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Liu R, Hu C, Gao D, Li M, Yuan X, Chen L, Shu Q, Wang Z, Yang X, Dai Z, Yu H, Yang F, Zheng A, Lv M, Garg V, Jiao C, Zhang H, Hou W, Teng C, Zhou X, Du C, Xiang C, Xu D, Tang Y, Chitikineni A, Duan Y, Maalouf F, Agrawal SK, Wei L, Zhao N, Barmukh R, Li X, Wang D, Ding H, Liu Y, Chen X, Varshney RK, He Y, Zong X, Yang T. A special short-wing petal faba genome and genetic dissection of floral and yield-related traits accelerate breeding and improvement of faba bean. Genome Biol 2025; 26:62. [PMID: 40098156 PMCID: PMC11916958 DOI: 10.1186/s13059-025-03532-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 03/06/2025] [Indexed: 03/19/2025] Open
Abstract
BACKGROUND A comprehensive study of the genome and genetics of superior germplasms is fundamental for crop improvement. As a widely adapted protein crop with high yield potential, the improvement in breeding and development of the seeds industry of faba bean have been greatly hindered by its giant genome size and high outcrossing rate. RESULTS To fully explore the genomic diversity and genetic basis of important agronomic traits, we first generate a de novo genome assembly and perform annotation of a special short-wing petal faba bean germplasm (VF8137) exhibiting a low outcrossing rate. Comparative genome and pan-genome analyses reveal the genome evolution characteristics and unique pan-genes among the three different faba bean genomes. In addition, the genome diversity of 558 accessions of faba bean germplasm reveals three distinct genetic groups and remarkable genetic differences between the southern and northern germplasms. Genome-wide association analysis identifies several candidate genes associated with adaptation- and yield-related traits. We also identify one candidate gene related to short-wing petals by combining quantitative trait locus mapping and bulked segregant analysis. We further elucidate its function through multiple lines of evidence from functional annotation, sequence variation, expression differences, and protein structure variation. CONCLUSIONS Our study provides new insights into the genome evolution of Leguminosae and the genomic diversity of faba bean. It offers valuable genomic and genetic resources for breeding and improvement of faba bean.
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Affiliation(s)
- Rong Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian District, Beijing, 100081, China
| | - Chaoqin Hu
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Dan Gao
- Smartgenomics Technology Institute, Tianjin, 301700, China
| | - Mengwei Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian District, Beijing, 100081, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Liyang Chen
- Smartgenomics Technology Institute, Tianjin, 301700, China
| | - Qin Shu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian District, Beijing, 100081, China
| | - Zonghe Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian District, Beijing, 100081, China
| | - Xin Yang
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Zhengming Dai
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Haitian Yu
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Feng Yang
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Aiqing Zheng
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Meiyuan Lv
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Vanika Garg
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Chengzhi Jiao
- Smartgenomics Technology Institute, Tianjin, 301700, China
| | - Hongyan Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, 810016, China
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, 810016, China
| | - Wanwei Hou
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, 810016, China
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, 810016, China
| | - Changcai Teng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, 810016, China
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, 810016, China
| | - Xianli Zhou
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, 810016, China
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, 810016, China
| | - Chengzhang Du
- Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Chao Xiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 610066, China
| | - Dongxu Xu
- Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou, Hebei, 075032, China
| | - Yongsheng Tang
- Qujing Academy of Agricultural Sciences, Qujingaq, Yunnan, 655000, China
| | - Annapurna Chitikineni
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Yinmei Duan
- Dali Academy of Agricultural Sciences, Dali, Yunnan, 671005, China
| | - Fouad Maalouf
- International Center for Agricultural Researchin the, Dry Areas (ICARDA), Beirut, 1108-2010, Lebanon
| | - Shiv Kumar Agrawal
- International Center for Agricultural Researchin the, Dry Areas (ICARDA), Beirut, 1108-2010, Lebanon
| | - Libin Wei
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, Jiangsu, 226541, China
| | - Na Zhao
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, Jiangsu, 226541, China
| | - Rutwik Barmukh
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Xiang Li
- Yuxi Academy of Agricultural Sciences, Yuxi, Yunnan, 653100, China
| | - Dong Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong, 250100, China
| | - Hanfeng Ding
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong, 250100, China
| | - Yujiao Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, 810016, China.
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China.
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Yuhua He
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China.
| | - Xuxiao Zong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian District, Beijing, 100081, China.
| | - Tao Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian District, Beijing, 100081, China.
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Boukteb A, Sato K, Gan P, Kharrat M, Sakouhi H, Shibata A, Shirasu K, Ichihashi Y, Bouhadida M. Global changes in gene expression during compatible and incompatible interactions of faba bean (Vicia faba L.) during Orobanche foetida parasitism. PLoS One 2024; 19:e0301981. [PMID: 38626155 PMCID: PMC11020376 DOI: 10.1371/journal.pone.0301981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/26/2024] [Indexed: 04/18/2024] Open
Abstract
Orobanche foetida Poiret is the main constraint facing faba bean crop in Tunisia. Indeed, in heavily infested fields with this parasitic plant, yield losses may reach 90%, and the recent estimation of the infested area is around 80,000 ha. Identifying genes involved in the Vicia faba/O. foetida interaction is crucial for the development of effective faba bean breeding programs. However, there is currently no available information on the transcriptome of faba bean responding to O. foetida parasitism. In this study, we employed RNA sequencing to explore the global gene expression changes associated with compatible and incompatible V. faba/O. foetida interactions. In this perspective, two faba bean varieties (susceptible and resistant) were examined at the root level across three stages of O. foetida development (Before Germination (BG), After Germination (AG) and Tubercule Stage (TS)). Our analyses presented an exploration of the transcriptomic profile, including comprehensive assessments of differential gene expression and Gene Ontology (GO) enrichment analyses. Specifically, we investigated key pathways revealing the complexity of molecular responses to O. foetida attack. In this study, we detected differential gene expression of pathways associated with secondary metabolites: flavonoids, auxin, thiamine, and jasmonic acid. To enhance our understanding of the global changes in V. faba response to O. foetida, we specifically examined WRKY genes known to play a role in plant host-parasitic plant interactions. Furthermore, considering the pivotal role of parasitic plant seed germination in this interaction, we investigated genes involved in the orobanchol biosynthesis pathway. Interestingly, we detected the gene expression of VuCYP722C homolog, coding for a key enzyme involved in orobanchol biosynthesis, exclusively in the susceptible host. Clearly, this study enriches our understanding of the V. faba/O. foetida interaction, shedding light on the main differences between susceptible and resistant faba bean varieties during O. foetida infestation at the gene expression level.
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Affiliation(s)
- Amal Boukteb
- Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Field Crop Laboratory, National Institute of Agricultural Research of Tunisia, Carthage University, Tunis, Tunisia
| | - Kazuki Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Pamela Gan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Mohamed Kharrat
- Field Crop Laboratory, National Institute of Agricultural Research of Tunisia, Carthage University, Tunis, Tunisia
| | - Hanen Sakouhi
- Field Crop Laboratory, National Institute of Agricultural Research of Tunisia, Carthage University, Tunis, Tunisia
| | - Arisa Shibata
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Mariem Bouhadida
- Field Crop Laboratory, National Institute of Agricultural Research of Tunisia, Carthage University, Tunis, Tunisia
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Jayakodi M, Golicz AA, Kreplak J, Fechete LI, Angra D, Bednář P, Bornhofen E, Zhang H, Boussageon R, Kaur S, Cheung K, Čížková J, Gundlach H, Hallab A, Imbert B, Keeble-Gagnère G, Koblížková A, Kobrlová L, Krejčí P, Mouritzen TW, Neumann P, Nadzieja M, Nielsen LK, Novák P, Orabi J, Padmarasu S, Robertson-Shersby-Harvie T, Robledillo LÁ, Schiemann A, Tanskanen J, Törönen P, Warsame AO, Wittenberg AHJ, Himmelbach A, Aubert G, Courty PE, Doležel J, Holm LU, Janss LL, Khazaei H, Macas J, Mascher M, Smýkal P, Snowdon RJ, Stein N, Stoddard FL, Stougaard J, Tayeh N, Torres AM, Usadel B, Schubert I, O'Sullivan DM, Schulman AH, Andersen SU. The giant diploid faba genome unlocks variation in a global protein crop. Nature 2023; 615:652-659. [PMID: 36890232 PMCID: PMC10033403 DOI: 10.1038/s41586-023-05791-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/03/2023] [Indexed: 03/10/2023]
Abstract
Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.
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Affiliation(s)
- Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Agnieszka A Golicz
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Jonathan Kreplak
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Lavinia I Fechete
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Deepti Angra
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Petr Bednář
- Department of Analytical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Elesandro Bornhofen
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus C, Denmark
| | - Hailin Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Raphaël Boussageon
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Kwok Cheung
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Asis Hallab
- IBG-4 Bioinformatics Forschungszentrum Jülich, Jülich, Germany
- Bingen Technical University of Applied Sciences, Bingen, Germany
| | - Baptiste Imbert
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | | | - Andrea Koblížková
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Lucie Kobrlová
- Department of Botany, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Petra Krejčí
- Department of Analytical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Troels W Mouritzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | | | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | | | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | - Laura Ávila Robledillo
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | | | | | - Petri Törönen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ahmed O Warsame
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Grégoire Aubert
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Liisa U Holm
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Luc L Janss
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus C, Denmark
| | - Hamid Khazaei
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Center of Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Frederick L Stoddard
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland, Córdoba, Spain
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Nadim Tayeh
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Ana M Torres
- Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), Área de Mejora y Biotecnología, Centro Alameda del Obispo, Córdoba, Spain
| | - Björn Usadel
- IBG-4 Bioinformatics Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science, CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | - Alan H Schulman
- Natural Resources Institute Finland (Luke), Helsinki, Finland.
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland, Córdoba, Spain.
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Zhang H, Mascher M, Abbo S, Jayakodi M. Advancing Grain Legumes Domestication and Evolution Studies with Genomics. PLANT & CELL PHYSIOLOGY 2022; 63:1540-1553. [PMID: 35534441 PMCID: PMC9680859 DOI: 10.1093/pcp/pcac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 06/14/2023]
Abstract
Grain legumes were domesticated in parallel with cereals in several regions of the world and formed the economic basis of early farming cultures. Since then, legumes have played a vital role in human and animal diets and in fostering agrobiodiversity. Increasing grain legume cultivation will be crucial to safeguard nutritional security and the resilience of agricultural ecosystems across the globe. A better understanding of the molecular underpinnings of domestication and crop evolution of grain legumes may be translated into practical approaches in modern breeding programs to stabilize yield, which is threatened by evolving pathogens and changing climates. During recent decades, domestication research in all crops has greatly benefited from the fast progress in genomic technologies. Yet still, many questions surrounding the domestication and diversification of legumes remain unanswered. In this review, we assess the potential of genomic approaches in grain legume research. We describe the centers of origin and the crucial domestication traits of grain legumes. In addition, we survey the effect of domestication on both above-ground and below-ground traits that have economic importance. Finally, we discuss open questions in grain legume domestication and diversification and outline how to bridge the gap between the preservation of historic crop diversity and their utilization in modern plant breeding.
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Affiliation(s)
- Hailin Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, Leipzig 04103, Germany
| | - Shahal Abbo
- The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
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Bohra A, Tiwari A, Kaur P, Ganie SA, Raza A, Roorkiwal M, Mir RR, Fernie AR, Smýkal P, Varshney RK. The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies. PLANT & CELL PHYSIOLOGY 2022; 63:1554-1572. [PMID: 35713290 PMCID: PMC9680861 DOI: 10.1093/pcp/pcac086] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 05/11/2023]
Abstract
Crop domestication is a co-evolutionary process that has rendered plants and animals significantly dependent on human interventions for survival and propagation. Grain legumes have played an important role in the development of Neolithic agriculture some 12,000 years ago. Despite being early companions of cereals in the origin and evolution of agriculture, the understanding of grain legume domestication has lagged behind that of cereals. Adapting plants for human use has resulted in distinct morpho-physiological changes between the wild ancestors and domesticates, and this distinction has been the focus of several studies aimed at understanding the domestication process and the genetic diversity bottlenecks created. Growing evidence from research on archeological remains, combined with genetic analysis and the geographical distribution of wild forms, has improved the resolution of the process of domestication, diversification and crop improvement. In this review, we summarize the significance of legume wild relatives as reservoirs of novel genetic variation for crop breeding programs. We describe key legume features, which evolved in response to anthropogenic activities. Here, we highlight how whole genome sequencing and incorporation of omics-level data have expanded our capacity to monitor the genetic changes accompanying these processes. Finally, we present our perspective on alternative routes centered on de novo domestication and re-domestication to impart significant agronomic advances of novel crops over existing commodities. A finely resolved domestication history of grain legumes will uncover future breeding targets to develop modern cultivars enriched with alleles that improve yield, quality and stress tolerance.
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Affiliation(s)
- Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Abha Tiwari
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kalyanpur, Kanpur 208024, India
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, Santiniketan Road, Bolpur 731235, India
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Manish Roorkiwal
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Sheik Khalifa Bin Zayed Street, Al Ain, Abu Dhabi 15551, UAE
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST, Shalimar, Srinagar 190025, India
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Křížkovského 511/8, Olomouc 78371, Czech Republic
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
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Adaptability and Stability of Faba Bean (Vicia faba L.) Accessions under Diverse Environments and Herbicide Treatments. PLANTS 2022; 11:plants11030251. [PMID: 35161237 PMCID: PMC8839948 DOI: 10.3390/plants11030251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/31/2021] [Accepted: 01/01/2022] [Indexed: 11/18/2022]
Abstract
The adaptability and stability of 37 faba bean (Vicia faba L.) accessions with different levels of tolerance to metribuzin or imazethapyr was assessed across 12 season–location–herbicide experiments. Significant Genotype x environment (GE) interaction was found for the days to flowering (DFLR), plant height (PLHT) and grain yield (GY). Performance and stability of the accessions regarding PLHT and GY were assessed using four different stability parameters: cultivar superiority, static stability, Wricke’s eco-valence and Finlay and Wilkinson’s regression model. The stability parameters ranked these genotypes differently suggesting that PLHT and GY stability should be assessed not only on a single or a few stability parameters but on a combination of them. GGE biplot analysis indicated that the environments representing metribuzin treatment at Marchouch 2014–2015 and the non-treated treatment at Terbol 2018–2019 are the ideal environments for evaluating faba bean genotypes. GGE biplots showed herbicide tolerant accession IG12983 with simultaneous average PLHT, GY and stability across the environments. The performance of other tolerant accessions, namely IG13945, IG13906, IG106453, FB2648, and FB1216 was less stable but superior under specific mega environments. Therefore, utilizing these accessions in faba bean breeding programs would help broaden the adaptability to diverse locations–season–herbicide treatments.
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Genomic regions associated with herbicide tolerance in a worldwide faba bean (Vicia faba L.) collection. Sci Rep 2022; 12:158. [PMID: 34996977 PMCID: PMC8741826 DOI: 10.1038/s41598-021-03861-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/09/2021] [Indexed: 01/18/2023] Open
Abstract
Weeds represent one of the major constraints for faba bean crop. The identification of molecular markers associated with key genes imparting tolerance to herbicides can facilitate and fasten the efficient and effective development of herbicide tolerant cultivars. We phenotyped 140 faba bean genotypes in three open field experiments at two locations in Lebanon and Morocco against three herbicide treatments (T1 metribuzin 250 g ai/ha; T2 imazethapyr 75 g ai/ha; T3 untreated) and one in greenhouse where T1 and T3 were applied. The same set was genotyped using genotyping by sequencing (GBS) which yield 10,794 high quality single nucleotide polymorphisms (SNPs). ADMIXTURE software was used to infer the population structure which revealed two ancestral subpopulations. To identify SNPs associated with phenological and yield related traits under herbicide treatments, Single-trait (ST) and Multi-trait (MT) Genome Wide Association Studies (GWAS) were fitted using GEMMA software, showing 10 and 14 highly significant associations, respectively. Genomic sequences containing herbicide tolerance associated SNPs were aligned against the NCBI database using BLASTX tool using default parameters to annotate candidate genes underlying the causal variants. SNPs from acidic endochitinase, LRR receptor-like serine/threonine-protein kinase RCH1, probable serine/threonine-protein kinase NAK, malate dehydrogenase, photosystem I core protein PsaA and MYB-related protein P-like were significantly associated with herbicide tolerance traits.
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Adhikari KN, Khazaei H, Ghaouti L, Maalouf F, Vandenberg A, Link W, O'Sullivan DM. Conventional and Molecular Breeding Tools for Accelerating Genetic Gain in Faba Bean ( Vicia Faba L.). FRONTIERS IN PLANT SCIENCE 2021; 12:744259. [PMID: 34721470 PMCID: PMC8548637 DOI: 10.3389/fpls.2021.744259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/09/2021] [Indexed: 05/11/2023]
Abstract
Faba bean is a cool-season grain legume crop, which is grown worldwide for food and feed. Despite a decrease in area under faba bean in the past, the interest in growing faba bean is increasing globally due to its high seed protein content and its excellent ecological service. The crop is, however, exposed to diverse biotic and abiotic stresses causing unstable, low grain yield. Although, sources of resistance to main diseases, such as ascochyta blight (Ascochyta fabae Speg.), rust (Uromyces viciae-fabae (Pers.) Schroet.), chocolate spot (Botrytis fabae Sard.) and gall disease (Physioderma viciae), have been identified, their resistance is only partial and cannot prevent grain yield losses without agronomical practices. Tightly associated DNA markers for host plant resistance genes are needed to enhance the level of resistance. Less progress has been made for abiotic stresses. Different breeding methods are proposed, but until now line breeding, based on the pedigree method, is the dominant practice in breeding programs. Nonetheless, the low seed multiplication coefficient and the requirement for growing under insect-proof enclosures to avoid outcrossing hampers breeding, along with the lack of tools such as double haploid system and cytoplasmic male sterility. This reduces breeding population size and speed of breeding hence the chances of capturing rare combinations of favorable alleles. Availability and use of the DNA markers such as vicine-convicine (vc -) and herbicide tolerance in breeding programs have encouraged breeders and given confidence in marker assisted selection. Closely linked QTL for several biotic and abiotic stress tolerance are available and their verification and conversion in breeder friendly platform will enhance the selection process. Recently, genomic selection and speed breeding techniques together with genomics have come within reach to accelerate the genetic gains in faba bean. Advancements in genomic resources with other breeding tools, methods and platforms will enable to accelerate the breeding process for enhancing genetic gain in this species.
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Affiliation(s)
- Kedar N. Adhikari
- The University of Sydney, School of Life and Environmental Science, Plant Breeding Institute, Narrabri, NSW, Australia
| | | | - Lamiae Ghaouti
- Institute of Agronomy and Veterinary Medicine Hassan II, Department of Plant Production, Protection and Biotechnology, Rabat, Morocco
| | - Fouad Maalouf
- International Center for Agricultural Research in Dry Areas, Beirut, Lebanon
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Wolfgang Link
- Department of Crop Sciences, Georg-August-Universität, Göttingen, Germany
| | - Donal M. O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
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Khazaei H, O'Sullivan DM, Stoddard FL, Adhikari KN, Paull JG, Schulman AH, Andersen SU, Vandenberg A. Recent advances in faba bean genetic and genomic tools for crop improvement. LEGUME SCIENCE 2021; 3:e75. [PMID: 34977588 PMCID: PMC8700193 DOI: 10.1002/leg3.75] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/10/2021] [Accepted: 02/02/2021] [Indexed: 05/04/2023]
Abstract
Faba bean (Vicia faba L.), a member of the Fabaceae family, is one of the important food legumes cultivated in cool temperate regions. It holds great importance for human consumption and livestock feed because of its high protein content, dietary fibre, and nutritional value. Major faba bean breeding challenges include its mixed breeding system, unknown wild progenitor, and genome size of ~13 Gb, which is the largest among diploid field crops. The key breeding objectives in faba bean include improved resistance to biotic and abiotic stress and enhanced seed quality traits. Regarding quality traits, major progress on reduction of vicine-convicine and seed coat tannins, the main anti-nutritional factors limiting faba bean seed usage, have been recently achieved through gene discovery. Genomic resources are relatively less advanced compared with other grain legume species, but significant improvements are underway due to a recent increase in research activities. A number of bi-parental populations have been constructed and mapped for targeted traits in the last decade. Faba bean now benefits from saturated synteny-based genetic maps, along with next-generation sequencing and high-throughput genotyping technologies that are paving the way for marker-assisted selection. Developing a reference genome, and ultimately a pan-genome, will provide a foundational resource for molecular breeding. In this review, we cover the recent development and deployment of genomic tools for faba bean breeding.
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Affiliation(s)
- Hamid Khazaei
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | | | - Frederick L. Stoddard
- Department of Agricultural Sciences, Viikki Plant Science Centre, and Helsinki Sustainability Science CentreUniversity of HelsinkiHelsinkiFinland
| | - Kedar N. Adhikari
- Plant Breeding Institute, Faculty of ScienceThe University of SydneyNarrabriNew South WalesAustralia
| | - Jeffrey G. Paull
- School of Agriculture, Food and WineThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Alan H. Schulman
- Production SystemsNatural Resources Institute Finland (Luke)HelsinkiFinland
- Institute of Biotechnology and Viikki Plant Science CentreUniversity of HelsinkiHelsinkiFinland
| | - Stig U. Andersen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Albert Vandenberg
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSaskatchewanCanada
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Tissue culture-based genetic improvement of fava bean (Vicia faba L.): analysis on previous achievements and future perspectives. Appl Microbiol Biotechnol 2021; 105:6531-6546. [PMID: 34427764 DOI: 10.1007/s00253-021-11517-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
Fava bean is an extremely important legume and serves immense potential to function as an ingredient as pulse proteins in human diet. Bearing the proficiency of yielding magnanimous amount of functional and nutritional ingredients, this bean deserves to replace any other leguminous crop too. The instability of fava bean in its yield makes breeding for crop improvement difficult, and its high susceptibility to a number of abiotic and biotic stresses additionally results in unstable yields. The self-incompatibility leads to the formation of a limited genetic pool and shows a slow progress in breeding. The plant is highly recalcitrant, making it an onerous task to micropropagate or regenerate fava beans under in vitro conditions. Another fly in the ointment is the release of phenolic compounds by the plant. There are several endeavours that have been made to establish in vitro regeneration, protoplast culture, and genetic transformation and to genetically improve this plant. Nonetheless there are a number of promising cutting-edge technologies that are yet to be harnessed in order to ensure its comprehensive and sustainable genetic improvement. The in vitro-based technologies of this legume and its untraveled path in the plant tissue culture-mediated approaches can assist further genetic manipulation of this plant species in a smoother manner and at an exponential rate. Creation of a single review comprising all the updates and genetic advancements in fava bean is an absolute necessity of the hour. Thus, the importance of this review remains at the peak as it covers a vast range of information, starting from the basic description to the utmost modern stages of advancement in the selected crop. Overall interpretation of the review is aimed at encouraging readers to focus on almost all possible dimensions of international research, already executed, and is being executed in fava bean, thereby helping to understand the demand and advantages of the crop, even at the molecular level.Key points• Fava bean, commonly known as "poor man's meat", is a protein-rich legume with multiple nutritional and pharmacological benefits.• Its highly recalcitrant response makes in vitro interventions quite challenging for its genetic improvement.• This review delves into biotechnological interventions for its advancements to date and highlights major hurdles and potential research solutions to ensure comprehensive genetic improvement.
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11
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Hierro JL, Callaway RM. The Ecological Importance of Allelopathy. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-051120-030619] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Allelopathy (i.e., chemical interaction among species) was originally conceived as inclusive of positive and negative effects of plants on other plants, and we adopt this view. Most studies of allelopathy have been phenomenological, but we focus on studies that have explored the ecological significance of this interaction. The literature suggests that studies of allelopathy have been particularly important for three foci in ecology: species distribution, conditionality of interactions, and maintenance of species diversity. There is evidence that allelopathy influences local distributions of plant species around the world. Allelopathic conditionality appears to arise through coevolution, and this is a mechanism for plant invasions. Finally, allelopathy promotes species coexistence via intransitive competition, modifications of direct interactions, and (co)evolution. Recent advances additionally suggest that coexistence might be favored through biochemical recognition. The preponderance of phenomenological studies notwithstanding, allelopathy has broad ecological consequences. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- José L. Hierro
- Laboratorio de Ecología, Biogeografía y Evolución Vegetal (LEByEV), Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)–Universidad Nacional de La Pampa (UNLPam), 6300 Santa Rosa, La Pampa, Argentina
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, UNLPam, 6300 Santa Rosa, La Pampa, Argentina
| | - Ragan M. Callaway
- Division of Biological Sciences and the Institute on Ecosystems, University of Montana, Missoula, Montana 59812, USA
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12
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Hruby K, Cendrowska M, Chasan R, Groman-Yaroslavski I, Rosenberg D. The function of the south-Levantine Late Chalcolithic and Early Bronze Age basalt vessels bearing circumferential depressions: Insights from use-wear analyses. PLoS One 2021; 16:e0252535. [PMID: 34086750 PMCID: PMC8177471 DOI: 10.1371/journal.pone.0252535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/17/2021] [Indexed: 11/23/2022] Open
Abstract
One of the most characteristic aspects of the Late Chalcolithic and Early Bronze Age periods in the southern Levant is the appearance of large assemblages of basalt vessels. These vessels, frequently meticulously made, appear sometimes a considerable distance from the raw material sources and are found mainly at habitation sites. While these and their prestigious value have been widely discussed in the past, their function is still obscure. In the current paper, we address their functionality through microscopic use-wear analysis. Emphasis was placed on basalt vessels with a distinct wear pattern–circumferential depressions, which appear along the perimeter of their interior bases. The documented traces were compared to results of an experimental study we conducted to characterize the effects of abrasion, grinding, and lubrication on basalt surfaces. The results of the comparative experimental study suggest that the circumferential depression was formed from a repetitive rotational activity using a narrow-ended tool. Further, it seems that two material types acted in combination as the circling device and processed material. One was hard and abrasive, such as stone, and the other was semi-resilient, such as wood or mineral powder. Water was likely used as a lubricant in the rotational process. While the actual function of the bowls bearing the circumferential depressions is not entirely clear, the use-wear analyses suggest that they may have been devices involved in craft industries, used for processing materials unrelated to food (minerals in particular). Whatever the exact function was, it clear that this use continued from the Chalcolithic through the Early Bronze Age, providing evidence for functional continuity between these two periods.
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Affiliation(s)
- Karolina Hruby
- Laboratory for Ground Stone Tools Research, Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
- * E-mail:
| | | | - Rivka Chasan
- Laboratory for Ground Stone Tools Research, Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Iris Groman-Yaroslavski
- The Use-Wear Analysis Laboratory, Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Danny Rosenberg
- Laboratory for Ground Stone Tools Research, Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
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13
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A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons. Proc Natl Acad Sci U S A 2021; 118:2101486118. [PMID: 34031154 DOI: 10.1073/pnas.2101486118] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Wild relatives or progenitors of crops are important resources for breeding and for understanding domestication. Identifying them, however, is difficult because of extinction, hybridization, and the challenge of distinguishing them from feral forms. Here, we use collection-based systematics, iconography, and resequenced accessions of Citrullus lanatus and other species of Citrullus to search for the potential progenitor of the domesticated watermelon. A Sudanese form with nonbitter whitish pulp, known as the Kordofan melon (C. lanatus subsp. cordophanus), appears to be the closest relative of domesticated watermelons and a possible progenitor, consistent with newly interpreted Egyptian tomb paintings that suggest that the watermelon may have been consumed in the Nile Valley as a dessert by 4360 BP. To gain insights into the genetic changes that occurred from the progenitor to the domesticated watermelon, we assembled and annotated the genome of a Kordofan melon at the chromosome level, using a combination of Pacific Biosciences and Illumina sequencing as well as Hi-C mapping technologies. The genetic signature of bitterness loss is present in the Kordofan melon genome, but the red fruit flesh color only became fixed in the domesticated watermelon. We detected 15,824 genome structural variants (SVs) between the Kordofan melon and a typical modern cultivar, "97103," and mapping the SVs in over 400 Citrullus accessions revealed shifts in allelic frequencies, suggesting that fruit sweetness has gradually increased over the course of watermelon domestication. That a likely progenitor of the watermelon still exists in Sudan has implications for targeted modern breeding efforts.
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14
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Fayek NM, Mekky RH, Dias CN, Kropf M, Heiss AG, Wessjohann LA, Farag MA. UPLC-MS Metabolome-Based Seed Classification of 16 Vicia Species: A Prospect for Phyto-Equivalency and Chemotaxonomy of Different Accessions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5252-5266. [PMID: 33877831 DOI: 10.1021/acs.jafc.0c06054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Seeds of domesticated Vicia (vetch) species (family Fabaceae-Faboideae) are produced and consumed worldwide for their nutritional value. Seed accessions belonging to 16 different species of Vicia-both domesticated and wild taxa-were subjected to a chemotaxonomic study using ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) analyzed by chemometrics. A total of 89 metabolites were observed in the examined Vicia accessions. Seventy-eight out of the 89 detected metabolites were annotated. Metabolites quantified belonged to several classes, viz., flavonoids, procyanidins, prodelphinidins, anthocyanins, stilbenes, dihydrochalcones, phenolic acids, coumarins, alkaloids, jasmonates, fatty acids, terpenoids, and cyanogenics, with flavonoids and fatty acids amounting to the major classes. Flavonoids, fatty acids, and anthocyanins showed up as potential chemotaxonomic markers in Vicia species discrimination. Fatty acids were more enriched in Vicia faba specimens, while the abundance of flavonoids was the highest in Vicia parviflora. Anthocyanins allowed for discrimination between Vicia hirsuta and Vicia sepium. To the best of our knowledge, this is the first report on employing UPLC-MS metabolomics to discern the diversity of metabolites at the intrageneric level among Vicia species.
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Affiliation(s)
- Nesrin M Fayek
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr El Aini Street, 11562 Cairo, Egypt
| | - Reham Hassan Mekky
- Department of Pharmacognosy, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo-Suez Road, 11829 Cairo, Egypt
| | - Clarice Noleto Dias
- Natural and Synthetic Bioactive Products Graduate Program, Federal University of Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Matthias Kropf
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, Vienna (BOKU), Gregor Mendel-Straße 33, 1180 Vienna, Austria
| | - Andreas G Heiss
- Department for Bioarchaeology, Austrian Archaeological Institute (ÖAI), Austrian Academy of Sciences (ÖAW), Franz Klein-Gasse 1, 1190 Vienna, Austria
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle - Saale, Germany
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr El Aini Street, 11562 Cairo, Egypt
- Department of Chemistry, School of Sciences & Engineering, The American University in Cairo, New Cairo 11835, Egypt
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15
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Rosenberg D, Gluhak TM, Kaufman D, Yeshurun R, Weinstein-Evron M. Exploring exchange and direct procurement strategies for Natufian food processing tools of el-Wad Terrace, Israel. Sci Rep 2021; 11:9480. [PMID: 33947889 PMCID: PMC8096842 DOI: 10.1038/s41598-021-88484-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/13/2021] [Indexed: 12/02/2022] Open
Abstract
We present the results of a detailed geochemical provenance study of 54 Natufian (ca. 15,000–11,700 cal. BP) basalt pestles from the site of el-Wad Terrace (EWT), Israel. It is the first time precise locations from where basalt raw materials were derived are provided. The results indicate that the Natufian hunter-gatherers used multiple sources of basaltic rocks, distributed over a large area surrounding the Sea of Galilee. This area is located at a considerable distance from EWT, ca. 60–120 km away, in a region where contemporaneous Natufian basecamps are few. We consider two possible models that suggest vehicles for the transportation of these artifacts to EWT, namely the exchange obtaining model (EOM) and the direct procurement model (DPM). We argue that these mechanisms are not mutually exclusive and may have operated together. We also suggest that at a time of increasing Natufian territoriality, a large area around the Sea of Galilee remained unclaimed. The paper concludes with a brief discussion of the implications for the two models. In particular, we note that the DPM implies that technological know-how for pestle production was maintained within the EWT community.
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Affiliation(s)
- Danny Rosenberg
- Laboratory for Ground Stone Tools Research, The Zinman Institute of Archaeology, University of Haifa, Haifa, Israel.
| | - Tatjana M Gluhak
- Römisch Germanisches Zentralmuseum, Ernst Ludwig Platz 2, 55124, Mainz, Germany
| | - Daniel Kaufman
- The Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Reuven Yeshurun
- The Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
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16
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Parker TA, Lo S, Gepts P. Pod shattering in grain legumes: emerging genetic and environment-related patterns. THE PLANT CELL 2021; 33:179-199. [PMID: 33793864 PMCID: PMC8136915 DOI: 10.1093/plcell/koaa025] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/26/2020] [Indexed: 05/25/2023]
Abstract
A reduction in pod shattering is one of the main components of grain legume domestication. Despite this, many domesticated legumes suffer serious yield losses due to shattering, particularly under arid conditions. Mutations related to pod shattering modify the twisting force of pod walls or the structural strength of the dehiscence zone in pod sutures. At a molecular level, a growing body of evidence indicates that these changes are controlled by a relatively small number of key genes that have been selected in parallel across grain legume species, supporting partial molecular convergence. Legume homologs of Arabidopsis thaliana silique shattering genes play only minor roles in legume pod shattering. Most domesticated grain legume species contain multiple shattering-resistance genes, with mutants of each gene typically showing only partial shattering resistance. Hence, crosses between varieties with different genes lead to transgressive segregation of shattering alleles, producing plants with either enhanced shattering resistance or atavistic susceptibility to the trait. The frequency of these resistance pod-shattering alleles is often positively correlated with environmental aridity. The continued development of pod-shattering-related functional information will be vital for breeding crops that are suited to the increasingly arid conditions expected in the coming decades.
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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
| | - Sassoum Lo
- Department of Plant Sciences/MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA 95616-8780
| | - Paul Gepts
- Department of Plant Sciences/MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA 95616-8780
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17
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Elamine Y, Torres-Salas V, Messai A, Girón-Calle J, Alaiz M, Vioque J. Purification, Characterization, and Antiproliferative Activity of a Single-Chain Lectin from Vicia palaestina (Fabaceae) Seeds. Chem Biodivers 2021; 18:e2000827. [PMID: 33410600 DOI: 10.1002/cbdv.202000827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/11/2020] [Indexed: 11/06/2022]
Abstract
Vicia palaestina Boiss. is an annual herb that grows in dry areas of eastern Mediterranean countries. It belongs to section Cracca subgenus Vicilla, which is characterized by having a high content in the non-protein amino acid canavanine. The seeds from some of these vetches are also rich in lectins. The purification and characterization of a single-chain lectin from the seeds of V. palaestina is described here. This lectin was the most abundant protein in albumin extracts. It has affinity for the glycoconjugate N-acetylgalactosamine and inhibits proliferation of the cancerous Caco-2 and THP-1 cell lines. In addition to their high nutritional value, the seeds from V. palaestina represent a source of lectins with health promoting and pharmacological potential because of their antiproliferative activity.
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Affiliation(s)
- Youssef Elamine
- Food Phytochemistry Department, Instituto de la Grasa (C.S.I.C.), Campus Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41089, Sevilla, Spain
| | - Verenice Torres-Salas
- Departamento de Ingeniería Agroindustrial, Universidad Autónoma Chapingo, Km. 38.5 Carretera México-Texcoco, 56230, Chapingo, Estado de México, Mexico
| | - Alima Messai
- Food Phytochemistry Department, Instituto de la Grasa (C.S.I.C.), Campus Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41089, Sevilla, Spain
| | - Julio Girón-Calle
- Food Phytochemistry Department, Instituto de la Grasa (C.S.I.C.), Campus Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41089, Sevilla, Spain
| | - Manuel Alaiz
- Food Phytochemistry Department, Instituto de la Grasa (C.S.I.C.), Campus Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41089, Sevilla, Spain
| | - Javier Vioque
- Food Phytochemistry Department, Instituto de la Grasa (C.S.I.C.), Campus Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41089, Sevilla, Spain
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Caracuta V, Alex B, Regev L, Regev J, Mintz E, Barzilai O, Hershkovitz I, Boaretto E. The Marine Isotope Stage 3 landscape around Manot Cave (Israel) and the food habits of anatomically modern humans: New insights from the anthracological record and stable carbon isotope analysis of wild almond (Amygdalus sp.). J Hum Evol 2020; 160:102868. [DOI: 10.1016/j.jhevol.2020.102868] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 01/29/2023]
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Serendipitous In Situ Conservation of Faba Bean Landraces in Tunisia: A Case Study. Genes (Basel) 2020; 11:genes11020236. [PMID: 32102450 PMCID: PMC7074078 DOI: 10.3390/genes11020236] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 12/19/2022] Open
Abstract
Cultivation of faba bean (Vicia faba L.) in Tunisia is largely based on improved varieties of the crop. However, a few farmers continue to produce local cultivars or landraces. The National Gene Bank of Tunisia (NGBT) recently launched a collection project for faba bean landraces, with special focus on the regions of the North West, traditionally devoted to cultivating grain legumes, and where around 80% of the total national faba bean cultivation area is located. The seed phenotypic features of the collected samples were studied, and the genetic diversity and population structure analyzed using simple sequence repeat markers. The genetic constitution of the present samples was compared to that of faba bean samples collected by teams of the International Center for Agricultural Research in the Dry Areas (ICARDA) in the 1970s in the same region, and stored at the ICARDA gene bank. The results of the diversity analysis demonstrate that the recently collected samples and those stored at ICARDA largely overlap, thus demonstrating that over the past 50 years, little genetic change has occurred to the local faba bean populations examined. These findings suggest that farmers serendipitously applied international best practices for in situ conservation of agricultural crops.
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Karkanis A, Ntatsi G, Lepse L, Fernández JA, Vågen IM, Rewald B, Alsiņa I, Kronberga A, Balliu A, Olle M, Bodner G, Dubova L, Rosa E, Savvas D. Faba Bean Cultivation - Revealing Novel Managing Practices for More Sustainable and Competitive European Cropping Systems. FRONTIERS IN PLANT SCIENCE 2018; 9:1115. [PMID: 30116251 PMCID: PMC6083270 DOI: 10.3389/fpls.2018.01115] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/11/2018] [Indexed: 05/14/2023]
Abstract
Faba beans are highly nutritious because of their high protein content: they are a good source of mineral nutrients, vitamins, and numerous bioactive compounds. Equally important is the contribution of faba bean in maintaining the sustainability of agricultural systems, as it is highly efficient in the symbiotic fixation of atmospheric nitrogen. This article provides an overview of factors influencing faba bean yield and quality, and addresses the main biotic and abiotic constraints. It also reviews the factors relating to the availability of genetic material and the agronomic features of faba bean production that contribute to high yield and the improvement of European cropping systems. Emphasis is to the importance of using new high-yielding cultivars that are characterized by a high protein content, low antinutritional compound content, and resistance to biotic and abiotic stresses. New cultivars should combine several of these characteristics if an increased and more stable production of faba bean in specific agroecological zones is to be achieved. Considering that climate change is also gradually affecting many European regions, it is imperative to breed elite cultivars that feature a higher abiotic-biotic stress resistance and nutritional value than currently used cultivars. Improved agronomical practices for faba bean crops, such as crop establishment and plant density, fertilization and irrigation regime, weed, pest and disease management, harvesting time, and harvesting practices are also addressed, since they play a crucial role in both the production and quality of faba bean.
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Affiliation(s)
- Anestis Karkanis
- Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, Volos, Greece
| | - Georgia Ntatsi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Athens, Greece
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER, Thessaloniki, Greece
| | - Liga Lepse
- Pūre Horticultural Research Centre, Pūre, Latvia
- Institute of Horticulture, Latvia University of Agriculture, Jelgava, Latvia
| | - Juan A. Fernández
- Department of Horticulture, Technical University of Cartagena, Cartagena, Spain
| | - Ingunn M. Vågen
- Department of Horticulture, Division of Food Production and Society, Norwegian Institute of Bioeconomy Research (NIBIO), Oslo, Norway
| | - Boris Rewald
- Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ina Alsiņa
- Institute of Soil and Plant Sciences, Latvia University of Agriculture, Jelgava, Latvia
| | - Arta Kronberga
- Department of Plant Breeding and Genetics, Institute of Agricultural Resources and Economics, Priekuli, Latvia
| | - Astrit Balliu
- Department of Horticulture and Landscape Architecture, Agricultural University of Tirana, Tirana, Albania
| | - Margit Olle
- Estonian Crop Research Institute, Jõgeva, Estonia
| | - Gernot Bodner
- Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Laila Dubova
- Institute of Soil and Plant Sciences, Latvia University of Agriculture, Jelgava, Latvia
| | - Eduardo Rosa
- UTAD-CITAB – Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Dimitrios Savvas
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Athens, Greece
- *Correspondence: Dimitrios Savvas,
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Caracuta V, Vardi J, Paz Y, Boaretto E. Farming legumes in the pre-pottery Neolithic: New discoveries from the site of Ahihud (Israel). PLoS One 2017; 12:e0177859. [PMID: 28542358 PMCID: PMC5443508 DOI: 10.1371/journal.pone.0177859] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 04/28/2017] [Indexed: 11/30/2022] Open
Abstract
New discoveries of legumes in the lower Galilee at the prehistoric site of Ahihud in Israel shed light on early farming systems in the southern Levant. Radiocarbon dating of twelve legumes from pits and floors indicate that the farming of legumes was practiced in southern Levant as early as 10.240-10.200 (1σ) ago. The legumes were collected from pits and other domestic contexts dated to the Early Pre-Pottery Neolithic B. The legumes identified include Vicia faba L. (faba bean), V. ervilia (bitter vetch), V. narbonensis (narbon vetch), Lens sp. (lentil), Pisum sp. (pea), Lathyrus inconspicuus (inconspicuous pea) and L. hirosolymitanus (jerusalem vetchling). Comparison with coeval sites in the region show how the presence of peas, narbon vetches, inconspicuous peas, jerusalem vetchlings and bitter vetches together with faba bean and lentils is unique to the Pre-Pottery Neolithic, and might indicate specific patterns in farming or storing at the onset of agriculture.
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Affiliation(s)
- Valentina Caracuta
- Max Planck-Weizmann Center for Integrative Archaeology and Anthropology, Rehovot, Israel
- D-REAMS Radiocarbon Laboratory, Rehovot, Israel
| | - Jacob Vardi
- Israel Antiquity Authority, Jerusalem, Israel
| | - Ytzhak Paz
- Israel Antiquity Authority, Jerusalem, Israel
| | - Elisabetta Boaretto
- Max Planck-Weizmann Center for Integrative Archaeology and Anthropology, Rehovot, Israel
- D-REAMS Radiocarbon Laboratory, Rehovot, Israel
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