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Talbot SC, Vining KJ, Snelling JW, Clevenger J, Mehlenbacher SA. A haplotype-resolved chromosome-level assembly and annotation of European hazelnut (C. avellana cv. Jefferson) provides insight into mechanisms of eastern filbert blight resistance. G3 (BETHESDA, MD.) 2024; 14:jkae021. [PMID: 38325326 DOI: 10.1093/g3journal/jkae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024]
Abstract
European hazelnut (Corylus avellana L.) is an important tree nut crop. Hazelnut production in North America is currently limited in scalability due to Anisogramma anomala, a fungal pathogen that causes Eastern Filbert Blight (EFB) disease in hazelnut. Successful deployment of EFB resistant cultivars has been limited to the state of Oregon, where the breeding program at Oregon State University (OSU) has released cultivars with a dominant allele at a single resistance locus identified by classical breeding, linkage mapping, and molecular markers. C. avellana cultivar "Jefferson" is resistant to the predominant EFB biotype in Oregon and has been selected by the OSU breeding program as a model for hazelnut genetic and genomic research. Here, we present a near complete, haplotype-resolved chromosome-level hazelnut genome assembly for "Jefferson". This new assembly is a significant improvement over a previously published genome draft. Analysis of genomic regions linked to EFB resistance and self-incompatibility confirmed haplotype splitting and identified new gene candidates that are essential for downstream molecular marker development, thereby facilitating breeding efforts.
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Affiliation(s)
- Samuel C Talbot
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
| | - Kelly J Vining
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
| | - Jacob W Snelling
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
| | - Josh Clevenger
- Hudson Alpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Shawn A Mehlenbacher
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
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Lucas SJ, Kahraman K, Avşar B, Buggs RJA, Bilge I. A chromosome-scale genome assembly of European hazel (Corylus avellana L.) reveals targets for crop improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1413-1430. [PMID: 33249676 DOI: 10.1111/tpj.15099] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 11/09/2020] [Indexed: 05/20/2023]
Abstract
The European hazelnut (Corylus avellana L.) is a tree crop of economic importance worldwide, but especially for northern Turkey, where the majority of production takes place. Hazelnut production is currently challenged by environmental stresses, such as a recent outbreak of severe powdery mildew disease; furthermore, allergy to hazelnuts is an increasing health concern in some regions. In order to provide a foundation for using the available hazelnut genetic resources for crop improvement, we produced a fully assembled genome sequence and annotation for a hazelnut species, from C. avellana cv. 'Tombul', one of the most important Turkish varieties. A hybrid sequencing strategy, combining short reads, long reads and proximity ligation methods, enabled us to resolve heterozygous regions and produce a high-quality 370-Mb assembly that agrees closely with cytogenetic studies and genetic maps of the 11 C. avellana chromosomes, and covers 97.8% of the estimated genome size. The genome includes 27 270 high-confidence protein-coding genes, over 20 000 of which were functionally annotated based on homology with known plant proteins. We focused particularly on gene families encoding hazelnut allergens, and the Mildew resistance Locus O (MLO) proteins that are an important susceptibility factor for powdery mildew. The complete assembly enabled us to differentiate between members of these families and to identify homologues that may be important in mildew disease and hazelnut allergy. These findings provide examples of how the genome can be used to guide research and to develop effective strategies for crop improvement in C. avellana.
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Affiliation(s)
- Stuart J Lucas
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Istanbul, Turkey
| | - Kadriye Kahraman
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Istanbul, Turkey
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Bihter Avşar
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Istanbul, Turkey
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Richard J A Buggs
- Jodrell Laboratory, Royal Botanic Gardens, Kew, London, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ipek Bilge
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Istanbul, Turkey
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
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Ascari L, Cristofori V, Macrì F, Botta R, Silvestri C, De Gregorio T, Huerta ES, Di Berardino M, Kaufmann S, Siniscalco C. Hazelnut Pollen Phenotyping Using Label-Free Impedance Flow Cytometry. FRONTIERS IN PLANT SCIENCE 2020; 11:615922. [PMID: 33370424 PMCID: PMC7753158 DOI: 10.3389/fpls.2020.615922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/13/2020] [Indexed: 05/23/2023]
Abstract
Impedance flow cytometry (IFC) is a versatile lab-on-chip technology which enables fast and label-free analysis of pollen grains in various plant species, promising new research possibilities in agriculture and plant breeding. Hazelnut is a monoecious, anemophilous species, exhibiting sporophytic self-incompatibility. Its pollen is dispersed by wind in midwinter when temperatures are still low and relative humidity is usually high. Previous research found that hazelnut can be characterized by high degrees of pollen sterility following a reciprocal chromosome translocation occurring in some cultivated genotypes. In this study, IFC was used for the first time to characterize hazelnut pollen biology. IFC was validated via dye exclusion in microscopy and employed to (i) follow pollen hydration over time to define the best pre-hydration treatment for pollen viability evaluation; (ii) test hazelnut pollen viability and sterility on 33 cultivars grown in a collection field located in central Italy, and two wild hazelnuts. The accessions were also characterized by their amount and distribution of catkins in the tree canopy. Pollen sterility rate greatly varied among hazelnut accessions, with one main group of highly sterile cultivars and a second group, comprising wild genotypes and the remaining cultivars, producing good quality pollen. The results support the hypothesis of recurring reciprocal translocation events in Corylus avellana cultivars, leading to the observed gametic semi-sterility. The measured hazelnut pollen viability was also strongly influenced by pollen hydration (R adj 2 = 0.83, P ≤ 0.0001) and reached its maximum at around 6 h of pre-hydration in humid chambers. Viable and dead pollen were best discriminated at around the same time of pollen pre-hydration, suggesting that high humidity levels are required for hazelnut pollen to maintain its functionality. Altogether, our results detail the value of impedance flow cytometry for high throughput phenotyping of hazelnut pollen. Further research is required to clarify the causes of pollen sterility in hazelnut, to confirm the role of reciprocal chromosome translocations and to investigate its effects on plant productivity.
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Affiliation(s)
- Lorenzo Ascari
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Valerio Cristofori
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Federico Macrì
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Roberto Botta
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
| | - Cristian Silvestri
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | | | | | | | | | - Consolata Siniscalco
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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She CW, Wei L, Jiang XH. Molecular cytogenetic characterization and comparison of the two cultivated Canavalia species (Fabaceae). COMPARATIVE CYTOGENETICS 2017; 11:579-600. [PMID: 29114355 PMCID: PMC5672272 DOI: 10.3897/compcytogen.v11i4.13604] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/07/2017] [Indexed: 05/25/2023]
Abstract
The two cultivated Canavalia (Adanson, 1763) species, Canavalia gladiata (N. J. von Jacquin, 1788) A. P. de Candolle, 1825 and Canavalia ensiformis (Linnaeus, 1753) A. P. de Candolle, 1825 are closely related based on morphological and molecular phylogenetic data. However, the similarities and differences in genome organization between them have not been evaluated at molecular cytogenetic level. Here, detailed karyotypes of both species were constructed using combined PI and DAPI (CPD) staining, rDNA-FISH and self-genomic in situ hybridization (sGISH). For further comparison, comparative genomic in situ hybridization (cGISH) and sequence analysis of 5S rDNA were applied. Their chromosomes were accurately identified by sGISH and rDNA-FISH signals. Both species had the karyotype formula 2n = 22 = 18m + 4m-SAT, but the karyotype of C. ensiformis was shorter and more asymmetric than that of C. gladiata. They displayed similar CPD bands at all 45S rDNA sites and centromeres. C. gladiata had ten centromeric 5S rDNA loci and two SC (secondary constriction)-associated 45S rDNA loci. C. ensiformis had nine centromeric and one interstitial 5S loci, two SC-associated and one proximal 45S loci. Their sGISH signal patterns displayed both basic similarities and distinct differences. Reciprocal cGISH generated prominent signals in all pericentromeric regions and 45S sites. There was lower level of sequence identity of the non-transcribed spacer between their 5S rDNA repeats. These data confirmed the evolutionary closeness between C. gladiata and C. ensiformis and demonstrated obvious differentiation between their genomes, and supported the opinion that C. ensiformis is more advanced in evolution than C. gladiata.
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Affiliation(s)
- Chao-Wen She
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, Huaihua, Hunan, 418008, China
- Key Laboratory of Xiangxi Medicinal Plant and Ethnobotany of Hunan Higher Education, Huaihua University, Huaihua, Hunan, 418008, China
- College of Biological and Food Engineering, Huaihua University, Huaihua, Hunan, 418008, China
| | - Lin Wei
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, Huaihua, Hunan, 418008, China
- Key Laboratory of Xiangxi Medicinal Plant and Ethnobotany of Hunan Higher Education, Huaihua University, Huaihua, Hunan, 418008, China
- College of Biological and Food Engineering, Huaihua University, Huaihua, Hunan, 418008, China
| | - Xiang-Hui Jiang
- Key Laboratory of Xiangxi Medicinal Plant and Ethnobotany of Hunan Higher Education, Huaihua University, Huaihua, Hunan, 418008, China
- College of Biological and Food Engineering, Huaihua University, Huaihua, Hunan, 418008, China
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Zheng JS, Sun CZ, Zhang SN, Hou XL, Bonnema G. Cytogenetic Diversity of Simple Sequences Repeats in Morphotypes of Brassica rapa ssp. chinensis. FRONTIERS IN PLANT SCIENCE 2016; 7:1049. [PMID: 27507974 PMCID: PMC4961004 DOI: 10.3389/fpls.2016.01049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 07/04/2016] [Indexed: 05/29/2023]
Abstract
A significant fraction of the nuclear DNA of all eukaryotes is comprised of simple sequence repeats (SSRs). Although these sequences are widely used for studying genetic variation, linkage mapping and evolution, little attention had been paid to the chromosomal distribution and cytogenetic diversity of these sequences. In this paper, we report the distribution characterization of mono-, di-, and tri-nucleotide SSRs in Brassica rapa ssp. chinensis. Fluorescence in situ hybridization was used to characterize the cytogenetic diversity of SSRs among morphotypes of B. rapa ssp. chinensis. The proportion of different SSR motifs varied among morphotypes of B. rapa ssp. chinensis, with tri-nucleotide SSRs being more prevalent in the genome of B. rapa ssp. chinensis. We determined the chromosomal locations of mono-, di-, and tri-nucleotide repeat loci. The results showed that the chromosomal distribution of SSRs in the different morphotypes is non-random and motif-dependent, and allowed us to characterize the relative variability in terms of SSR numbers and similar chromosomal distributions in centromeric/peri-centromeric heterochromatin. The differences between SSR repeats with respect to abundance and distribution indicate that SSRs are a driving force in the genomic evolution of B. rapa species. Our results provide a comprehensive view of the SSR sequence distribution and evolution for comparison among morphotypes B. rapa ssp. chinensis.
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Affiliation(s)
- Jin-shuang Zheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Horticulture, Nanjing Agricultural University, NanjingChina
- Hebei Normal University of Science and Technology, QinhuangdaoChina
| | - Cheng-zhen Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Horticulture, Nanjing Agricultural University, NanjingChina
- Hebei Normal University of Science and Technology, QinhuangdaoChina
| | - Shu-ning Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Horticulture, Nanjing Agricultural University, NanjingChina
| | - Xi-lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Horticulture, Nanjing Agricultural University, NanjingChina
| | - Guusje Bonnema
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, WageningenNetherlands
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