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Ho WK, Tanzi AS, Sang F, Tsoutsoura N, Shah N, Moore C, Bhosale R, Wright V, Massawe F, Mayes S. A genomic toolkit for winged bean Psophocarpus tetragonolobus. Nat Commun 2024; 15:1901. [PMID: 38429275 PMCID: PMC10907731 DOI: 10.1038/s41467-024-45048-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 01/12/2024] [Indexed: 03/03/2024] Open
Abstract
A sustainable supply of plant protein is critical for future generations and needs to be achieved while reducing green house gas emissions from agriculture and increasing agricultural resilience in the face of climate volatility. Agricultural diversification with more nutrient-rich and stress tolerant crops could provide the solution. However, this is often hampered by the limited availability of genomic resources and the lack of understanding of the genetic structure of breeding germplasm and the inheritance of important traits. One such crop with potential is winged bean (Psophocarpus tetragonolobus), a high seed protein tropical legume which has been termed 'the soybean for the tropics'. Here, we present a chromosome level winged bean genome assembly, an investigation of the genetic diversity of 130 worldwide accessions, together with two linked genetic maps and a trait QTL analysis (and expression studies) for regions of the genome with desirable ideotype traits for breeding, namely architecture, protein content and phytonutrients.
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Affiliation(s)
- Wai Kuan Ho
- Future Food Beacon, School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- Crops for the Future (UK) CIC, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Alberto Stefano Tanzi
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Fei Sang
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Niki Tsoutsoura
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Niraj Shah
- Digital and Technology Services, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Christopher Moore
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Rahul Bhosale
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Victoria Wright
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Festo Massawe
- Future Food Beacon, School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Sean Mayes
- Crops for the Future (UK) CIC, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
- International Centre for Research in the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India.
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Lachenmeier DW, Montagnon C. Convention on Biological Diversity (CBD) and the Nagoya Protocol: Implications and Compliance Strategies for the Global Coffee Community. Foods 2024; 13:254. [PMID: 38254555 PMCID: PMC10814485 DOI: 10.3390/foods13020254] [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: 12/07/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
The Nagoya Protocol on Access and Benefit-sharing (ABS) of the Convention on Biological Diversity (CBD) is a fundamental international agreement that plays a crucial role in the protection and equitable utilization of plant genetic resources. While this agreement is essential for conservation and sustainable use, it presents specific challenges to coffee research and industry. One major issue is the requirement to obtain prior informed consent (PIC) from the source country or community, which can be a complex and time-consuming process, especially in regions with limited governance capacity. Additionally, the mandates of this agreement necessitate benefit-sharing with the source community, a requirement that poses implementation challenges, particularly for small businesses or individual researchers. Despite these challenges, the importance of the Nagoya Protocol in the coffee sector cannot be overstated. It contributes significantly to the conservation of coffee genetic resources and the sustainable utilization of these resources, ensuring fair distribution of benefits. To address the complexities presented by this international framework, coffee researchers and industry need to engage proactively with source countries and communities. This includes developing clear and equitable benefit-sharing and implementing strategies for compliance. This article explores the impact of the Nagoya Protocol on the coffee industry, particularly emphasizing the need for balancing scientific investigation with the ethical considerations of resource sharing. It also discusses practical strategies for navigating the complexities of this agreement, including research focused on authenticity control and the challenges in conducting large-scale coffee studies. The conclusion underscores the potential for international collaboration, particularly through platforms like the International Coffee Organization (ICO), to harmonize research activities with the ethical imperatives of the Nagoya Protocol.
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Affiliation(s)
- Dirk W. Lachenmeier
- Chemisches und Veterinäruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, 76187 Karlsruhe, Germany
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Davis AP, Kiwuka C, Faruk A, Mulumba J, Kalema J. A review of the indigenous coffee resources of Uganda and their potential for coffee sector sustainability and development. FRONTIERS IN PLANT SCIENCE 2023; 13:1057317. [PMID: 36874918 PMCID: PMC9982753 DOI: 10.3389/fpls.2022.1057317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/01/2022] [Indexed: 06/18/2023]
Abstract
Uganda is a major global coffee exporter and home to key indigenous (wild) coffee resources. A comprehensive survey of Uganda's wild coffee species was undertaken more than 80 years ago (in 1938) and thus a contemporary evaluation is required, which is provided here. We enumerate four indigenous coffee species for Uganda: Coffea canephora, C. eugenioides, C. liberica (var. dewevrei) and C. neoleroyi. Based on ground point data from various sources, survey of natural forests, and literature reviews we summarise taxonomy, geographical distribution, ecology, conservation, and basic climate characteristics, for each species. Using literature review and farm survey we also provide information on the prior and exiting uses of Uganda's wild coffee resources for coffee production. Three of the indigenous species (excluding C. neoleroyi) represent useful genetic resources for coffee crop development (e.g. via breeding, or selection), including: adaptation to a changing climate, pest and disease resistance, improved agronomic performance, and market differentiation. Indigenous C. canephora has already been pivotal in the establishment and sustainability of the robusta coffee sector in Uganda and worldwide, and has further potential for the development of this crop species. Coffea liberica var. dewevrei (excelsa coffee) is emerging as a commercially viable coffee crop plant in its own right, and may offer substantial potential for lowland coffee farmers, i.e. in robusta coffee growing areas. It may also provide useful stock material for the grafting of robusta and Arabica coffee, and possibly other species. Preliminary conservation assessments indicate that C. liberica var. dewevrei and C. neoleroyi are at risk of extinction at the country-level (Uganda). Adequate protection of Uganda's humid forests, and thus its coffee natural capital, is identified as a conservation priority for Uganda and the coffee sector in general.
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Affiliation(s)
- Aaron P. Davis
- Crops & Global Change, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Catherine Kiwuka
- Plant Genetic Resources Centre, National Agricultural Research Organization, Entebbe, Uganda
| | - Aisyah Faruk
- Partnerships (Conservation), Millennium Seed Bank (Royal Botanic Gardens, Kew), Wakehurst, Sussex, United Kingdom
| | - John Mulumba
- Plant Genetic Resources Centre, National Agricultural Research Organization, Entebbe, Uganda
| | - James Kalema
- Department of Plant Sciences, Microbiology and Biotechnology, College of Natural Sciences, Makerere University, Kampala, Uganda
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Bar I, Sambasivam PT, Davidson J, Farfan-Caceres LM, Lee RC, Hobson K, Moore K, Ford R. Current population structure and pathogenicity patterns of Ascochyta rabiei in Australia. Microb Genom 2021; 7:000627. [PMID: 34283013 PMCID: PMC8477395 DOI: 10.1099/mgen.0.000627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/09/2021] [Indexed: 12/19/2022] Open
Abstract
Ascochyta blight disease, caused by the necrotrophic fungus Ascochyta rabiei, is a major biotic constraint to chickpea production in Australia and worldwide. Detailed knowledge of the structure of the pathogen population and its potential to adapt to our farming practices is key to informing optimal management of the disease. This includes understanding the molecular diversity among isolates and the frequency and distribution of the isolates that have adapted to overcome host resistance across agroecologically distinct regions. Thanks to continuous monitoring efforts over the past 6 years, a comprehensive collection of A. rabiei isolates was collated from the major Australian chickpea production regions. To determine the molecular structure of the entire population, representative isolates from each collection year and growing region have been genetically characterized using a DArTseq genotyping-by-sequencing approach. The genotyped isolates were further phenotyped to determine their pathogenicity levels against a differential set of chickpea cultivars and genotype-phenotype associations were inferred. Overall, the Australian A. rabiei population displayed a far lower genetic diversity (average Nei's gene diversity of 0.047) than detected in other populations worldwide. This may be explained by the presence of a single mating-type in Australia, MAT1-2, limiting its reproduction to a clonal mode. Despite the low detected molecular diversity, clonal selection appears to have given rise to a subset of adapted isolates that are highly pathogenic on commonly employed resistance sources, and that are occurring at an increasing frequency. Among these, a cluster of genetically similar isolates was identified, with a higher proportion of highly aggressive isolates than in the general population. The discovery of distinct genetic clusters associated with high and low isolate pathogenicity forms the foundation for the development of a molecular pathotyping tool for the Australian A. rabiei population. Application of such a tool, along with continuous monitoring of the genetic structure of the population will provide crucial information for the screening of breeding material and integrated disease management packages.
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Affiliation(s)
- Ido Bar
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, QLD 4111, Australia
| | | | - Jenny Davidson
- South Australian Research and Development Institute, Hartley Grove, Urrbrae SA 5064, Australia
| | - Lina M. Farfan-Caceres
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Robert C. Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Kristy Hobson
- Department of Primary Industries Tamworth Agricultural Institute, Calala, NSW 2340, Australia
| | - Kevin Moore
- Department of Primary Industries Tamworth Agricultural Institute, Calala, NSW 2340, Australia
| | - Rebecca Ford
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, QLD 4111, Australia
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Pruvot-Woehl S, Krishnan S, Solano W, Schilling T, Toniutti L, Bertrand B, Montagnon C. Authentication of Coffea arabica Varieties through DNA Fingerprinting and its Significance for the Coffee Sector. J AOAC Int 2021; 103:325-334. [PMID: 33241280 DOI: 10.1093/jaocint/qsz003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 11/14/2022]
Abstract
BACKGROUND Locating the optimal varieties for coffee cultivation is increasingly considered a key condition for sustainable production and marketing. Variety performance varies when it comes to susceptibility to coffee leaf rust and other diseases, adaptation to climate change and high cup quality for specialty markets. But because of poor organization and the lack of a professional coffee seed sector, most existing coffee farms (and even seed lots and nurseries) do not know which varieties they are using. DNA fingerprinting of coffee planting material will contribute to professionalize the coffee seed sector. OBJECTIVE The objective of this paper is i) to check in a large scale the robustness of the existing coffee DNA fingerprinting method based on eight Single Sequence Repeats markers (SRR) and ii) to describe how it can help in moving the needle towards a more professional seed sector. METHOD 2533 samples representing all possible genetic background of Arabica varieties were DNA fingerprinted with 8 SRR markers. The genetic diversity was analyzed and the genetic conformity to varietal references was assessed. RESULTS The DNA fingerprinting method proved to be robust in authenticating varieties and trace back the history of C. arabica breeding and of the movement of C. arabica varieties. The genetic conformity of two important coffee varieties, Marseillesa and Gesha, proved to be 91% and 39% respectively. CONCLUSIONS DNA fingerprinting provides different actors in the coffee sector with a powerful new tool-farmers can verify the identity of their cultivated varieties, coffee roasters can be assured that marketing claims related to varieties are correct, and most of all, those looking to establish the a more professional and reliable coffee seed sector have a reliable new monitoring tool to establish and check genetic purity of seed stock and nursery plants. HIGHLIGHTS While C. arabica is primarily self-pollinating, even fixed line varieties appear to be drifting away from their original genetic reference due to uncontrolled cross pollination. A set of 8 SSR markers applied to the largest possible genetically diverse set of samples prove to discriminate between a wide range of varieties Figures confirm that genetic non conformity of coffee varieties can represent up to 61% of checked samples.
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Affiliation(s)
- Solène Pruvot-Woehl
- World Coffee Research, 5 Avenue du Grand Chêne, 34270 Saint Mathieu de Tréviers, France
| | - Sarada Krishnan
- Denver Botanic Garden, 909 York Street, Denver, CO 80206, USA
| | - William Solano
- Tropical Agricultural Research and Higher Education Center (CATIE), Turrialba 30501, Costa Rica
| | - Tim Schilling
- World Coffee Research, Babel Community, 70 Avenue de la République, 13000 Marseille, France
| | - Lucile Toniutti
- World Coffee Research, 5 Avenue du Grand Chêne, 34270 Saint Mathieu de Tréviers, France
| | - Benoit Bertrand
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR IPME, Montpellier, France
| | - Christophe Montagnon
- World Coffee Research, 5 Avenue du Grand Chêne, 34270 Saint Mathieu de Tréviers, France
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Akpertey A, Padi FK, Meinhardt L, Zhang D. Effectiveness of Single Nucleotide Polymorphism Markers in Genotyping Germplasm Collections of Coffea canephora Using KASP Assay. FRONTIERS IN PLANT SCIENCE 2021; 11:612593. [PMID: 33569071 PMCID: PMC7868401 DOI: 10.3389/fpls.2020.612593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Accurate genotype identification is imperative for effective use of Coffea canephora L. germplasm to breed new varieties with tolerance or resistance to biotic and abiotic stresses (including moisture stress and pest and disease stresses such as coffee berry borer and rust) and for high yield and improved cup quality. The present study validated 192 published single nucleotide polymorphism (SNP) markers and selected a panel of 120 loci to examine parentage and labeling errors, genetic diversity, and population structure in 400 C. canephora accessions assembled from different coffee-producing countries and planted in a field gene bank in Ghana. Of the 400 genotypes analyzed, both synonymous (trees with same SNP profiles but different names, 12.8%) and homonymous (trees with same name but different SNP profiles, 5.8%) mislabeling were identified. Parentage analysis showed that 33.3% of the progenies derived from controlled crossing and 0% of the progenies derived from an open pollinated biclonal seed garden had parentage (both parents) corresponding to breeder records. The results suggest mislabeling of the mother trees used in seed gardens and pollen contamination from unwanted paternal parents. After removing the duplicated accessions, Bayesian clustering analysis partitioned the 270 unique genotypes into two main populations. Analysis of molecular variance (AMOVA) showed that the between-population variation accounts for 41% of the total molecular variation and the genetic divergence was highly significant (Fst = 0.256; P < 0.001). Taken together, our results demonstrate the effectiveness of using the selected SNP panel in gene bank management, varietal identification, seed garden management, nursery verification, and coffee bean authentication for C. canephora breeding programs.
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Affiliation(s)
| | | | - Lyndel Meinhardt
- Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
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Coffee Berry Borer ( Hypothenemus hampei), a Global Pest of Coffee: Perspectives from Historical and Recent Invasions, and Future Priorities. INSECTS 2020; 11:insects11120882. [PMID: 33322763 PMCID: PMC7763606 DOI: 10.3390/insects11120882] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 01/30/2023]
Abstract
Coffee berry borer (Hypothenemus hampei (Ferrari), CBB) has invaded nearly every coffee-producing country in the world, and it is commonly recognized as the most damaging insect pest of coffee. While research has been conducted on this pest in individual coffee-growing regions, new insights may be gained by comparing and contrasting patterns of invasion and response across its global distribution. In this review, we explore the existing literature and focus on common themes in the invasion biology of CBB by examining (1) how it was introduced into each particular region and the response to its invasion, (2) flight activity and infestation patterns, (3) economic impacts, and (4) management strategies. We highlight research conducted over the last ten years in Hawaii as a case study for the development and implementation of an effective integrated pest management (IPM) program for CBB, and also discuss biosecurity issues contributing to incursion and establishment. Potential areas for future research in each of the five major components of CBB IPM (monitoring and sampling, cultural, biological, chemical, and physical controls) are also presented. Finally, we emphasize that outreach efforts are crucial to the successful implementation of CBB IPM programs. Future research programs should strive to include coffee growers as much as possible to ensure that management options are feasible and cost-effective.
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Kath J, Byrareddy VM, Craparo A, Nguyen-Huy T, Mushtaq S, Cao L, Bossolasco L. Not so robust: Robusta coffee production is highly sensitive to temperature. GLOBAL CHANGE BIOLOGY 2020; 26:3677-3688. [PMID: 32223007 DOI: 10.1111/gcb.15097] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/30/2020] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
Coffea canephora (robusta coffee) is the most heat-tolerant and 'robust' coffee species and therefore considered more resistant to climate change than other types of coffee production. However, the optimum production range of robusta has never been quantified, with current estimates of its optimal mean annual temperature range (22-30°C) based solely on the climatic conditions of its native range in the Congo basin, Central Africa. Using 10 years of yield observations from 798 farms across South East Asia coupled with high-resolution precipitation and temperature data, we used hierarchical Bayesian modeling to quantify robusta's optimal temperature range for production. Our climate-based models explained yield variation well across the study area with a cross-validated mean R2 = .51. We demonstrate that robusta has an optimal temperature below 20.5°C (or a mean minimum/maximum of ≤16.2/24.1°C), which is markedly lower, by 1.5-9°C than current estimates. In the middle of robusta's currently assumed optimal range (mean annual temperatures over 25.1°C), coffee yields are 50% lower compared to the optimal mean of ≤20.5°C found here. During the growing season, every 1°C increase in mean minimum/maximum temperatures above 16.2/24.1°C corresponded to yield declines of ~14% or 350-460 kg/ha (95% credible interval). Our results suggest that robusta coffee is far more sensitive to temperature than previously thought. Current assessments, based on robusta having an optimal temperature range over 22°C, are likely overestimating its suitable production range and its ability to contribute to coffee production as temperatures increase under climate change. Robusta supplies 40% of the world's coffee, but its production potential could decline considerably as temperatures increase under climate change, jeopardizing a multi-billion dollar coffee industry and the livelihoods of millions of farmers.
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Affiliation(s)
- Jarrod Kath
- Centre for Applied Climate Sciences, University of Southern Queensland, Toowoomba, Qld, Australia
| | - Vivekananda M Byrareddy
- Centre for Applied Climate Sciences, University of Southern Queensland, Toowoomba, Qld, Australia
| | - Alessandro Craparo
- International Center for Tropical Agriculture (CIAT), Hanoi, Vietnam
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Cali, Colombia
| | - Thong Nguyen-Huy
- Centre for Applied Climate Sciences, University of Southern Queensland, Toowoomba, Qld, Australia
- Vietnam National Space Center, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Shahbaz Mushtaq
- Centre for Applied Climate Sciences, University of Southern Queensland, Toowoomba, Qld, Australia
| | - Loc Cao
- Sustainable Management Services, ECOM Agroindustrial, Ho Chi Minh City, Vietnam
| | - Laurent Bossolasco
- Sustainable Management Services, ECOM Agroindustrial, Ho Chi Minh City, Vietnam
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Talamantes-Becerra B, Carling J, Kilian A, Georges A. Discovery of thermophilic Bacillales using reduced-representation genotyping for identification. BMC Microbiol 2020; 20:114. [PMID: 32404118 PMCID: PMC7222431 DOI: 10.1186/s12866-020-01800-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Abstract
Background This study demonstrates the use of reduced-representation genotyping to provide preliminary identifications for thermophilic bacterial isolates. The approach combines restriction enzyme digestion and PCR with next-generation sequencing to provide thousands of short-read sequences from across the bacterial genomes. Isolates were obtained from compost, hot water systems, and artesian bores of the Great Artesian Basin. Genomic DNA was double-digested with two combinations of restriction enzymes followed by PCR amplification, using a commercial provider of DArTseq™, Diversity Arrays Technology Pty Ltd. (Canberra, Australia). The resulting fragments which formed a reduced-representation of approximately 2.3% of the genome were sequenced. The sequence tags obtained were aligned against all available RefSeq bacterial genome assemblies by BLASTn to identify the nearest reference genome. Results Based on the preliminary identifications, a total of 99 bacterial isolates were identified to species level, from which 8 isolates were selected for whole-genome sequencing to assess the identification results. Novel species and strains were discovered within this set of isolates. The preliminary identifications obtained by reduced-representation genotyping, as well as identifications obtained by BLASTn alignment of the 16S rRNA gene sequence, were compared with those derived from the whole-genome sequence data, using the same RefSeq sequence database for the three methods. Identifications obtained with reduced-representation sequencing agreed with the identifications provided by whole-genome sequencing in 100% of cases. The identifications produced by BLASTn alignment of 16S rRNA gene sequence to the same database differed from those provided by whole-genome sequencing in 37.5% of cases, and produced ambiguous identifications in 50% of cases. Conclusions Previously, this method has been successfully demonstrated for use in bacterial identification for medical microbiology. This study demonstrates the first successful use of DArTseq™ for preliminary identification of thermophilic bacterial isolates, providing results in complete agreement with those obtained from whole-genome sequencing of the same isolates. The growing database of bacterial genome sequences provides an excellent resource for alignment of reduced-representation sequence data for identification purposes, and as the available sequenced genomes continue to grow, the technique will become more effective.
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Affiliation(s)
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, Canberra, ACT, 2617, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, Canberra, ACT, 2617, Australia
| | - Arthur Georges
- Institute of Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
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Huang L, Wang X, Dong Y, Long Y, Hao C, Yan L, Shi T. Resequencing 93 accessions of coffee unveils independent and parallel selection during Coffea species divergence. PLANT MOLECULAR BIOLOGY 2020; 103:51-61. [PMID: 32072392 DOI: 10.1007/s11103-020-00974-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Coffea arabica, C. canephora and C. excelsa, with differentiated morphological traits and distinct agro-climatic conditions, compose the majority of the global coffee plantation. To comprehensively understand their genetic diversity and divergence for future genetic improvement requires high-density markers. Here, we sequenced 93 accessions encompassing these three Coffea species, uncovering 15,367,960 single-nucleotide polymorphisms (SNPs). These SNPs are unequally distributed across different genomic regions and gene families, with two disease-resistant gene families showing the highest SNP density, suggesting strong balancing selection. Meanwhile, the allotetraploid C. arabica exhibits greater nucleotide diversity, followed by C. canephora and C. excelsa. Population divergence (FST), population stratification and phylogeny all support strong divergence among species, with C. arabica and its parental species C. canephora being closer genetically. Scanning of genomic islands with elevated FST and structure-disruptive SNPs contributing to species divergence revealed that most of the selected genes in each lineage are independent, with a few being selected in parallel for two or three species, such as genes in root hair cell development, flavonols accumulation and disease-resistant genes. Moreover, some of the SNPs associated with coffee lipids exhibit significantly biased allele frequency among species, being valuable for interspecific breeding. Overall, our study not only uncovers the key population genomic patterns among species but also contributes a substantial genomic resource for coffee breeding.
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Affiliation(s)
- Lifang Huang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, 571533, China
| | - Xiaoyang Wang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, 571533, China
| | - Yunping Dong
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, 571533, China
| | - Yuzhou Long
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, 571533, China
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, 571533, China
| | - Lin Yan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China.
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, China.
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, 571533, China.
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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Scalabrin S, Toniutti L, Di Gaspero G, Scaglione D, Magris G, Vidotto M, Pinosio S, Cattonaro F, Magni F, Jurman I, Cerutti M, Suggi Liverani F, Navarini L, Del Terra L, Pellegrino G, Ruosi MR, Vitulo N, Valle G, Pallavicini A, Graziosi G, Klein PE, Bentley N, Murray S, Solano W, Al Hakimi A, Schilling T, Montagnon C, Morgante M, Bertrand B. A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm. Sci Rep 2020; 10:4642. [PMID: 32170172 PMCID: PMC7069947 DOI: 10.1038/s41598-020-61216-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/20/2020] [Indexed: 11/09/2022] Open
Abstract
The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma’s D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.
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Affiliation(s)
- Simone Scalabrin
- IGA Technology Services S.r.l., via Jacopo Linussio 51, I-33100, Udine, Italy
| | - Lucile Toniutti
- World Coffee Research, 5 avenue du grand chêne, 34270, Saint-Mathieu-de-Tréviers, France.
| | - Gabriele Di Gaspero
- Istituto di Genomica Applicata, via Jacopo Linussio 51, I-33100, Udine, Italy
| | - Davide Scaglione
- IGA Technology Services S.r.l., via Jacopo Linussio 51, I-33100, Udine, Italy
| | - Gabriele Magris
- Istituto di Genomica Applicata, via Jacopo Linussio 51, I-33100, Udine, Italy.,University of Udine, Department of Agricultural Food, Environmental and Animal Sciences, via delle scienze 206, I-33100, Udine, Italy
| | - Michele Vidotto
- IGA Technology Services S.r.l., via Jacopo Linussio 51, I-33100, Udine, Italy
| | - Sara Pinosio
- Istituto di Genomica Applicata, via Jacopo Linussio 51, I-33100, Udine, Italy.,Institute of Biosciences and Bioresources, National Research Council, via Madonna del Piano 10, I-50019, Sesto Fiorentino (FI), Italy
| | - Federica Cattonaro
- IGA Technology Services S.r.l., via Jacopo Linussio 51, I-33100, Udine, Italy
| | - Federica Magni
- IGA Technology Services S.r.l., via Jacopo Linussio 51, I-33100, Udine, Italy
| | - Irena Jurman
- Istituto di Genomica Applicata, via Jacopo Linussio 51, I-33100, Udine, Italy
| | - Mario Cerutti
- Luigi Lavazza S.p.A., Innovation Center, I-10156, Torino, Italy
| | - Furio Suggi Liverani
- Illycaffè S.p.A., Research & Innovation, via Flavia 110, I-34147, Trieste, Italy
| | - Luciano Navarini
- Illycaffè S.p.A., Research & Innovation, via Flavia 110, I-34147, Trieste, Italy
| | - Lorenzo Del Terra
- Illycaffè S.p.A., Research & Innovation, via Flavia 110, I-34147, Trieste, Italy
| | | | | | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Giorgio Valle
- CRIBI, Università degli Studi di Padova, viale G. Colombo 3, I-35121, Padova, Italy
| | | | - Giorgio Graziosi
- Department of Life Sciences, University of Trieste, I-34148, Trieste, Italy
| | - Patricia E Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
| | - Nolan Bentley
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
| | - Seth Murray
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | - Amin Al Hakimi
- Faculty of Agriculture, Sana'a University, Sana'a, Yemen
| | - Timothy Schilling
- World Coffee Research, 5 avenue du grand chêne, 34270, Saint-Mathieu-de-Tréviers, France
| | - Christophe Montagnon
- World Coffee Research, 5 avenue du grand chêne, 34270, Saint-Mathieu-de-Tréviers, France
| | - Michele Morgante
- Istituto di Genomica Applicata, via Jacopo Linussio 51, I-33100, Udine, Italy.,University of Udine, Department of Agricultural Food, Environmental and Animal Sciences, via delle scienze 206, I-33100, Udine, Italy
| | - Benoit Bertrand
- CIRAD, IPME, 34 398, Montpellier, France.,UMR IPME, Univ. Montpellier, IRD, CIRAD, 34 398, Montpellier, France
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12
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Garot E, Joët T, Combes MC, Lashermes P. Genetic diversity and population divergences of an indigenous tree (Coffea mauritiana) in Reunion Island: role of climatic and geographical factors. Heredity (Edinb) 2019; 122:833-847. [PMID: 30478354 PMCID: PMC6781115 DOI: 10.1038/s41437-018-0168-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/09/2018] [Indexed: 01/23/2023] Open
Abstract
Oceanic islands are commonly considered as natural laboratories for studies on evolution and speciation. The evolutionary specificities of islands associated with species biology provide unique scenarios to study the role of geography and climate in driving population divergence. However, few studies have addressed this subject in small oceanic islands with heterogeneous climates. Being widely distributed in Reunion Island forest, Coffea mauritiana represents an interesting model case for investigating patterns of within-island differentiation at small spatial scale. In this study, we examined the genetic diversity and population divergences of C. mauritiana using SNP markers obtained from 323 individuals across 34 locations in Reunion Island. Using redundancy analysis, we further evaluated the contribution of geographic and climatic factors to shaping genetic divergence among populations. Genetic diversity analyses revealed that accessions clustered according to the source population, with further grouping in regional clusters. Genetic relationships among the regional clusters underlined a recent process of expansion in the form of step-by-step colonization on both sides of the island. Divergence among source populations was mostly driven by the joint effect of geographic distance and climatic heterogeneity. The pattern of isolation-by-geography was in accordance with the dispersal characteristics of the species, while isolation-by-environment was mostly explained by the heterogeneous rainfall patterns, probably associated with an asynchronous flowering among populations. These findings advance our knowledge on the patterns of genetic diversity and factors of population differentiation of species native to Reunion Island, and will also usefully guide forest management for conservation.
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Affiliation(s)
- Edith Garot
- IRD, University of Montpellier, DIADE, Montpellier, France
| | - Thierry Joët
- IRD, University of Montpellier, DIADE, Montpellier, France
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13
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Talamantes-Becerra B, Carling J, Kennedy K, Gahan ME, Georges A. Identification of bacterial isolates from a public hospital in Australia using complexity-reduced genotyping. J Microbiol Methods 2019; 160:11-19. [PMID: 30894330 DOI: 10.1016/j.mimet.2019.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/16/2019] [Accepted: 03/17/2019] [Indexed: 11/25/2022]
Abstract
Bacterial identification methods used in routine identification of pathogens in medical microbiology include a combination approach of biochemical tests, mass spectrometry or molecular biology techniques. Extensive publicly-available databases of DNA sequence data from pathogenic bacteria have been amassed in recent years; this provides an opportunity for using bacterial genome sequencing for identification purposes. Whole genome sequencing is increasing in popularity, although at present it remains a relatively expensive approach to bacterial identification and typing. Complexity-reduced bacterial genome sequencing provides an alternative. We evaluate genomic complexity-reduction using restriction enzymes and sequencing to identify bacterial isolates. A total of 165 bacterial isolates from hospital patients in the Australian Capital Territory, between 2013 and 2015 were used in this study. They were identified and typed by the Microbiology Department of Canberra Public Hospital, and represented 14 bacterial species. DNA extractions from these samples were processed using a combination of the restriction enzymes PstI with MseI, PstI with HpaII and MseI with HpaII. The resulting sequences (length 30-69 bp) were aligned against publicly available bacterial genome and plasmid sequences. Results of the alignment were processed using a bioinformatics pipeline developed for this project, Currito3.1 DNA Fragment Analysis Software. All 165 samples were correctly identified to genus and species by each of the three combinations of restriction enzymes. A further 35 samples typed to the level of strain identified and compared for consistency with MLST typing data and in silico MLST data derived from the nearest sequenced candidate reference. The high level of agreement between bacterial identification using complexity-reduced genome sequencing and standard hospital identifications indicating that this new approach is a viable alternative for identification of bacterial isolates derived from pathology specimens. The effectiveness of species identification and in particular, strain typing, depends on access to a comprehensive and taxonomically accurate bacterial genome sequence database containing relevant bacterial species and strains.
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Affiliation(s)
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, Canberra, ACT 2617, Australia
| | - Karina Kennedy
- Canberra Health Services, Departments of Microbiology and Infectious Diseases, Canberra Hospital, Yamba Drive, Garran 2605, Australia
| | - Michelle E Gahan
- National Centre for Forensic Studies, University of Canberra, ACT, 2617, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, ACT 2601, Australia
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14
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Davis AP, Chadburn H, Moat J, O’Sullivan R, Hargreaves S, Nic Lughadha E. High extinction risk for wild coffee species and implications for coffee sector sustainability. SCIENCE ADVANCES 2019; 5:eaav3473. [PMID: 30746478 PMCID: PMC6357749 DOI: 10.1126/sciadv.aav3473] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/19/2018] [Indexed: 05/14/2023]
Abstract
Wild coffee species are critical for coffee crop development and, thus, for sustainability of global coffee production. Despite this fact, the extinction risk and conservation priority status of the world's coffee species are poorly known. Applying IUCN Red List of Threatened Species criteria to all (124) wild coffee species, we undertook a gap analysis for germplasm collections and protected areas and devised a crop wild relative (CWR) priority system. We found that at least 60% of all coffee species are threatened with extinction, 45% are not held in any germplasm collection, and 28% are not known to occur in any protected area. Existing conservation measures, including those for key coffee CWRs, are inadequate. We propose that wild coffee species are extinction sensitive, especially in an era of accelerated climatic change.
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Affiliation(s)
- Aaron P. Davis
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Corresponding author.
| | - Helen Chadburn
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Justin Moat
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- School of Geography, University of Nottingham, Nottingham NG7 2RD, UK
| | - Robert O’Sullivan
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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15
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Rossetto M, Bragg J, Kilian A, McPherson H, van der Merwe M, Wilson PD. Restore and Renew: a genomics‐era framework for species provenance delimitation. Restor Ecol 2018. [DOI: 10.1111/rec.12898] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Maurizio Rossetto
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
| | - Jason Bragg
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
| | - Andrzej Kilian
- Diversity Arrays TechnologyUniversity of Canberra Bruce ACT 2617 Australia
| | - Hannah McPherson
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
| | - Marlien van der Merwe
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
| | - Peter D. Wilson
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
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16
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Fayaz F, Aghaee Sarbarzeh M, Talebi R, Azadi A. Genetic Diversity and Molecular Characterization of Iranian Durum Wheat Landraces (Triticum turgidum durum (Desf.) Husn.) Using DArT Markers. Biochem Genet 2018; 57:98-116. [PMID: 30051349 DOI: 10.1007/s10528-018-9877-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 07/14/2018] [Indexed: 01/07/2023]
Abstract
Durum wheat is grown mainly in rain-fed regions of Iran and the Mediterranean district under stressful conditions. Different environmental conditions and agricultural practices among ancient communities have led to the development of locally adapted genotypes known as landraces. Landraces are a valued source of genetic variety and show definite adaptation to local environmental conditions according to their home of origin. This study aimed to explore linkage disequilibrium (LD) analysis and the population structure and genetic diversity of Iranian durum wheat landraces. In this study, population structure and genome-wide LD were investigated in 129 durum landrace accessions using 1500 DArT markers. Both structure and discriminant analysis of principal components obviously subdivided the sample collection into seven distinct groups centered on key ancestors and regions of origin of the germplasm. Genetic diversity among the populations was primarily within population (68 vs. 32%). Mean LD values across the entire population sample decayed below r2 of 0.11 after 1 cM. LD decay of genomes A and B of Iranian durum wheat landrace is approximately 2-3 cM (r2 = 0.11) and approximately 0.5 cM (r2 = 0.12), respectively. Altogether, low LD decay, a high number of subpopulations, and the high existence of genetic diversity among and within populations were characteristics of the Iranian durum landrace collection. Hence, the existing genetic diversity within the population can be associated with the very long evolutionary history of plants in Iran. The populations we studied are hence presented as a valuable resource that can be used in basic and applied research in durum wheat breeding.
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Affiliation(s)
- Farzad Fayaz
- Department of Agronomy & Plant Breeding, College of Agriculture, Islamic Azad University, Sanandaj Branch, Sanandaj, Iran.
| | - Mostafa Aghaee Sarbarzeh
- Seed and Plant Improvement Institute, Agriculture Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Reza Talebi
- Department of Agronomy & Plant Breeding, College of Agriculture, Islamic Azad University, Sanandaj Branch, Sanandaj, Iran
| | - Amin Azadi
- Department of Plant Breeding, Yadegar-e-Imam Khomeini (RAH), Islamic Azad University, Shahre Rey Branch, Tehran, Iran
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17
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Borzęcka E, Hawliczek-Strulak A, Bolibok L, Gawroński P, Tofil K, Milczarski P, Stojałowski S, Myśków B, Targońska-Karasek M, Grądzielewska A, Smolik M, Kilian A, Bolibok-Brągoszewska H. Effective BAC clone anchoring with genotyping-by-sequencing and Diversity Arrays Technology in a large genome cereal rye. Sci Rep 2018; 8:8428. [PMID: 29849048 PMCID: PMC5976670 DOI: 10.1038/s41598-018-26541-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/16/2018] [Indexed: 11/09/2022] Open
Abstract
Identification of bacterial artificial chromosome (BAC) clones containing specific sequences is a prerequisite for many applications, such as physical map anchoring or gene cloning. Existing BAC library screening strategies are either low-throughput or require a considerable initial input of resources for platform establishment. We describe a high-throughput, reliable, and cost-effective BAC library screening approach deploying genotyping platforms which are independent from the availability of sequence information: a genotyping-by-sequencing (GBS) method DArTSeq and the microarray-based Diversity Arrays Technology (DArT). The performance of these methods was tested in a very large and complex rye genome. The DArTseq approach delivered superior results: a several fold higher efficiency of addressing genetic markers to BAC clones and anchoring of BAC clones to genetic map and also a higher reliability. Considering the sequence independence of the platform, the DArTseq-based library screening can be proposed as an attractive method to speed up genomics research in resource poor species.
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Affiliation(s)
- Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Anna Hawliczek-Strulak
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Leszek Bolibok
- Department of Silviculture, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Paweł Milczarski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Stefan Stojałowski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Beata Myśków
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Małgorzata Targońska-Karasek
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Agnieszka Grądzielewska
- Institute of Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
| | - Miłosz Smolik
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Kirinari st, ACT 2617, Bruce, Australia
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland.
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18
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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: 0.7] [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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19
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Zhou G, Jian J, Wang P, Li C, Tao Y, Li X, Renshaw D, Clements J, Sweetingham M, Yang H. Construction of an ultra-high density consensus genetic map, and enhancement of the physical map from genome sequencing in Lupinus angustifolius. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:209-223. [PMID: 29051970 DOI: 10.1007/s00122-017-2997-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/01/2017] [Indexed: 05/04/2023]
Abstract
An ultra-high density genetic map containing 34,574 sequence-defined markers was developed in Lupinus angustifolius. Markers closely linked to nine genes of agronomic traits were identified. A physical map was improved to cover 560.5 Mb genome sequence. Lupin (Lupinus angustifolius L.) is a recently domesticated legume grain crop. In this study, we applied the restriction-site associated DNA sequencing (RADseq) method to genotype an F9 recombinant inbred line population derived from a wild type × domesticated cultivar (W × D) cross. A high density linkage map was developed based on the W × D population. By integrating sequence-defined DNA markers reported in previous mapping studies, we established an ultra-high density consensus genetic map, which contains 34,574 markers consisting of 3508 loci covering 2399 cM on 20 linkage groups. The largest gap in the entire consensus map was 4.73 cM. The high density W × D map and the consensus map were used to develop an improved physical map, which covered 560.5 Mb of genome sequence data. The ultra-high density consensus linkage map, the improved physical map and the markers linked to genes of breeding interest reported in this study provide a common tool for genome sequence assembly, structural genomics, comparative genomics, functional genomics, QTL mapping, and molecular plant breeding in lupin.
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Affiliation(s)
- Gaofeng Zhou
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jianbo Jian
- Beijing Genome Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Penghao Wang
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia
| | - Chengdao Li
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia
| | - Ye Tao
- BIOZERON Biotechnology Co., Ltd.-Shanghai, Xingxian Road, 1180-7, Shanghai, 210880, China
| | - Xuan Li
- Beijing Genome Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Daniel Renshaw
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Jonathan Clements
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Mark Sweetingham
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Huaan Yang
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia.
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