Parra L, Lizama M, Seguel I, Urzúa A, Quiroz A. Plant Flavonoid Content Modified by Domestication. ENVIRONMENTAL ENTOMOLOGY 2017; 46:1080-1089. [PMID: 28981645 DOI: 10.1093/ee/nvx126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Indexed: 06/07/2023]
Abstract
Plant domestication can modify and weaken defensive chemical traits, reducing chemical defenses in plants and consequently their resistance against pests. We characterized and quantified the major defensive flavonols and isoflavonoids present in both wild and cultivated murtilla plants (Ugni molinae Turcz), established in a common garden. We examined their effects on the larvae of Chilesia rudis (Butler) (Lepidoptera: Arctiidae). Insect community and diversity indices were also evaluated. We hypothesized that domestication reduces flavonoid contents and modifies C. rudis preference, the insect community, and diversity. Methanolic extracts were obtained from leaves of U. molinae plants and analyzed by high performance liquid chromatography. Results showed higher insect numbers (86.48%) and damage index (1.72 ± 0.16) in cultivated plants. Four new first records of insects were found associated with U. molinae. Diversity indices, such as Simpson, Shannon, and Margalef, were higher in cultivated plants than in wild plants. Furthermore, eight isoflavonoids were identified in U. molinae leaves for the first time. The five flavonols showed higher concentrations in wild U. molinae leaves (89.8 µg/g) than in cultivated plants (75.2 µg/g); however, no differences were found in isoflavonoids between wild and cultivated plants. The larvae of C. rudis consumed more leaf material of cultivated plants than wild plants in choice (3.8 vs. 0.8 mm2) and no-choice (7.5 vs. 3.0 mm2) assays. Our study demonstrates that domestication in U. molinae reduces the amount of flavonoids in leaves, increasing the preference of C. rudis and the insect community.
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Affiliation(s)
- Manuel Chacón-Fuentes
- Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco, Chile
- Laboratorio de Química Ecológica, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
| | - Leonardo Parra
- Laboratorio de Química Ecológica, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
- Centro de Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
- Scientific and Technological Bioresources Nucleus, BIOREN -UFRO, Universidad de La Frontera, Temuco, Chile
| | - Marcelo Lizama
- Laboratorio de Química Ecológica, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
- Centro de Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
| | - Ivette Seguel
- Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación Carillanca, Temuco, Chile
| | - Alejandro Urzúa
- Laboratorio de Química Ecológica, Departamento de Ciencias del Ambiente, Universidad de Santiago de Chile, Av. Bernardo O' Higgins 3363, Santiago, Chile
| | - Andrés Quiroz
- Laboratorio de Química Ecológica, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
- Centro de Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
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Assessing elements of an extended evolutionary synthesis for plant domestication and agricultural origin research. Proc Natl Acad Sci U S A 2017; 114:6429-6437. [PMID: 28576881 DOI: 10.1073/pnas.1703658114] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The development of agricultural societies, one of the most transformative events in human and ecological history, was made possible by plant and animal domestication. Plant domestication began 12,000-10,000 y ago in a number of major world areas, including the New World tropics, Southwest Asia, and China, during a period of profound global environmental perturbations as the Pleistocene epoch ended and transitioned into the Holocene. Domestication is at its heart an evolutionary process, and for many prehistorians evolutionary theory has been foundational in investigating agricultural origins. Similarly, geneticists working largely with modern crops and their living wild progenitors have documented some of the mechanisms that underwrote phenotypic transformations from wild to domesticated species. Ever-improving analytic methods for retrieval of empirical data from archaeological sites, together with advances in genetic, genomic, epigenetic, and experimental research on living crop plants and wild progenitors, suggest that three fields of study currently little applied to plant domestication processes may be necessary to understand these transformations across a range of species important in early prehistoric agriculture. These fields are phenotypic (developmental) plasticity, niche construction theory, and epigenetics with transgenerational epigenetic inheritance. All are central in a controversy about whether an Extended Evolutionary Synthesis is needed to reconceptualize how evolutionary change occurs. An exploration of their present and potential utility in domestication study shows that all three fields have considerable promise in elucidating important issues in plant domestication and in agricultural origin and dispersal research and should be increasingly applied to these issues.
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Brandenburg JT, Mary-Huard T, Rigaill G, Hearne SJ, Corti H, Joets J, Vitte C, Charcosset A, Nicolas SD, Tenaillon MI. Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. PLoS Genet 2017; 13:e1006666. [PMID: 28301472 PMCID: PMC5373671 DOI: 10.1371/journal.pgen.1006666] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 03/30/2017] [Accepted: 03/01/2017] [Indexed: 12/27/2022] Open
Abstract
Through the local selection of landraces, humans have guided the adaptation of crops to a vast range of climatic and ecological conditions. This is particularly true of maize, which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges worldwide. Here, we sequenced 67 genomes with an average sequencing depth of 18x to document routes of introduction, admixture and selective history of European maize and its American counterparts. To avoid the confounding effects of recent breeding, we targeted germplasm (lines) directly derived from landraces. Among our lines, we discovered 22,294,769 SNPs and between 0.9% to 4.1% residual heterozygosity. Using a segmentation method, we identified 6,978 segments of unexpectedly high rate of heterozygosity. These segments point to genes potentially involved in inbreeding depression, and to a lesser extent to the presence of structural variants. Genetic structuring and inferences of historical splits revealed 5 genetic groups and two independent European introductions, with modest bottleneck signatures. Our results further revealed admixtures between distinct sources that have contributed to the establishment of 3 groups at intermediate latitudes in North America and Europe. We combined differentiation- and diversity-based statistics to identify both genes and gene networks displaying strong signals of selection. These include genes/gene networks involved in flowering time, drought and cold tolerance, plant defense and starch properties. Overall, our results provide novel insights into the evolutionary history of European maize and highlight a major role of admixture in environmental adaptation, paralleling recent findings in humans.
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Affiliation(s)
- Jean-Tristan Brandenburg
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| | - Tristan Mary-Huard
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
- UMR 518 AgroParisTech/INRA, France
| | - Guillem Rigaill
- Institute of Plant Sciences Paris-Saclay, UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot, Sorbonne Paris-Cité, France
| | - Sarah J. Hearne
- CIMMYT (International Maize and Wheat Improvement Centre), El Batan, Texcoco, Edo de Mexico, Mexico
| | - Hélène Corti
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| | - Johann Joets
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| | - Clémentine Vitte
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| | - Alain Charcosset
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| | - Stéphane D. Nicolas
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| | - Maud I. Tenaillon
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
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van de Wiel CCM, Schaart JG, Lotz LAP, Smulders MJM. New traits in crops produced by genome editing techniques based on deletions. PLANT BIOTECHNOLOGY REPORTS 2017; 11:1-8. [PMID: 28386301 PMCID: PMC5360818 DOI: 10.1007/s11816-017-0425-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 01/23/2017] [Indexed: 05/21/2023]
Abstract
One of the most promising New Plant Breeding Techniques is genome editing (also called gene editing) with the help of a programmable site-directed nuclease (SDN). In this review, we focus on SDN-1, which is the generation of small deletions or insertions (indels) at a precisely defined location in the genome with zinc finger nucleases (ZFN), TALENs, or CRISPR-Cas9. The programmable nuclease is used to induce a double-strand break in the DNA, while the repair is left to the plant cell itself, and mistakes are introduced, while the cell is repairing the double-strand break using the relatively error-prone NHEJ pathway. From a biological point of view, it could be considered as a form of targeted mutagenesis. We first discuss improvements and new technical variants for SDN-1, in particular employing CRISPR-Cas, and subsequently explore the effectiveness of targeted deletions that eliminate the function of a gene, as an approach to generate novel traits useful for improving agricultural sustainability, including disease resistances. We compare them with examples of deletions that resulted in novel functionality as known from crop domestication and classical mutation breeding (both using radiation and chemical mutagens). Finally, we touch upon regulatory and access and benefit sharing issues regarding the plants produced.
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Affiliation(s)
| | - J. G. Schaart
- Wageningen University and Research, Wageningen, The Netherlands
| | - L. A. P. Lotz
- Wageningen University and Research, Wageningen, The Netherlands
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