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Schilbert HM, Busche M, Sáez V, Angeli A, Weisshaar B, Martens S, Stracke R. Generation and characterisation of an Arabidopsis thaliana f3h/fls1/ans triple mutant that accumulates eriodictyol derivatives. BMC PLANT BIOLOGY 2024; 24:99. [PMID: 38331743 PMCID: PMC10854054 DOI: 10.1186/s12870-024-04787-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Flavonoids are plant specialised metabolites, which derive from phenylalanine and acetate metabolism. They possess a variety of beneficial characteristics for plants and humans. Several modification steps in the synthesis of tricyclic flavonoids cause for the amazing diversity of flavonoids in plants. The 2-oxoglutarate-dependent dioxygenases (2-ODDs) flavanone 3-hydroxylase (F3H, synonym FHT), flavonol synthase (FLS) and anthocyanidin synthase (ANS, synonym leucoanthocyanidin dioxygenase (LDOX)), catalyse oxidative modifications to the central C ring. They are highly similar and have been shown to catalyse, at least in part, each other's reactions. FLS and ANS have been identified as bifunctional enzymes in many species, including Arabidopsis thaliana, stressing the capability of plants to bypass missing or mutated reaction steps on the way to flavonoid production. However, little is known about such bypass reactions and the flavonoid composition of plants lacking all three central flavonoid 2-ODDs. RESULTS To address this issue, we generated a f3h/fls1/ans mutant, as well as the corresponding double mutants and investigated the flavonoid composition of this mutant collection. The f3h/fls1/ans mutant was further characterised at the genomic level by analysis of a nanopore DNA sequencing generated genome sequence assembly and at the transcriptomic level by RNA-Seq analysis. The mutant collection established, including the novel double mutants f3h/fls1 and f3h/ans, was used to validate and analyse the multifunctionalities of F3H, FLS1, and ANS in planta. Metabolite analyses revealed the accumulation of eriodictyol and additional glycosylated derivatives in mutants carrying the f3h mutant allele, resulting from the conversion of naringenin to eriodictyol by flavonoid 3'-hydroxylase (F3'H) activity. CONCLUSIONS We describe the in planta multifunctionality of the three central flavonoid 2-ODDs from A. thaliana and identify a bypass in the f3h/fls1/ans triple mutant that leads to the formation of eriodictyol derivatives. As (homo-)eriodictyols are known as bitter taste maskers, the annotated eriodictyol (derivatives) and in particular the observations made on their in planta production, could provide valuable insights for the creation of novel food supplements.
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Affiliation(s)
- Hanna Marie Schilbert
- Faculty of Biology, Genetics and Genomics of Plants, Bielefeld University, 33615, Bielefeld, Germany
| | - Mareike Busche
- Faculty of Biology, Genetics and Genomics of Plants, Bielefeld University, 33615, Bielefeld, Germany
| | - Vania Sáez
- Research and Innovation Centre, Fondazione Edmund Mach, 38098, San Michele all'Adige (TN), Italy
| | - Andrea Angeli
- Research and Innovation Centre, Fondazione Edmund Mach, 38098, San Michele all'Adige (TN), Italy
| | - Bernd Weisshaar
- Faculty of Biology, Genetics and Genomics of Plants, Bielefeld University, 33615, Bielefeld, Germany
| | - Stefan Martens
- Research and Innovation Centre, Fondazione Edmund Mach, 38098, San Michele all'Adige (TN), Italy
| | - Ralf Stracke
- Faculty of Biology, Genetics and Genomics of Plants, Bielefeld University, 33615, Bielefeld, Germany.
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Diouf M, Zoclanclounon YAB, Mboup PA, Diouf D, Malédon E, Rivallan R, Chair H, Dossa K. Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD. THE PLANT GENOME 2024:e20428. [PMID: 38234122 DOI: 10.1002/tpg2.20428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 12/04/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024]
Abstract
Microsatellite markers are widely used in population genetics and breeding. Despite the economic significance of yams in developing countries, there is a paucity of microsatellite markers, and as of now, no comprehensive microsatellite marker database exists. In this study, we conducted genome-wide microsatellite marker development across four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam researchers. The screening of Dioscorea alata, Dioscorea rotundata, Dioscorea dumetorum, and Dioscorea zingiberensis genomes resulted in 318,713, 322,501, 307,040, and 253,856 microsatellites, respectively. Mono-, di-, and tri-nucleotides were the most important types of repeats in the different species, and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, 17 out of 18 randomly selected were experimentally validated with good discriminatory power, regardless of the species and ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at https://y2md.ucad.sn/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. This study represents the first comprehensive microsatellite marker mining across several yam species and will contribute to advancing yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam researchers.
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Affiliation(s)
- Moussa Diouf
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | | | - Pape Adama Mboup
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Erick Malédon
- UMR AGAP Institut, CIRAD, Petit Bourg, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Ronan Rivallan
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Hâna Chair
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Komivi Dossa
- UMR AGAP Institut, CIRAD, Petit Bourg, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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Salava H, Deák T, Czepe C, Maghuly F. Sample and Library Preparation for PacBio Long-Read Sequencing in Grapevine. Methods Mol Biol 2024; 2787:183-197. [PMID: 38656490 DOI: 10.1007/978-1-0716-3778-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
PacBio long-read sequencing is a third-generation technology that generates long reads up to 20 kilobases (kb), unlike short-read sequencing instruments that produce up to 600 bases. Long-read sequencing is particularly advantageous in higher organisms, such as humans and plants, where repetitive regions in the genome are more abundant. The PacBio long-read sequencing uses a single molecule, real-time approach where the SMRT cells contain several zero-mode waveguides (ZMWs). Each ZMW contains a single DNA molecule bound by a DNA polymerase. All ZMWs are flushed with deoxy nucleotides with a fluorophore specific to each nucleotide. As the sequencing proceeds, the detector detects the wavelength of the fluorescence and the nucleotides are read in real-time. This chapter describes the sample and library preparation for PacBio long-read sequencing for grapevine.
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Affiliation(s)
- Hymavathi Salava
- Plant Functional Genomics Lab, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Tamás Deák
- Institute of Viticulture and Oenology, Hungarian University of Agriculture and Life Sciences (MATE), Budapest, Hungary
| | - Carmen Czepe
- Next Generation Sequencing Unit, Vienna Biocenter Core Facilities (VBCF), Vienna, Austria
| | - Fatemeh Maghuly
- Plant Functional Genomics Lab, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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Yaqoob H, Tariq A, Bhat BA, Bhat KA, Nehvi IB, Raza A, Djalovic I, Prasad PVV, Mir RA. Integrating genomics and genome editing for orphan crop improvement: a bridge between orphan crops and modern agriculture system. GM CROPS & FOOD 2023; 14:1-20. [PMID: 36606637 PMCID: PMC9828793 DOI: 10.1080/21645698.2022.2146952] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Domestication of orphan crops could be explored by editing their genomes. Genome editing has a lot of promise for enhancing agricultural output, and there is a lot of interest in furthering breeding in orphan crops, which are sometimes plagued with unwanted traits that resemble wild cousins. Consequently, applying model crop knowledge to orphan crops allows for the rapid generation of targeted allelic diversity and innovative breeding germplasm. We explain how plant breeders could employ genome editing as a novel platform to accelerate the domestication of semi-domesticated or wild plants, resulting in a more diversified base for future food and fodder supplies. This review emphasizes both the practicality of the strategy and the need to invest in research that advances our understanding of plant genomes, genes, and cellular systems. Planting more of these abandoned orphan crops could help alleviate food scarcities in the challenge of future climate crises.
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Affiliation(s)
- Huwaida Yaqoob
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Jammu and Kashmir, India
| | - Arooj Tariq
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Jammu and Kashmir, India
| | - Basharat Ahmad Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Kaisar Ahmad Bhat
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Jammu and Kashmir, India
| | - Iqra Bashir Nehvi
- Department of Clinical Biochemistry, SKIMS, Srinagar, Jammu and Kashmir, India
| | - Ali Raza
- College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China,Ali Raza College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Novi Sad, Serbia
| | - PV Vara Prasad
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, Kansas, USA
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Jammu and Kashmir, India,CONTACT Rakeeb Ahmad MirDepartment of Biotechnology, School of Life Sciences, Central University of Kashmir, Jammu and Kashmir, India
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Thoben C, Pucker B. Automatic annotation of the bHLH gene family in plants. BMC Genomics 2023; 24:780. [PMID: 38102570 PMCID: PMC10722790 DOI: 10.1186/s12864-023-09877-2] [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: 05/10/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND The bHLH transcription factor family is named after the basic helix-loop-helix (bHLH) domain that is a characteristic element of their members. Understanding the function and characteristics of this family is important for the examination of a wide range of functions. As the availability of genome sequences and transcriptome assemblies has increased significantly, the need for automated solutions that provide reliable functional annotations is emphasised. RESULTS A phylogenetic approach was adapted for the automatic identification and functional annotation of the bHLH transcription factor family. The bHLH_annotator, designed for the automated functional annotation of bHLHs, was implemented in Python3. Sequences of bHLHs described in literature were collected to represent the full diversity of bHLH sequences. Previously described orthologs form the basis for the functional annotation assignment to candidates which are also screened for bHLH-specific motifs. The pipeline was successfully deployed on the two Arabidopsis thaliana accessions Col-0 and Nd-1, the monocot species Dioscorea dumetorum, and a transcriptome assembly of Croton tiglium. Depending on the applied search parameters for the initial candidates in the pipeline, species-specific candidates or members of the bHLH family which experienced domain loss can be identified. CONCLUSIONS The bHLH_annotator allows a detailed and systematic investigation of the bHLH family in land plant species and classifies candidates based on bHLH-specific characteristics, which distinguishes the pipeline from other established functional annotation tools. This provides the basis for the functional annotation of the bHLH family in land plants and the systematic examination of a wide range of functions regulated by this transcription factor family.
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Affiliation(s)
- Corinna Thoben
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & Braunschweig Integrated, Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & Braunschweig Integrated, Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany.
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Sielemann K, Pucker B, Orsini E, Elashry A, Schulte L, Viehöver P, Müller AE, Schechert A, Weisshaar B, Holtgräwe D. Genomic characterization of a nematode tolerance locus in sugar beet. BMC Genomics 2023; 24:748. [PMID: 38057719 DOI: 10.1186/s12864-023-09823-2] [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: 07/07/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Infection by beet cyst nematodes (BCN, Heterodera schachtii) causes a serious disease of sugar beet, and climatic change is expected to improve the conditions for BCN infection. Yield and yield stability under adverse conditions are among the main breeding objectives. Breeding of BCN tolerant sugar beet cultivars offering high yield in the presence of the pathogen is therefore of high relevance. RESULTS To identify causal genes providing tolerance against BCN infection, we combined several experimental and bioinformatic approaches. Relevant genomic regions were detected through mapping-by-sequencing using a segregating F2 population. DNA sequencing of contrasting F2 pools and analyses of allele frequencies for variant positions identified a single genomic region which confers nematode tolerance. The genomic interval was confirmed and narrowed down by genotyping with newly developed molecular markers. To pinpoint the causal genes within the potential nematode tolerance locus, we generated long read-based genome sequence assemblies of the tolerant parental breeding line Strube U2Bv and the susceptible reference line 2320Bv. We analyzed continuous sequences of the potential locus with regard to functional gene annotation and differential gene expression upon BCN infection. A cluster of genes with similarity to the Arabidopsis thaliana gene encoding nodule inception protein-like protein 7 (NLP7) was identified. Gene expression analyses confirmed transcriptional activity and revealed clear differences between susceptible and tolerant genotypes. CONCLUSIONS Our findings provide new insights into the genomic basis of plant-nematode interactions that can be used to design and accelerate novel management strategies against BCN.
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Affiliation(s)
- Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615, Bielefeld, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, 38106, Braunschweig, Germany
| | - Elena Orsini
- Strube Research GmbH & Co. KG, Hauptstraße 1, 38387, Söllingen, Germany
| | | | - Lukas Schulte
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Prisca Viehöver
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Andreas E Müller
- Strube Research GmbH & Co. KG, Hauptstraße 1, 38387, Söllingen, Germany
| | - Axel Schechert
- Strube Research GmbH & Co. KG, Hauptstraße 1, 38387, Söllingen, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.
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Wolff K, Friedhoff R, Schwarzer F, Pucker B. Data literacy in genome research. J Integr Bioinform 2023; 20:jib-2023-0033. [PMID: 38047760 PMCID: PMC10777367 DOI: 10.1515/jib-2023-0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023] Open
Abstract
With an ever increasing amount of research data available, it becomes constantly more important to possess data literacy skills to benefit from this valuable resource. An integrative course was developed to teach students the fundamentals of data literacy through an engaging genome sequencing project. Each cohort of students performed planning of the experiment, DNA extraction, nanopore sequencing, genome sequence assembly, prediction of genes in the assembled sequence, and assignment of functional annotation terms to predicted genes. Students learned how to communicate science through writing a protocol in the form of a scientific paper, providing comments during a peer-review process, and presenting their findings as part of an international symposium. Many students enjoyed the opportunity to own a project and to work towards a meaningful objective.
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Affiliation(s)
- Katharina Wolff
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
| | - Ronja Friedhoff
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
| | - Friderieke Schwarzer
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
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Rempel A, Choudhary N, Pucker B. KIPEs3: Automatic annotation of biosynthesis pathways. PLoS One 2023; 18:e0294342. [PMID: 37972102 PMCID: PMC10653506 DOI: 10.1371/journal.pone.0294342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/28/2023] [Indexed: 11/19/2023] Open
Abstract
Flavonoids and carotenoids are pigments involved in stress mitigation and numerous other processes. Both pigment classes can contribute to flower and fruit coloration. Flavonoid aglycones and carotenoids are produced by a pathway that is largely conserved across land plants. Glycosylations, acylations, and methylations of the flavonoid aglycones can be species-specific and lead to a plethora of biochemically diverse flavonoids. We previously developed KIPEs for the automatic annotation of biosynthesis pathways and presented an application on the flavonoid aglycone biosynthesis. KIPEs3 is an improved version with additional features and the potential to identify not just the core biosynthesis players, but also candidates involved in the decoration steps and in the transport of flavonoids. Functionality of KIPEs3 is demonstrated through the analysis of the flavonoid biosynthesis in Arabidopsis thaliana Nd-1, Capsella grandiflora, and Dioscorea dumetorum. We demonstrate the applicability of KIPEs to other pathways by adding the carotenoid biosynthesis to the repertoire. As a technical proof of concept, the carotenoid biosynthesis was analyzed in the same species and Daucus carota. KIPEs3 is available as an online service to enable access without prior bioinformatics experience. KIPEs3 facilitates the automatic annotation and analysis of biosynthesis pathways with a consistent and high quality in a large number of plant species. Numerous genome sequencing projects are generating a huge amount of data sets that can be analyzed to identify evolutionary patterns and promising candidate genes for biotechnological and breeding applications.
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Affiliation(s)
- Andreas Rempel
- Genome Informatics, Faculty of Technology & Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Graduate School “Digital Infrastructure for the Life Sciences” (DILS), Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, Bielefeld, Germany
| | - Nancy Choudhary
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
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Meckoni SN, Nass B, Pucker B. Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data. BMC Res Notes 2023; 16:187. [PMID: 37626355 PMCID: PMC10464454 DOI: 10.1186/s13104-023-06459-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
OBJECTIVE Eutrophication poses a mounting concern in today's world. Ceratophyllum submersum L. is one of many plants capable of living in eutrophic conditions, therefore it could play a critical role in addressing the problem of eutrophication. This study aimed to take a first genomic look at C. submersum. RESULTS Sequencing of gDNA from C. submersum yielded enough reads to assemble a plastome. Subsequent annotation and phylogenetic analysis validated existing information regarding angiosperm relationships and the positioning of Ceratophylalles in a wider phylogenetic context.
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Affiliation(s)
- Samuel Nestor Meckoni
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology, TU Braunschweig, 38106, Braunschweig, Germany
| | - Benneth Nass
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology, TU Braunschweig, 38106, Braunschweig, Germany
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 - Suchdol, CZ-165 21, Prague, Czech Republic
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology, TU Braunschweig, 38106, Braunschweig, Germany.
- Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, 38106, Braunschweig, Germany.
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Schilbert HM, Holzenkamp K, Viehöver P, Holtgräwe D, Möllers C. Homoeologous non-reciprocal translocation explains a major QTL for seed lignin content in oilseed rape (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:172. [PMID: 37439815 PMCID: PMC10345078 DOI: 10.1007/s00122-023-04407-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/22/2023] [Indexed: 07/14/2023]
Abstract
A homoeologous non-reciprocal translocation was identified in the major QTL for seed lignin content in the low lignin line SGDH14. The lignin biosynthetic gene PAL4 was deleted. Oilseed rape is a major oil crop and a valuable protein source for animal and human nutrition. Lignin is a non-digestible, major component of the seed coat with negative effect on sensory quality, bioavailability and usage of oilseed rape's protein. Hence, seed lignin reduction is of economic and nutritional importance. In this study, the major QTL for reduced lignin content found on chromosome C05 in the DH population SGDH14 x Express 617 was further examined. SGDH14 had lower seed lignin content than Express 617. Harvested seeds from a F2 population of the same cross were additionally field tested and used for seed quality analysis. The F2 population showed a bimodal distribution for seed lignin content. F2 plants with low lignin content had thinner seed coats compared to high lignin lines. Both groups showed a dark seed colour with a slightly lighter colour in the low lignin group indicating that a low lignin content is not necessarily associated with yellow seed colour. Mapping of genomic long-reads from SGDH14 against the Express 617 genome assembly revealed a homoeologous non-reciprocal translocation (HNRT) in the confidence interval of the major QTL for lignin content. A homologous A05 region is duplicated and replaced the C05 region in SGDH14. As consequence several genes located in the C05 region were lost in SGDH14. Thus, a HNRT was identified in the major QTL region for reduced lignin content in the low lignin line SGDH14. The most promising candidate gene related to lignin biosynthesis on C05, PAL4, was deleted.
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Affiliation(s)
- Hanna Marie Schilbert
- Genetics and Genomics of Plants, CeBiTec and Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany.
| | - Karin Holzenkamp
- Department of Crop Sciences, Division of Crop Plant Genetics, Georg-August-University, Göttingen, Germany
| | - Prisca Viehöver
- Genetics and Genomics of Plants, CeBiTec and Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, CeBiTec and Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Christian Möllers
- Department of Crop Sciences, Division of Crop Plant Genetics, Georg-August-University, Göttingen, Germany
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Ngo Ngwe F, Siljak-Yakovlev S. Sex Determination in Dioscorea dumetorum: Evidence of Heteromorphic Sex Chromosomes and Sex-Linked NORs. PLANTS (BASEL, SWITZERLAND) 2023; 12:228. [PMID: 36678940 PMCID: PMC9861523 DOI: 10.3390/plants12020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Yams (Dioscorea spp.) are a pantropical genus located worldwide that constitute an important source of nutrients and pharmaceutical substances. Some Dioscorea crop species are widely grown in West Africa. One species that is mainly cultivated in Cameroon is Dioscorea dumetorum. This is a dioecious root crop whose sex-determining system was unknown until now. To address the possible presence of sex chromosomes in D. dumetorum, we performed a karyotype characterization of male and female individuals using classical and molecular cytogenetic approaches. It was determined that 2n = 40 was the most common number of chromosomes in all of the investigated samples. One chromosome pair was longer than the others in the chromosome set and was a heteromorph in male and homomorph in female individuals. This pair corresponded to sex chromosomes, and we also confirmed this with molecular cytogenetic experiments. The results of chromomycin banding revealed the presence of strong positive signals on this chromosome pair. The signals, corresponding to GC-rich DNA regions, were similar in size on the chromosomes of the female individuals, whereas they were different in size in the male individuals. This size difference in the GC-rich heterochromatin regions was also apparent in the interphase nuclei as one small and one large fluorescent spot. The results of the in situ hybridization experiment showed that these chromomycin positive signals on the sex chromosomes also corresponded to the 35S rDNA cluster. The mean 2C DNA value (genome size) obtained for D. dumentorum was 0.71 pg (±0.012), which represents a small genome size. We found no difference in the genome size between the male and female individuals. The results of this study contribute to increasing our knowledge of sex determination in D. dumetorum (standard sex-determining XX/XY system) and may have some agronomic applications.
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Affiliation(s)
- Florence Ngo Ngwe
- Biodiversity Division, Institute of Agricultural Research for Development, Yaoundé 2123, Cameroon
| | - Sonja Siljak-Yakovlev
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, 91190 Gif-sur-Yvette, France
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Dmitriev AA, Pushkova EN, Melnikova NV. Plant Genome Sequencing: Modern Technologies and Novel Opportunities for Breeding. Mol Biol 2022. [DOI: 10.1134/s0026893322040045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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13
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Chapman MA, He Y, Zhou M. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. THE NEW PHYTOLOGIST 2022; 234:1583-1597. [PMID: 35318683 PMCID: PMC9994440 DOI: 10.1111/nph.18021] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/22/2022] [Indexed: 04/14/2023]
Abstract
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
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Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Yuqi He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| | - Meiliang Zhou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
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14
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Tripathi L, Dhugga KS, Ntui VO, Runo S, Syombua ED, Muiruri S, Wen Z, Tripathi JN. Genome Editing for Sustainable Agriculture in Africa. Front Genome Ed 2022; 4:876697. [PMID: 35647578 PMCID: PMC9133388 DOI: 10.3389/fgeed.2022.876697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/21/2022] [Indexed: 12/25/2022] Open
Abstract
Sustainable intensification of agriculture in Africa is essential for accomplishing food and nutritional security and addressing the rising concerns of climate change. There is an urgent need to close the yield gap in staple crops and enhance food production to feed the growing population. In order to meet the increasing demand for food, more efficient approaches to produce food are needed. All the tools available in the toolbox, including modern biotechnology and traditional, need to be applied for crop improvement. The full potential of new breeding tools such as genome editing needs to be exploited in addition to conventional technologies. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based genome editing has rapidly become the most prevalent genetic engineering approach for developing improved crop varieties because of its simplicity, efficiency, specificity, and easy to use. Genome editing improves crop variety by modifying its endogenous genome free of any foreign gene. Hence, genome-edited crops with no foreign gene integration are not regulated as genetically modified organisms (GMOs) in several countries. Researchers are using CRISPR/Cas-based genome editing for improving African staple crops for biotic and abiotic stress resistance and improved nutritional quality. Many products, such as disease-resistant banana, maize resistant to lethal necrosis, and sorghum resistant to the parasitic plant Striga and enhanced quality, are under development for African farmers. There is a need for creating an enabling environment in Africa with science-based regulatory guidelines for the release and adoption of the products developed using CRISPR/Cas9-mediated genome editing. Some progress has been made in this regard. Nigeria and Kenya have recently published the national biosafety guidelines for the regulation of gene editing. This article summarizes recent advances in developments of tools, potential applications of genome editing for improving staple crops, and regulatory policies in Africa.
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Affiliation(s)
- Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- *Correspondence: Leena Tripathi,
| | | | - Valentine O. Ntui
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | | | - Easter D. Syombua
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Samwel Muiruri
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- Kenyatta University, Nairobi, Kenya
| | - Zhengyu Wen
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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15
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Bredeson JV, Lyons JB, Oniyinde IO, Okereke NR, Kolade O, Nnabue I, Nwadili CO, Hřibová E, Parker M, Nwogha J, Shu S, Carlson J, Kariba R, Muthemba S, Knop K, Barton GJ, Sherwood AV, Lopez-Montes A, Asiedu R, Jamnadass R, Muchugi A, Goodstein D, Egesi CN, Featherston J, Asfaw A, Simpson GG, Doležel J, Hendre PS, Van Deynze A, Kumar PL, Obidiegwu JE, Bhattacharjee R, Rokhsar DS. Chromosome evolution and the genetic basis of agronomically important traits in greater yam. Nat Commun 2022; 13:2001. [PMID: 35422045 PMCID: PMC9010478 DOI: 10.1038/s41467-022-29114-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 02/08/2022] [Indexed: 12/14/2022] Open
Abstract
The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Jessica B Lyons
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Ibukun O Oniyinde
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Nneka R Okereke
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - Olufisayo Kolade
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Ikenna Nnabue
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | | | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900, Olomouc, Czech Republic
| | - Matthew Parker
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Jeremiah Nwogha
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | | | | | - Robert Kariba
- World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- African Orphan Crops Consortium, Nairobi, Kenya
| | - Samuel Muthemba
- World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- African Orphan Crops Consortium, Nairobi, Kenya
| | - Katarzyna Knop
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Anna V Sherwood
- School of Life Sciences, University of Dundee, Dundee, UK
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Antonio Lopez-Montes
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
- International Trade Center, Accra, Ghana
| | - Robert Asiedu
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Ramni Jamnadass
- World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- African Orphan Crops Consortium, Nairobi, Kenya
| | - Alice Muchugi
- World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- African Orphan Crops Consortium, Nairobi, Kenya
| | | | - Chiedozie N Egesi
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- Cornell University, Ithaca, NY, 14850, USA
| | | | - Asrat Asfaw
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Gordon G Simpson
- School of Life Sciences, University of Dundee, Dundee, UK
- James Hutton Institute, Dundee, UK
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900, Olomouc, Czech Republic
| | - Prasad S Hendre
- World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- African Orphan Crops Consortium, Nairobi, Kenya
| | | | - Pullikanti Lava Kumar
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Jude E Obidiegwu
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria.
| | - Ranjana Bhattacharjee
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria.
| | - Daniel S Rokhsar
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
- DOE Joint Genome Institute, Berkeley, CA, USA.
- Okinawa Institute of Science and Technology, Onna, Okinawa, Japan.
- Chan-Zuckerberg BioHub, 499 Illinois St., San Francisco, CA, 94158, USA.
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16
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A Review of Viruses Infecting Yam ( Dioscorea spp.). Viruses 2022; 14:v14040662. [PMID: 35458392 PMCID: PMC9033002 DOI: 10.3390/v14040662] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Yam is an important food staple for millions of people globally, particularly those in the developing countries of West Africa and the Pacific Islands. To sustain the growing population, yam production must be increased amidst the many biotic and abiotic stresses. Plant viruses are among the most detrimental of plant pathogens and have caused great losses of crop yield and quality, including those of yam. Knowledge and understanding of virus biology and ecology are important for the development of diagnostic tools and disease management strategies to combat the spread of yam-infecting viruses. This review aims to highlight current knowledge on key yam-infecting viruses by examining their characteristics, genetic diversity, disease symptoms, diagnostics, and elimination to provide a synopsis for consideration in developing diagnostic strategy and disease management for yam.
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17
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Automatic identification and annotation of MYB gene family members in plants. BMC Genomics 2022; 23:220. [PMID: 35305581 PMCID: PMC8933966 DOI: 10.1186/s12864-022-08452-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND MYBs are among the largest transcription factor families in plants. Consequently, members of this family are involved in a plethora of processes including development and specialized metabolism. The MYB families of many plant species were investigated in the last two decades since the first investigation looked at Arabidopsis thaliana. This body of knowledge and characterized sequences provide the basis for the identification, classification, and functional annotation of candidate sequences in new genome and transcriptome assemblies. RESULTS A pipeline for the automatic identification and functional annotation of MYBs in a given sequence data set was implemented in Python. MYB candidates are identified, screened for the presence of a MYB domain and other motifs, and finally placed in a phylogenetic context with well characterized sequences. In addition to technical benchmarking based on existing annotation, the transcriptome assembly of Croton tiglium and the annotated genome sequence of Castanea crenata were screened for MYBs. Results of both analyses are presented in this study to illustrate the potential of this application. The analysis of one species takes only a few minutes depending on the number of predicted sequences and the size of the MYB gene family. This pipeline, the required bait sequences, and reference sequences for a classification are freely available on github: https://github.com/bpucker/MYB_annotator . CONCLUSIONS This automatic annotation of the MYB gene family in novel assemblies makes genome-wide investigations consistent and paves the way for comparative studies in the future. Candidate genes for in-depth analyses are presented based on their orthology to previously characterized sequences which allows the functional annotation of the newly identified MYBs with high confidence. The identification of orthologs can also be harnessed to detect duplication and deletion events.
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18
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Chourasia KN, More SJ, Kumar A, Kumar D, Singh B, Bhardwaj V, Kumar A, Das SK, Singh RK, Zinta G, Tiwari RK, Lal MK. Salinity responses and tolerance mechanisms in underground vegetable crops: an integrative review. PLANTA 2022; 255:68. [PMID: 35169941 DOI: 10.1007/s00425-022-03845-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 01/25/2022] [Indexed: 05/04/2023]
Abstract
The present review gives an insight into the salinity stress tolerance responses and mechanisms of underground vegetable crops. Phytoprotectants, agronomic practices, biofertilizers, and modern biotechnological approaches are crucial for salinity stress management. Underground vegetables are the source of healthy carbohydrates, resistant starch, antioxidants, vitamins, mineral, and nutrients which benefit human health. Soil salinity is a serious threat to agriculture that severely affects the growth, development, and productivity of underground vegetable crops. Salt stress induces several morphological, anatomical, physiological, and biochemical changes in crop plants which include reduction in plant height, leaf area, and biomass. Also, salinity stress impedes the growth of the underground organs, which ultimately reduces crop yield. Moreover, salt stress is detrimental to photosynthesis, membrane integrity, nutrient balance, and leaf water content. Salt tolerance mechanisms involve a complex interplay of several genes, transcription factors, and proteins that are involved in the salinity tolerance mechanism in underground crops. Besides, a coordinated interaction between several phytoprotectants, phytohormones, antioxidants, and microbes is needed. So far, a comprehensive review of salinity tolerance responses and mechanisms in underground vegetables is not available. This review aims to provide a comprehensive view of salt stress effects on underground vegetable crops at different levels of biological organization and discuss the underlying salt tolerance mechanisms. Also, the role of multi-omics in dissecting gene and protein regulatory networks involved in salt tolerance mechanisms is highlighted, which can potentially help in breeding salt-tolerant underground vegetable crops.
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Affiliation(s)
- Kumar Nishant Chourasia
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, West Bengal, India
| | | | - Ashok Kumar
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, Maharashtra, India
| | - Dharmendra Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Awadhesh Kumar
- Division of Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | | | - Rajesh Kumar Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientifc and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Gaurav Zinta
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.
- Academy of Scientifc and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
| | - Rahul Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India.
- ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India.
- ICAR-Indian Agricultural Research Institute, New Delhi, India.
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19
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Pucker B, Irisarri I, de Vries J, Xu B. Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions. QUANTITATIVE PLANT BIOLOGY 2022; 3:e5. [PMID: 37077982 PMCID: PMC10095996 DOI: 10.1017/qpb.2021.18] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/24/2021] [Accepted: 12/21/2021] [Indexed: 05/03/2023]
Abstract
Third-generation long-read sequencing is transforming plant genomics. Oxford Nanopore Technologies and Pacific Biosciences are offering competing long-read sequencing technologies and enable plant scientists to investigate even large and complex plant genomes. Sequencing projects can be conducted by single research groups and sequences of smaller plant genomes can be completed within days. This also resulted in an increased investigation of genomes from multiple species in large scale to address fundamental questions associated with the origin and evolution of land plants. Increased accessibility of sequencing devices and user-friendly software allows more researchers to get involved in genomics. Current challenges are accurately resolving diploid or polyploid genome sequences and better accounting for the intra-specific diversity by switching from the use of single reference genome sequences to a pangenome graph.
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Affiliation(s)
- Boas Pucker
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany
- Author for correspondence: Boas Pucker E-mail:
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Göttingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Göttingen, Germany
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB), University of Goettingen, Göttingen, Germany
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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20
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Syombua ED, Tripathi JN, Obiero GO, Nguu EK, Yang B, Wang K, Tripathi L. Potential applications of the CRISPR/Cas technology for genetic improvement of yam (
Dioscorea
spp.). Food Energy Secur 2021. [DOI: 10.1002/fes3.330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Easter D. Syombua
- International Institute of Tropical Agriculture (IITA) Nairobi Kenya
- Centre for Biotechnology and Bioinformatics (CEBIB) University of Nairobi Nairobi Kenya
| | | | - George O. Obiero
- Centre for Biotechnology and Bioinformatics (CEBIB) University of Nairobi Nairobi Kenya
| | - Edward K. Nguu
- Department of Biochemistry University of Nairobi Nairobi Kenya
| | - Bing Yang
- Division of Plant Sciences Bond Life Sciences Center University of Missouri Columbia MO USA
- Donald Danforth Plant Science Center St. Louis MO USA
| | - Kan Wang
- Department of Agronomy Iowa State University Ames IA USA
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA) Nairobi Kenya
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21
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Pucker B, Kleinbölting N, Weisshaar B. Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. BMC Genomics 2021; 22:599. [PMID: 34362298 PMCID: PMC8348815 DOI: 10.1186/s12864-021-07877-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 07/06/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Experimental proof of gene function assignments in plants is based on mutant analyses. T-DNA insertion lines provided an invaluable resource of mutants and enabled systematic reverse genetics-based investigation of the functions of Arabidopsis thaliana genes during the last decades. RESULTS We sequenced the genomes of 14 A. thaliana GABI-Kat T-DNA insertion lines, which eluded flanking sequence tag-based attempts to characterize their insertion loci, with Oxford Nanopore Technologies (ONT) long reads. Complex T-DNA insertions were resolved and 11 previously unknown T-DNA loci identified, resulting in about 2 T-DNA insertions per line and suggesting that this number was previously underestimated. T-DNA mutagenesis caused fusions of chromosomes along with compensating translocations to keep the gene set complete throughout meiosis. Also, an inverted duplication of 800 kbp was detected. About 10 % of GABI-Kat lines might be affected by chromosomal rearrangements, some of which do not involve T-DNA. Local assembly of selected reads was shown to be a computationally effective method to resolve the structure of T-DNA insertion loci. We developed an automated workflow to support investigation of long read data from T-DNA insertion lines. All steps from DNA extraction to assembly of T-DNA loci can be completed within days. CONCLUSIONS Long read sequencing was demonstrated to be an effective way to resolve complex T-DNA insertions and chromosome fusions. Many T-DNA insertions comprise not just a single T-DNA, but complex arrays of multiple T-DNAs. It is becoming obvious that T-DNA insertion alleles must be characterized by exact identification of both T-DNA::genome junctions to generate clear genotype-to-phenotype relations.
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Affiliation(s)
- Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
- Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Nils Kleinbölting
- Bioinformatics Resource Facility, Center for Biotechnology (CeBiTec, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
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22
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Kamenya SN, Mikwa EO, Song B, Odeny DA. Genetics and breeding for climate change in Orphan crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1787-1815. [PMID: 33486565 PMCID: PMC8205878 DOI: 10.1007/s00122-020-03755-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/16/2020] [Indexed: 05/17/2023]
Abstract
Climate change is rapidly changing how we live, what we eat and produce, the crops we breed and the target traits. Previously underutilized orphan crops that are climate resilient are receiving much attention from the crops research community, as they are often the only crops left in the field after periods of extreme weather conditions. There are several orphan crops with incredible resilience to biotic and abiotic stresses. Some are nutritious, while others provide good sources of biofuel, medicine and other industrial raw materials. Despite these benefits, orphan crops are still lacking in important genetic and genomic resources that could be used to fast track their improvement and make their production profitable. Progress has been made in generating draft genomes of at least 28 orphan crops over the last decade, thanks to the reducing cost of sequencing. The implementation of a structured breeding program that takes advantage of additional modern crop improvement tools such as genomic selection, speed breeding, genome editing, high throughput phenotyping and breeding digitization would make rapid improvement of these orphan crops possible, but would require coordinated research investment. Other production challenges such as lack of adequate germplasm conservation, poor/non-existent seed systems and agricultural extension services, as well as poor marketing channels will also need to be improved if orphan crops were to be profitable. We review the importance of breeding orphan crops under the increasing effects of climate change, highlight existing gaps that need to be addressed and share some lessons to be learned from major crops.
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Affiliation(s)
- Sandra Ndagire Kamenya
- African Center of Excellence in Agroecology and Livelihood Systems, Uganda Martyrs University, Kampala, Uganda
| | - Erick Owuor Mikwa
- The International Crops Research Institute for the Semi-Arid Tropics - Eastern and Southern Africa, Nairobi, Kenya
| | - Bo Song
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute At Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518060, People's Republic of China.
| | - Damaris Achieng Odeny
- The International Crops Research Institute for the Semi-Arid Tropics - Eastern and Southern Africa, Nairobi, Kenya.
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23
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Siadjeu C, Mayland-Quellhorst E, Pande S, Laubinger S, Albach DC. Transcriptome Sequence Reveals Candidate Genes Involving in the Post-Harvest Hardening of Trifoliate Yam Dioscorea dumetorum. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10040787. [PMID: 33923758 PMCID: PMC8074181 DOI: 10.3390/plants10040787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Storage ability of trifoliate yam (Dioscorea dumetorum) is restricted by a severe post-harvest hardening (PHH) phenomenon, which starts within the first 24 h after harvest and renders tubers inedible. Previous work has only focused on the biochemical changes affecting PHH in D. dumetorum. To the best of our knowledge, the candidate genes responsible for the hardening of D. dumetorum have not been identified. Here, transcriptome analyses of D. dumetorum tubers were performed in yam tubers of four developmental stages: 4 months after emergence (4MAE), immediately after harvest (AH), 3 days after harvest (3DAH) and 14 days after harvest (14DAH) of four accessions (Bangou 1, Bayangam 2, Fonkouankem 1, and Ibo sweet 3) using RNA-Seq. In total, between AH and 3DAH, 165, 199, 128 and 61 differentially expressed genes (DEGs) were detected in Bayangam 2, Fonkouankem 1, Bangou 1 and Ibo sweet 3, respectively. Functional analysis of DEGs revealed that genes encoding for CELLULOSE SYNTHASE A (CESA), XYLAN O-ACETYLTRANSFERASE (XOAT), CHLOROPHYLL A/B BINDING PROTEIN1, 2, 3, 4 (LHCB1, LHCB2, LHCB3, and LCH4) and an MYB transcription factor were predominantly and significantly up-regulated 3DAH, implying that these genes were potentially involved in the PHH as confirmed by qRT-PCR. A hypothetical mechanism of this phenomenon and its regulation has been proposed. These findings provide the first comprehensive insights into gene expression in yam tubers after harvest and valuable information for molecular breeding against the PHH.
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Ye CY, Fan L. Orphan Crops and their Wild Relatives in the Genomic Era. MOLECULAR PLANT 2021; 14:27-39. [PMID: 33346062 DOI: 10.1016/j.molp.2020.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 05/06/2023]
Abstract
More than half of the calories consumed by humans are provided by three major cereal crops (rice, maize, and wheat). Orphan crops are usually well adapted to low-input agricultural conditions, and they not only play vital roles in local areas but can also contribute to food and nutritional needs worldwide. Interestingly, many wild relatives of orphan crops are important weeds of major crops. Although orphan crops and their wild relatives have received little attentions from researchers for many years, genomic studies have recently been performed on these plants. Here, we provide an overview of genomic studies on orphan crops, with a focus on orphan cereals and their wild relatives. The genomes of at least 12 orphan cereals and/or their wild relatives have been sequenced. In addition to genomic benefits for orphan crop breeding, we discuss the potential ways for mutual utilization of genomic data from major crops, orphan crops, and their wild relatives (including weeds) and provide perspectives on genetic improvement of both orphan and major crops (including de novo domestication of orphan crops) in the coming genomic era.
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Affiliation(s)
- Chu-Yu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572024, China.
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Danelli T, Laura M, Savona M, Landoni M, Adani F, Pilu R. Genetic Improvement of Arundo donax L.: Opportunities and Challenges. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1584. [PMID: 33207586 PMCID: PMC7696946 DOI: 10.3390/plants9111584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/09/2020] [Accepted: 11/13/2020] [Indexed: 12/29/2022]
Abstract
Arundo donax L., the giant reed-being a long-duration, low-cost, non-food energy crop able to grow in marginal lands-has emerged as a potential alternative to produce biomass for both energy production, with low carbon emissions, and industrial bioproducts. In recent years, pioneering efforts have been made to genetically improve this very promising energy crop. This review analyses the recent advances and challenges encountered in using clonal selection, mutagenesis/somaclonal variation and transgenesis/genome editing. Attempts to improve crop yield, in vitro propagation efficiency, salt and heavy metal tolerance by clonal selection were carried out, although limited by the species' low genetic diversity and availability of mutants. Mutagenesis and somaclonal variation have also been attempted on this species; however, since Arundo donax is polyploid, it is very difficult to induce and select promising mutations. In more recent years, genomics and transcriptomics data are becoming available in Arundo, closing the gap to make possible the genetic manipulation of this energy crop in the near future. The challenge will regard the functional characterization of the genes/sequences generated by genomic sequencing and transcriptomic analysis in a complex polyploid genome.
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Affiliation(s)
- Tommaso Danelli
- Gruppo Ricicla Labs—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (T.D.); (F.A.)
- Agricultural Genetics Group—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
| | - Marina Laura
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso Degli Inglesi 508, 18038 Sanremo, Italy; (M.L.); (M.S.)
| | - Marco Savona
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso Degli Inglesi 508, 18038 Sanremo, Italy; (M.L.); (M.S.)
| | - Michela Landoni
- Department of Biosciences, Università’ Degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy;
| | - Fabrizio Adani
- Gruppo Ricicla Labs—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (T.D.); (F.A.)
- Agricultural Genetics Group—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
| | - Roberto Pilu
- Gruppo Ricicla Labs—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (T.D.); (F.A.)
- Agricultural Genetics Group—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
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Epping J, Laibach N. An underutilized orphan tuber crop-Chinese yam : a review. PLANTA 2020; 252:58. [PMID: 32959173 PMCID: PMC7505826 DOI: 10.1007/s00425-020-03458-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 09/11/2020] [Indexed: 05/09/2023]
Abstract
MAIN CONCLUSION The diversification of food crops can improve our diets and address the effects of climate change, and in this context the orphan crop Chinese yam shows significant potential as a functional food. As the effects of climate change become increasingly visible even in temperate regions, there is an urgent need to diversify our crops in order to address hunger and malnutrition. This has led to the re-evaluation of neglected species such as Chinese yam (Dioscorea polystachya Turcz.), which has been cultivated for centuries in East Asia as a food crop and as a widely-used ingredient in traditional Chinese medicine. The tubers are rich in nutrients, but also contain bioactive metabolites such as resistant starches, steroidal sapogenins (like diosgenin), the storage protein dioscorin, and mucilage polysaccharides. These health-promoting products can help to prevent cardiovascular disease, diabetes, and disorders of the gut microbiome. Whereas most edible yams are tropical species, Chinese yam could be cultivated widely in Europe and other temperate regions to take advantage of its nutritional and bioactive properties. However, this is a laborious process and agronomic knowledge is fragmented. The underground tubers contain most of the starch, but are vulnerable to breaking and thus difficult to harvest. Breeding to improve tuber shape is complex given the dioecious nature of the species, the mostly vegetative reproduction via bulbils, and the presence of more than 100 chromosomes. Protocols have yet to be established for in vitro cultivation and genetic transformation, which limits the scope of research. This article summarizes the sparse research landscape and evaluates the nutritional and medical applications of Chinese yam. By highlighting the potential of Chinese yam tubers, we aim to encourage the adoption of this orphan crop as a novel functional food.
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Affiliation(s)
- Janina Epping
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, 48143, Muenster, Germany.
| | - Natalie Laibach
- Institute for Food and Resource Economics, University of Bonn, Meckenheimer Allee 174, 53115, Bonn, Germany
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27
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Dumschott K, Schmidt MHW, Chawla HS, Snowdon R, Usadel B. Oxford Nanopore sequencing: new opportunities for plant genomics? JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5313-5322. [PMID: 32459850 PMCID: PMC7501810 DOI: 10.1093/jxb/eraa263] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 05/25/2020] [Indexed: 05/06/2023]
Abstract
DNA sequencing was dominated by Sanger's chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. However, today's long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.
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Affiliation(s)
- Kathryn Dumschott
- Institute for Biology I, BioSC, RWTH Aachen University, Aachen, Germany
- IBG-4 Bioinformatics, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Maximilian H-W Schmidt
- Institute for Biology I, BioSC, RWTH Aachen University, Aachen, Germany
- IBG-4 Bioinformatics, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Björn Usadel
- Institute for Biology I, BioSC, RWTH Aachen University, Aachen, Germany
- IBG-4 Bioinformatics, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Obidiegwu JE, Lyons JB, Chilaka CA. The Dioscorea Genus (Yam)-An Appraisal of Nutritional and Therapeutic Potentials. Foods 2020; 9:E1304. [PMID: 32947880 PMCID: PMC7555206 DOI: 10.3390/foods9091304] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 12/19/2022] Open
Abstract
The quest for a food secure and safe world has led to continuous effort toward improvements of global food and health systems. While the developed countries seem to have these systems stabilized, some parts of the world still face enormous challenges. Yam (Dioscorea species) is an orphan crop, widely distributed globally; and has contributed enormously to food security especially in sub-Saharan Africa because of its role in providing nutritional benefits and income. Additionally, yam has non-nutritional components called bioactive compounds, which offer numerous health benefits ranging from prevention to treatment of degenerative diseases. Pharmaceutical application of diosgenin and dioscorin, among other compounds isolated from yam, has shown more prospects recently. Despite the benefits embedded in yam, reports on the nutritional and therapeutic potentials of yam have been fragmented and the diversity within the genus has led to much confusion. An overview of the nutritional and health importance of yam will harness the crop to meet its potential towards combating hunger and malnutrition, while improving global health. This review makes a conscious attempt to provide an overview regarding the nutritional, bioactive compositions and therapeutic potentials of yam diversity. Insights on how to increase its utilization for a greater impact are elucidated.
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Affiliation(s)
- Jude E. Obidiegwu
- National Root Crops Research Institute, Umudike, Km 8 Umuahia-Ikot Ekpene Road, P.M.B 7006 Umuahia, Abia State, Nigeria
| | - Jessica B. Lyons
- Department of Molecular and Cell Biology and Innovative Genomics Institute, University of California, Berkeley, 142 Weill Hall #3200, Berkeley, CA 94720-3200, USA;
| | - Cynthia A. Chilaka
- Institute of Pharmacology and Toxicology, Julius Maximilian University of Würzburg, Versbacher Straβe 9, 97078 Würzburg, Germany; or
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