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de los Cobos FP, García-Gómez BE, Orduña-Rubio L, Batlle I, Arús P, Matus JT, Eduardo I. Exploring large-scale gene coexpression networks in peach ( Prunus persica L.): a new tool for predicting gene function. Hortic Res 2024; 11:uhad294. [PMID: 38487296 PMCID: PMC10939413 DOI: 10.1093/hr/uhad294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/17/2023] [Indexed: 03/17/2024]
Abstract
Peach is a model for Prunus genetics and genomics, however, identifying and validating genes associated to peach breeding traits is a complex task. A gene coexpression network (GCN) capable of capturing stable gene-gene relationships would help researchers overcome the intrinsic limitations of peach genetics and genomics approaches and outline future research opportunities. In this study, we created four GCNs from 604 Illumina RNA-Seq libraries. We evaluated the performance of every GCN in predicting functional annotations using an algorithm based on the 'guilty-by-association' principle. The GCN with the best performance was COO300, encompassing 21 956 genes. To validate its performance predicting gene function, we performed two case studies. In case study 1, we used two genes involved in fruit flesh softening: the endopolygalacturonases PpPG21 and PpPG22. Genes coexpressing with both genes were extracted and referred to as melting flesh (MF) network. Finally, we performed an enrichment analysis of MF network and compared the results with the current knowledge regarding peach fruit softening. The MF network mostly included genes involved in cell wall expansion and remodeling, and with expressions triggered by ripening-related phytohormones, such as ethylene, auxin, and methyl jasmonate. In case study 2, we explored potential targets of the anthocyanin regulator PpMYB10.1 by comparing its gene-centered coexpression network with that of its grapevine orthologues, identifying a common regulatory network. These results validated COO300 as a powerful tool for peach and Prunus research. This network, renamed as PeachGCN v1.0, and the scripts required to perform a function prediction analysis are available at https://github.com/felipecobos/PeachGCN.
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Affiliation(s)
- Felipe Pérez de los Cobos
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA) , Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Beatriz E García-Gómez
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Luis Orduña-Rubio
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, 46908, Valencia, Spain
| | - Ignasi Batlle
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA) , Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
| | - Pere Arús
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, 46908, Valencia, Spain
| | - Iban Eduardo
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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Pradas N, Jurado-Ruiz F, Onielfa C, Arús P, Aranzana MJ. PERSEUS: an interactive and intuitive web-based tool for pedigree visualization. Bioinformatics 2024; 40:btae060. [PMID: 38310342 PMCID: PMC10898331 DOI: 10.1093/bioinformatics/btae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 02/05/2024] Open
Abstract
SUMMARY Pedigree-based analyses' prime role is to unravel relationships between individuals in breeding programs and germplasms. This is critical information for decoding the genetics underlying main inherited traits of relevance, and unlocking the genotypic variability of a species to carry out genomic selections and predictions. Despite the great interest, current lineage visualizations become quite limiting in terms of public display, exploration, and tracing of traits up to ancestral donors. PERSEUS is a user-friendly, intuitive, and interactive web-based tool for pedigree visualizations represented as directed graph networks distributed using a force-repulsion method. The visualizations do not only showcase individual relationships among accessions, but also facilitate a seamless search and download of phenotypic traits along the pedigrees. PERSEUS is a promising tool for breeders and scientists, advantageous for evolutionary, genealogy, and diversity analyses among related accessions and species. AVAILABILITY AND IMPLEMENTATION PERSEUS is freely accessible at https://bioinformatics.cragenomica.es/perseus and GitHub code is available at https://github.com/aranzana-lab/PERSEUS.
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Affiliation(s)
- Nicole Pradas
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Federico Jurado-Ruiz
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Carles Onielfa
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 0814 Barcelona, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 0814 Barcelona, Spain
| | - Maria José Aranzana
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 0814 Barcelona, Spain
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Pérez de los Cobos F, Coindre E, Dlalah N, Quilot-Turion B, Batlle I, Arús P, Eduardo I, Duval H. Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time. Hortic Res 2023; 10:uhad193. [PMID: 37927408 PMCID: PMC10623407 DOI: 10.1093/hr/uhad193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/14/2023] [Indexed: 11/07/2023]
Abstract
Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide association studies (GWASs) are a powerful tool to detect these alleles of interest (and so QTLs). In this study, we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions. Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups, all formed by accessions with a common origin. One of these groups was formed exclusively by Spanish accessions, while the rest were mainly formed by accessions from China, Italy, France, and the USA. These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases: Asiatic, Mediterranean, Californian, and southern hemisphere. In total, we found 13 independent QTLs for nut weight, crack-out percentage, double kernels percentage, and blooming time. Of the 13 QTLs found, only one had an additive effect. Through candidate gene analysis, we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage, Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage, and Prudul26A000954 as a candidate gene for the QTL found in blooming time. Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.
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Affiliation(s)
- Felipe Pérez de los Cobos
- Fruticultura, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | | | | | | | - Ignasi Batlle
- Fruticultura, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
| | - Pere Arús
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Iban Eduardo
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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Zaracho N, Reig G, Kalluri N, Arús P, Eduardo I. Inheritance of Fruit Red-Flesh Patterns in Peach. Plants (Basel) 2023; 12:plants12020394. [PMID: 36679108 PMCID: PMC9862646 DOI: 10.3390/plants12020394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 06/01/2023]
Abstract
Fruit color is an important trait in peach from the point of view of consumer preference, nutritional content, and diversification of fruit typologies. Several genes and phenotypes have been described for peach flesh and skin color, and although peach color knowledge has increased in the last few years, some fruit color patterns observed in peach breeding programs have not been carefully described. In this work, we first describe some peach mesocarp color patterns that have not yet been described in a collection of commercial peach cultivars, and we also study the genetic inheritance of the red dots present in the flesh (RDF) and red color around the stone (CAS) in several intra- and interspecific segregating populations for both traits. For RDF, we identified a QTL at the beginning of G5 in two intraspecific populations, and for CAS we identified a major QTL in G4 in both an intraspecific and an interspecific population between almond and peach. Finally, we discuss the interaction between these QTLs and some other genes previously identified in peach, such as dominant blood flesh (DBF), color around the stone (Cs), subacid (D) and the maturity date (MD), and the implications for peach breeding. The results obtained here will help peach germplasm curators and breeders to better characterize their plant materials and to develop an integrated system of molecular markers to select these traits.
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Affiliation(s)
- Nathalia Zaracho
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Gemma Reig
- Institut de Recerca i Tecnologia Agroalimentaria (IRTA) Fruitcentre, Programa Fructicultura, PCiTAL, Parc Gardeny, 25003 Lleida, Spain
| | - Naveen Kalluri
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentaria (IRTA), Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Iban Eduardo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentaria (IRTA), Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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Duval H, Coindre E, Ramos-Onsins SE, Alexiou KG, Rubio-Cabetas MJ, Martínez-García PJ, Wirthensohn M, Dhingra A, Samarina A, Arús P. Development and Evaluation of an Axiom TM 60K SNP Array for Almond ( Prunus dulcis). Plants (Basel) 2023; 12:242. [PMID: 36678957 PMCID: PMC9866729 DOI: 10.3390/plants12020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach × almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits.
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Affiliation(s)
- Henri Duval
- Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRAE (French National Research Institute for Agriculture, Food and Environment), 84143 Montfavet, France
| | - Eva Coindre
- Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRAE (French National Research Institute for Agriculture, Food and Environment), 84143 Montfavet, France
| | - Sebastian E. Ramos-Onsins
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Konstantinos G. Alexiou
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain
- IRTA (Institute of Agrifood Research and Technology), Campus UAB, Edifici CRAG, Cerdanyola del Valles (Bellaterra), 08193 Barcelona, Spain
| | - Maria J. Rubio-Cabetas
- CITA (Agrifood Research and Technology Centre of Aragon), Department of Plant Science, Avda. Montañana 930, 50059 Zaragoza, Spain
| | - Pedro J. Martínez-García
- CEBAS (Centro de Edafología y Biología Aplicada del Segura), CSIC, Department of Plant Breeding, Campus Universitario de Espinardo, 30100 Espinardo, Spain
| | - Michelle Wirthensohn
- Waite Research Institute, University of Adelaide, PMB 1 Glen, Osmond, SA 5064, Australia
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Anna Samarina
- Thermo Fisher Scientific, Frankfurter Str. 129B, 64293 Darmstadt, Germany
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain
- IRTA (Institute of Agrifood Research and Technology), Campus UAB, Edifici CRAG, Cerdanyola del Valles (Bellaterra), 08193 Barcelona, Spain
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Kalluri N, Serra O, Donoso JM, Picañol R, Howad W, Eduardo I, Arús P. Construction of a collection of introgression lines of "Texas" almond DNA fragments in the "Earlygold" peach genetic background. Hortic Res 2022; 9:uhac070. [PMID: 35669708 PMCID: PMC9157678 DOI: 10.1093/hr/uhac070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/09/2022] [Indexed: 06/15/2023]
Abstract
Peach [Prunus persica L. Batsch] is one of the major temperate fruit tree species, the commercial materials of which have a low level of genetic variability. Almond [P. dulcis (Mill) DA Webb], a close relative of peach cultivated for its kernels, has a much higher level of diversity. The species are inter-compatible and often produce fertile hybrids, almond being a possible source of new genes for peach that could provide biotic and abiotic stress tolerance traits. In this paper we describe the development of a collection of peach-almond introgression lines (ILs) having a single fragment of almond (cv. Texas) in the peach background (cv. Earlygold). Lines with few introgressions were selected with markers from successive generations from a "Texas" × "Earlygold" F1 hybrid, initially using a set of SSRs and later with the 18 k peach SNP chip, allowing for the final extraction of 67 lines, 39 with almond heterozygous introgressions covering 99% of the genome, and 28 with homozygous introgressions covering 83% of the genome. As a proof of concept, four major genes and four quantitative characters were examined in the selected ILs giving results generally consistent with previous information on the genetics of these characters. This collection is the first of its kind produced in a woody perennial species and promises to be a valuable tool for genetic analyses, including dissection of quantitative traits, positional cloning, epistasis and as prebreeding material to introgress almond genes of interest into the peach commercial gene pool.
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Affiliation(s)
- Naveen Kalluri
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Octávio Serra
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Banco Português de Germoplasma Vegetal (BPGV), Braga, Portugal
| | - José Manuel Donoso
- Instituto de Investigaciones Agropecuarias (INIA), Centro Regional de Investigación Rayentué, Av. Salamanca s/n Sector Los Choapinos, Rengo 2940000, Chile
| | - Roger Picañol
- Rijk Zwaan Ibérica S.A. Finca La Marina-PJ Lo Contreras 30395, La Puebla|Cartagena (Murcia), Spain
| | - Werner Howad
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- IRTA, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Iban Eduardo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- IRTA, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- IRTA, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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Jin J, Gan K, Zhao L, Jia H, Zhu Y, Li X, Yang Z, Ye Z, Cao K, Wang Z, Yu M, Zhang Y, Ma Z, Liu H, Arús P, Akkerdaas JH, Gao Z, van Ree R. Peach allergen Pru p 1 content is generally low in fruit but with large variation in different varieties. Clin Transl Allergy 2021; 11:e12034. [PMID: 34025984 PMCID: PMC8120414 DOI: 10.1002/clt2.12034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/05/2021] [Accepted: 04/26/2021] [Indexed: 01/22/2023] Open
Abstract
Background Pru p 1 is a major allergen in peach and nectarine, and the different content in varieties may affect the degree of allergic reactions. This study aimed to quantify Pru p 1 levels in representative peach varieties and select hypoallergenic Pru p 1 varieties. Methods To obtain monoclonal and polyclonal antibodies, mice and rabbits, respectively, were immunized with recombinant Pru p 1.01 and Pru p 1.02. The Pru p 1 levels in fruits from 83 representative peach varieties was quantified by sandwich enzyme-linked immunosorbent assay (sELISA). nPru p 1 was obtained through specific monoclonal antibody affinity purification and confirmed by Western blot and mass spectrometry. The variable Pru p 1 content of selected varieties was evaluated by Western blot and the expression level of encoding Pru p 1 genes by quantitative polymerase chain reaction. Results A sELISA method with monoclonal and polyclonal antibodies was built for quantifying Pru p 1 levels in peach. Pru p 1 was mainly concentrated in the peel (0.20-73.44 μg/g, fresh weight), being very low in the pulp (0.05-9.62 μg/g) and not detected in wild peach. For the 78 peach and nectarine varieties, Pru p 1 content varied widely from 0.12 to 6.45 μg/g in whole fruit. We verified that natural Pru p 1 is composed of 1.01 and 1.02 isoallergens, and the Pru p 1 expression level and Pru p 1 band intensity in the immunoblots were in agreement with protein quantity determined by ELISA for some tested varieties. In some cases, the reduced levels of Pru p 1 did not coincide with low Pru p 3 in the same variety in whole fruit, while some ancient wild peach and nectarines contained low levels of both allergens, and late-ripening yellow flesh varieties were usually highly allergenic. Conclusion Pru p 1 content is generally low in peach compared to Pru p 3. Several hypoallergenic Pru p 1 and Pru p 3 varieties, "Zi Xue Tao," "Wu Yue Xian," and "May Fire," were identified, which could be useful in trials for peach allergy patients.
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Affiliation(s)
- Jing Jin
- Allergy Research Center Zhejiang University Hangzhou China.,College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Kexin Gan
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Lan Zhao
- Allergy Research Center Zhejiang University Hangzhou China.,College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Huijuan Jia
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Yifan Zhu
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Xiongwei Li
- Forest & Fruit Tree Institute Shanghai Academy of Agricultural Sciences Shanghai China
| | - Zhaowei Yang
- State Key Laboratory of Respiratory Disease The First Affiliated Hospital of Guangzhou Medical University Guangzhou China
| | - Zhengwen Ye
- Forest & Fruit Tree Institute Shanghai Academy of Agricultural Sciences Shanghai China
| | - Ke Cao
- Zhengzhou Fruit Research Institute China Academy of Agricultural Sciences Zhengzhou China
| | - Zhiqiang Wang
- Zhengzhou Fruit Research Institute China Academy of Agricultural Sciences Zhengzhou China
| | - Mingliang Yu
- Fruit Tree Institute Jiangsu Academy of Agricultural Sciences Nanjing China
| | - Yuyan Zhang
- Fruit Tree Institute Jiangsu Academy of Agricultural Sciences Nanjing China
| | - Zhisheng Ma
- Shijiazhuang Pomology Institute Hebei Academy of Agriculture and Forestry Sciences Shijiazhuang Hebei China
| | - Hangkong Liu
- College of Horticulture Northwest A&F University Yangling Shaanxi China
| | - Pere Arús
- IRTA Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB Campus UAB - Edifici CRAG Barcelona Spain
| | - Jaap H Akkerdaas
- Departments of Experimental Immunology and Otorhinolaryngology Amsterdam UMC University of Amsterdam Amsterdam The Netherlands
| | - Zhongshan Gao
- Allergy Research Center Zhejiang University Hangzhou China.,College of Agriculture and Biotechnology Zhejiang University Hangzhou China.,Departments of Experimental Immunology and Otorhinolaryngology Amsterdam UMC University of Amsterdam Amsterdam The Netherlands
| | - Ronald van Ree
- Departments of Experimental Immunology and Otorhinolaryngology Amsterdam UMC University of Amsterdam Amsterdam The Netherlands
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Li Y, Cao K, Li N, Zhu G, Fang W, Chen C, Wang X, Guo J, Wang Q, Ding T, Wang J, Guan L, Wang J, Liu K, Guo W, Arús P, Huang S, Fei Z, Wang L. Genomic analyses provide insights into peach local adaptation and responses to climate change. Genome Res 2021; 31:592-606. [PMID: 33687945 PMCID: PMC8015852 DOI: 10.1101/gr.261032.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 01/25/2021] [Indexed: 01/30/2023]
Abstract
The environment has constantly shaped plant genomes, but the genetic bases underlying how plants adapt to environmental influences remain largely unknown. We constructed a high-density genomic variation map of 263 geographically representative peach landraces and wild relatives. A combination of whole-genome selection scans and genome-wide environmental association studies (GWEAS) was performed to reveal the genomic bases of peach adaptation to diverse climates. A total of 2092 selective sweeps that underlie local adaptation to both mild and extreme climates were identified, including 339 sweeps conferring genomic pattern of adaptation to high altitudes. Using genome-wide environmental association studies (GWEAS), a total of 2755 genomic loci strongly associated with 51 specific environmental variables were detected. The molecular mechanism underlying adaptive evolution of high drought, strong UVB, cold hardiness, sugar content, flesh color, and bloom date were revealed. Finally, based on 30 yr of observation, a candidate gene associated with bloom date advance, representing peach responses to global warming, was identified. Collectively, our study provides insights into molecular bases of how environments have shaped peach genomes by natural selection and adds candidate genes for future studies on evolutionary genetics, adaptation to climate changes, and breeding.
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Affiliation(s)
- Yong Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430000, China
| | - Ke Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Nan Li
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Gengrui Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Weichao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Changwen Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Xinwei Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jian Guo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Qi Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Tiyu Ding
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jiao Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Liping Guan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Junxiu Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Kuozhan Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Wenwu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430000, China
| | - Pere Arús
- IRTA-Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB-UB), Barcelona 08193, Spain
| | - Sanwen Huang
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA.,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Lirong Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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9
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Pérez de Los Cobos F, Martínez-García PJ, Romero A, Miarnau X, Eduardo I, Howad W, Mnejja M, Dicenta F, Socias I Company R, Rubio-Cabetas MJ, Gradziel TM, Wirthensohn M, Duval H, Holland D, Arús P, Vargas FJ, Batlle I. Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars. Hortic Res 2021; 8:11. [PMID: 33384415 PMCID: PMC7775440 DOI: 10.1038/s41438-020-00444-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/04/2020] [Accepted: 11/13/2020] [Indexed: 05/16/2023]
Abstract
Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: "Tuono", "Cristomorto", and "Nonpareil". Descendants from "Tuono" or "Cristomorto" number 76 (sharing 34 descendants), while "Nonpareil" has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.125, with "Tuono" as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.
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Affiliation(s)
- Felipe Pérez de Los Cobos
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120, Constantí, Tarragona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Pedro J Martínez-García
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), P.O. Box 164, 30100, Espinardo, Murcia, Spain
| | - Agustí Romero
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120, Constantí, Tarragona, Spain
| | - Xavier Miarnau
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Fruitcentre, PCiTAL, Gardeny Park, Fruitcentre Building, 25003, Lleida, Spain
| | - Iban Eduardo
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Werner Howad
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Mourad Mnejja
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Federico Dicenta
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), P.O. Box 164, 30100, Espinardo, Murcia, Spain
| | - Rafel Socias I Company
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059, Zaragoza, Instituto Agroalimentario de Aragón IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Maria J Rubio-Cabetas
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059, Zaragoza, Instituto Agroalimentario de Aragón IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | | | - Michelle Wirthensohn
- University of Adelaide, Waite Research, School of Agriculture, Food and Wine, PMB 1, Glen Osmond, Adelaide, SA, 5064, Australia
| | - Henri Duval
- Institut National de la Recherche Agronomique (INRA), Domain St. Maurice CS 60094, 84143, Montfavet Cedex, France
| | - Doron Holland
- Agricultural Research Organization, Newe-Ya'ar Research Center, P.O. Box 1021, Ramat Yishad, 30095, Israel
| | - Pere Arús
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Francisco J Vargas
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120, Constantí, Tarragona, Spain
| | - Ignasi Batlle
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120, Constantí, Tarragona, Spain.
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10
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Marimon N, Luque J, Arús P, Eduardo I. Fine mapping and identification of candidate genes for the peach powdery mildew resistance gene Vr3. Hortic Res 2020; 7:175. [PMID: 33328431 PMCID: PMC7603514 DOI: 10.1038/s41438-020-00396-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/18/2020] [Accepted: 08/30/2020] [Indexed: 06/12/2023]
Abstract
Powdery mildew is one of the major diseases of peach (Prunus persica), caused by the ascomycete Podosphaera pannosa. Currently, it is controlled through calendar-based fungicide treatments starting at petal fall, but an alternative is to develop resistant peach varieties. Previous studies mapped a resistance gene (Vr3) in interspecific populations between almond ('Texas') and peach ('Earlygold'). To obtain molecular markers highly linked to Vr3 and to reduce the number of candidate genes, we fine-mapped Vr3 to a genomic region of 270 kb with 27 annotated genes. To find evidence supporting one of these positional candidate genes as being responsible of Vr3, we analyzed the polymorphisms of the resequences of both parents and used near-isogenic lines (NILs) for expression analysis of the positional candidate genes in symptomatic or asymptomatic leaves. Genes differentially expressed between resistant and susceptible individuals were annotated as a Disease Resistance Protein RGA2 (Prupe2G111700) or an Eceriferum 1 protein involved in epicuticular wax biosynthesis (Prupe2G112800). Only Prupe2G111700 contained a variant predicted to have a disruptive effect on the encoded protein, and was overexpressed in both heterozygous and homozygous individuals containing the Vr3 almond allele, compared with susceptible individuals. This information was also useful to identify and validate molecular markers tightly linked and flanking Vr3. In addition, the NILs used in this work will facilitate the introgression of this gene into peach elite materials, alone or pyramided with other known resistance genes such as peach powdery mildew resistance gene Vr2.
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Grants
- RTA2015-00050-00-00 Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)
- RTA2013-00004-C03-01 Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)
- RTA2013-00004-C03-01 Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)
- RTA2015-00050-00-00 Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)
- COTPA-FRUIT3CAT Generalitat de Catalunya (Government of Catalonia)
- SEV-2015-0533 Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)
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Affiliation(s)
- Neus Marimon
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Plant Pathology, IRTA Cabrils, Carretera de Cabrils km 2, 08348, Cabrils, Spain
| | - Jordi Luque
- Plant Pathology, IRTA Cabrils, Carretera de Cabrils km 2, 08348, Cabrils, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
| | - Iban Eduardo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain.
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain.
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11
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Cirilli M, Micali S, Aranzana MJ, Arús P, Babini A, Barreneche T, Bink M, Cantin CM, Ciacciulli A, Cos-Terrer JE, Drogoudi P, Eduardo I, Foschi S, Giovannini D, Guerra W, Liverani A, Pacheco I, Pascal T, Quilot-Turion B, Verde I, Rossini L, Bassi D. The Multisite PeachRefPop Collection: A True Cultural Heritage and International Scientific Tool for Fruit Trees. Plant Physiol 2020; 184:632-646. [PMID: 32727910 PMCID: PMC7536698 DOI: 10.1104/pp.19.01412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/17/2020] [Indexed: 05/21/2023]
Abstract
Plants have evolved a range of adaptive mechanisms that adjust their development and physiology to variable external conditions, particularly in perennial species subjected to long-term interplay with the environment. Exploiting the allelic diversity within available germplasm and leveraging the knowledge of the mechanisms regulating genotype interaction with the environment are crucial to address climatic challenges and assist the breeding of novel cultivars with improved resilience. The development of multisite collections is of utmost importance for the conservation and utilization of genetic materials and will greatly facilitate the dissection of genotype-by-environment interaction. Such resources are still lacking for perennial trees, especially with the intrinsic difficulties of successful propagation, material exchange, and living collection maintenance. This work describes the concept, design, and realization of the first multisite peach (Prunus persica) reference collection (PeachRefPop) located across different European countries and sharing the same experimental design. Other than an invaluable tool for scientific studies in perennial species, PeachRefPop provides a milestone in an international collaborative project for the conservation and exploitation of European peach germplasm resources and, ultimately, as a true heritage for future generations.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
| | - Sabrina Micali
- Consiglio Per La Ricerca In Agricoltura E L'analisi Dell'Economia Agraria, Research Centre for Olive, Fruit, and Citrus Crops, 00134 Rome, Italy
| | - Maria José Aranzana
- Institut de Recerca i Tecnologia Agroalimentàries, Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas, Institut de Recerca i Tecnologia Agroalimentàries, Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus UAB, 08193 Barcelona, Spain
| | - Pere Arús
- Institut de Recerca i Tecnologia Agroalimentàries, Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas, Institut de Recerca i Tecnologia Agroalimentàries, Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus UAB, 08193 Barcelona, Spain
| | - Annarosa Babini
- Phytosanitary Service, Regione Emilia-Romagna, 40128 Bologna, Italy
| | - Teresa Barreneche
- Université de Bordeaux, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Marco Bink
- Hendrix Genetics Research, Technology, and Services, 5830 AC Boxmeer, The Netherlands
| | - Celia M Cantin
- Institut de Recerca i Tecnologia Agroalimentàries, Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas, Institut de Recerca i Tecnologia Agroalimentàries, Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus UAB, 08193 Barcelona, Spain
| | - Angelo Ciacciulli
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
| | | | - Pavlina Drogoudi
- Hellenic Agricultural Organization 'Demeter', Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, 59200 Naoussa, Greece
| | - Iban Eduardo
- Institut de Recerca i Tecnologia Agroalimentàries, Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas, Institut de Recerca i Tecnologia Agroalimentàries, Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus UAB, 08193 Barcelona, Spain
| | - Stefano Foschi
- Centro Ricerche Produzioni Vegetali, 47522 Cesena, Italy
| | - Daniela Giovannini
- Consiglio per la Ricerca in Agricoltura e L'Analisi Del'Economia Agraria, Research Centre for Olive, Fruit, and Citrus Crops, 47121 Forlì, Italy
| | | | - Alessandro Liverani
- Consiglio per la Ricerca in Agricoltura e L'Analisi Del'Economia Agraria, Research Centre for Olive, Fruit, and Citrus Crops, 47121 Forlì, Italy
| | - Igor Pacheco
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, 7830490 Macul, Chile
| | - Thierry Pascal
- Institut National de Recherche pour L'Agriculture, L'Alimentation et L'Environnement, Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | - Benedicte Quilot-Turion
- Institut National de Recherche pour L'Agriculture, L'Alimentation et L'Environnement, Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | - Ignazio Verde
- Consiglio Per La Ricerca In Agricoltura E L'analisi Dell'Economia Agraria, Research Centre for Olive, Fruit, and Citrus Crops, 00134 Rome, Italy
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
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12
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Eduardo I, Alegre S, Alexiou KG, Arús P. Resynthesis: Marker-Based Partial Reconstruction of Elite Genotypes in Clonally-Reproducing Plant Species. Front Plant Sci 2020; 11:1205. [PMID: 32849747 PMCID: PMC7427350 DOI: 10.3389/fpls.2020.01205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/24/2020] [Indexed: 06/02/2023]
Abstract
We propose a method for marker-based selection of cultivars of clonally-reproducing plant species which keeps the basic genetic architecture of a top-performing cultivar (usually a partly heterozygous genotype), with the addition of some agronomically relevant differences (such as production time, product appearance or quality), providing added value to the product or cultivation process. The method is based on selecting a) two complementary nearly-inbred lines from successive selfing generations (ideally only F2 and F3) of large size, that may generate individuals with most of their genome identical to the original cultivar but being homozygous for either of the two component haplotypes in the rest, and b) individuals with such characteristics already occurring in the F2. Option a) allows for introgressing genes from other individuals in one or both of these nearly-inbred lines. Peach, a woody-perennial, clonally-reproduced species, was chosen as a model for a proof of concept of the Resynthesis process due to its biological characteristics: self-compatibility, compact and genetically well-known genome, low recombination rates and relatively short intergeneration time (3-4 years). From 416 F2 seedlings from cultivar Sweet Dream (SD), we obtained seven individuals with 76-94% identity with SD, and selected five pairs of complementary lines with average homozygosity of the two parents ≥0.70 such that crossing would produce some individuals highly similar to SD. The application of this scheme to other species with more complex genomes or biological features, including its generalization to F1 hybrids, is discussed.
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Affiliation(s)
- Iban Eduardo
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | - Simó Alegre
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Parc Científic i Tecnològic Agroalimentari de Lleida, Lleida, Spain
| | - Konstantinos G. Alexiou
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | - Pere Arús
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
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13
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Jin J, Gao L, Zhao L, Gao Z, Li X, Xie H, Ni J, Gan K, Wu S, Ye Z, Luo J, Cao K, Ma R, Chen M, Arús P, Versteeg SA, Wang H, Liu ML, Jia H, Ree R. Selection of Pru p 3 hypoallergenic peach and nectarine varieties. Allergy 2020; 75:1256-1260. [PMID: 31710093 DOI: 10.1111/all.14102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/22/2019] [Accepted: 10/27/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Jing Jin
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Ling Gao
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Lan Zhao
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Zhong‐shan Gao
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
- Allergy Research Center Zhejiang University Hangzhou China
- Departments of Experimental Immunology and of Otorhinolaryngology Amsterdam UMC University of Amsterdam Amsterdam the Netherlands
| | - Xiong‐wei Li
- Forest & Fruit Tree Institute Shanghai Academy of Agricultural Sciences Shanghai China
| | - Han‐bing Xie
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Jun‐bei Ni
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Ke‐xin Gan
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Shan‐dong Wu
- Allergy Research Center Zhejiang University Hangzhou China
| | - Zheng‐wen Ye
- Forest & Fruit Tree Institute Shanghai Academy of Agricultural Sciences Shanghai China
| | - Jun Luo
- Forest & Fruit Tree Institute Shanghai Academy of Agricultural Sciences Shanghai China
| | - Ke Cao
- Zhengzhou Fruit Research Institute China Academy of Agricultural Sciences Zhengzhou China
| | - Rui‐juan Ma
- Horticultural Institute Jiangsu Academy of Agricultural Sciences Nanjing China
| | | | - Pere Arús
- IRTA Centre de Recerca en Agrigenòmica CSIC‐IRTA‐UAB‐UB, Campus UAB – Edifici CRAG Cerdanyola del Vallès (Bellaterra) Barcelona Spain
| | - Serge A. Versteeg
- Departments of Experimental Immunology and of Otorhinolaryngology Amsterdam UMC University of Amsterdam Amsterdam the Netherlands
| | - Hui‐ying Wang
- Department of Allergy the Second Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Mei-ling Liu
- Department of Allergy The Third People’s Hospital of Datong Datong China
| | - Hui‐juan Jia
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Ronald Ree
- Departments of Experimental Immunology and of Otorhinolaryngology Amsterdam UMC University of Amsterdam Amsterdam the Netherlands
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14
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Alioto T, Alexiou KG, Bardil A, Barteri F, Castanera R, Cruz F, Dhingra A, Duval H, Fernández i Martí Á, Frias L, Galán B, García JL, Howad W, Gómez‐Garrido J, Gut M, Julca I, Morata J, Puigdomènech P, Ribeca P, Rubio Cabetas MJ, Vlasova A, Wirthensohn M, Garcia‐Mas J, Gabaldón T, Casacuberta JM, Arús P. Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. Plant J 2020; 101:455-472. [PMID: 31529539 PMCID: PMC7004133 DOI: 10.1111/tpj.14538] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 05/19/2023]
Abstract
We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. Transposable elements may also be at the origin of important phenotypic differences between both species, and in particular for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.
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Affiliation(s)
- Tyler Alioto
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Konstantinos G. Alexiou
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Amélie Bardil
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Fabio Barteri
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Fernando Cruz
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Amit Dhingra
- Department of HorticultureWashington State University99164-6414PullmanWAUSA
| | - Henri Duval
- INRA, UR1052Unité de Génétique et Amélioration des Fruits et Légumes (GAFL)Domaine St. Maurice CS 6009484143Montfavet CedexFrance
| | - Ángel Fernández i Martí
- Department of Environmental Science Policy and ManagementUniversity of CaliforniaBerkeley94720CAUSA
- Innovative Genomics Institute (IGI)94720BerkeleyCAUSA
| | - Leonor Frias
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Beatriz Galán
- Department of Environmental BiologyCenter for Biological Research (CIB‐CSIC)Spanish National Research Council (CSIC)Ramiro de Maeztu 928040MadridSpain
| | - José L. García
- Department of Environmental BiologyCenter for Biological Research (CIB‐CSIC)Spanish National Research Council (CSIC)Ramiro de Maeztu 928040MadridSpain
| | - Werner Howad
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Jèssica Gómez‐Garrido
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Marta Gut
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Irene Julca
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
| | - Jordi Morata
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Pere Puigdomènech
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Paolo Ribeca
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- The Pirbright InstituteWokingSurreyGU24 0NFUK
| | - María J. Rubio Cabetas
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA)Unidad de HortofruticulturaGobierno de Aragón, Avda. Montañana 93050059ZaragozaSpain
- Instituto Agroalimentario de Aragón – IA2 (CITA‐Universidad de Zaragoza)Calle Miguel Servet 17750013ZaragozaSpain
| | - Anna Vlasova
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
| | - Michelle Wirthensohn
- University of AdelaideWaite Research InstituteSchool of Agriculture, Food and WinePMB 1Glen OsmondSA5064Australia
| | - Jordi Garcia‐Mas
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Toni Gabaldón
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Pg Lluís Companys 2308010BarcelonaSpain
| | - Josep M. Casacuberta
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Pere Arús
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
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Baró-Montel N, Eduardo I, Usall J, Casals C, Arús P, Teixidó N, Torres R. Exploring sources of resistance to brown rot in an interspecific almond × peach population. J Sci Food Agric 2019; 99:4105-4113. [PMID: 30784078 DOI: 10.1002/jsfa.9640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/29/2019] [Accepted: 02/11/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Monilinia spp. are responsible for brown rot, one of the most significant stone fruit diseases. Planting resistant cultivars seems a promising alternative, although most commercial cultivars are susceptible to brown rot. The aim of this study was to explore resistance to Monilinia fructicola over two seasons in a backcross one interspecific population between almond 'Texas' and peach 'Earlygold' (named T1E). RESULTS 'Texas' almond was resistant to brown rot inoculation, whereas peach was highly susceptible. Phenotypic data from the T1E population indicated wide differences in response to M. fructicola. Additionally, several non-wounded individuals exhibited resistance to brown rot. Quantitative trait loci (QTLs) were identified in several linkage groups, but only two proximal QTLs in G4 were detected over both seasons and accounted for 11.3-16.2% of the phenotypic variation. CONCLUSION Analysis of the progeny allowed the identification of resistant genotypes that could serve as a source of resistance in peach breeding programs. The finding of loci associated with brown rot resistance would shed light on implementing a strategy based on marker-assisted selection (MAS) for introgression of this trait into elite peach materials. New peach cultivars resistant to brown rot may contribute to the implementation of more sustainable crop protection strategies. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Núria Baró-Montel
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Josep Usall
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| | - Carla Casals
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Neus Teixidó
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| | - Rosario Torres
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
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16
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Carrasco-Valenzuela T, Muñoz-Espinoza C, Riveros A, Pedreschi R, Arús P, Campos-Vargas R, Meneses C. Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [ Prunus persica (L.) Batsch]. Front Plant Sci 2019; 10:1581. [PMID: 31850046 PMCID: PMC6901599 DOI: 10.3389/fpls.2019.01581] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/12/2019] [Indexed: 05/22/2023]
Abstract
Significant differences in softening rate have been reported between melting flesh in peach and nectarine varieties. This trait seems to be controlled by several genes. We aimed to identify candidate genes involved in fruit softening rate by integrating quantitative trait loci (QTL) and expression QTL (eQTL) analyses, comparing siblings with contrasting softening rates. We used a segregating population derived from nectarine cv. 'Venus' selfing, which was phenotyped for softening rate during three seasons. Six siblings with high (HSR) and six with low softening rate (LSR) were sequenced using RNA-Seq. A group of 5,041 differentially expressed genes was identified. Also, we found a QTL with a LOD (logarithm of odds) score of 9.7 on LG4 in all analyzed seasons. Furthermore, we detected 1,062 eQTLs, of which 133 were found co-localizing with the identified QTL. Gene Ontology (GO) analysis showed 'Response to auxin' as one the main over-represented categories. Our findings suggest over-expression of auxin biosynthetic related genes in the HSR group, which implies a higher expression and/or accumulation of auxin, thereby triggering fast softening. Conversely, the LSR phenotype might be explained by an altered auxin-homeostasis associated with low auxin levels. This work will contribute to unraveling the genetic mechanisms responsible for the softening rate in peaches and nectarines and lead to the development of molecular markers.
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Affiliation(s)
- Tomás Carrasco-Valenzuela
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Claudia Muñoz-Espinoza
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Aníbal Riveros
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Romina Pedreschi
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Quillota, Chile
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB-UB), Barcelona, Spain
| | - Reinaldo Campos-Vargas
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Santiago, Chile
- *Correspondence: Claudio Meneses,
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17
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Aranzana MJ, Decroocq V, Dirlewanger E, Eduardo I, Gao ZS, Gasic K, Iezzoni A, Jung S, Peace C, Prieto H, Tao R, Verde I, Abbott AG, Arús P. Prunus genetics and applications after de novo genome sequencing: achievements and prospects. Hortic Res 2019; 6:58. [PMID: 30962943 PMCID: PMC6450939 DOI: 10.1038/s41438-019-0140-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 05/04/2023]
Abstract
Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of Prunus genome evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement. Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.
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Affiliation(s)
- Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Véronique Decroocq
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Elisabeth Dirlewanger
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Zhong Shan Gao
- Allergy Research Center, Zhejiang University, 310058 Hangzhou, China
| | | | - Amy Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824-1325 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Research Station, Instituto de Investigaciones Agropecuarias, Santa Rosa, 11610 La Pintana, Santiago Chile
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) – Centro di ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Rome, Italy
| | - Albert G. Abbott
- University of Kentucky, 106 T. P. Cooper Hall, Lexington, KY 40546-0073 USA
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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18
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da Silva Linge C, Antanaviciute L, Abdelghafar A, Arús P, Bassi D, Rossini L, Ficklin S, Gasic K. High-density multi-population consensus genetic linkage map for peach. PLoS One 2018; 13:e0207724. [PMID: 30462743 PMCID: PMC6248993 DOI: 10.1371/journal.pone.0207724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/04/2018] [Indexed: 11/19/2022] Open
Abstract
Highly saturated genetic linkage maps are extremely helpful to breeders and are an essential prerequisite for many biological applications such as the identification of marker-trait associations, mapping quantitative trait loci (QTL), candidate gene identification, development of molecular markers for marker-assisted selection (MAS) and comparative genetic studies. Several high-density genetic maps, constructed using the 9K SNP peach array, are available for peach. However, each of these maps is based on a single mapping population and has limited use for QTL discovery and comparative studies. A consensus genetic linkage map developed from multiple populations provides not only a higher marker density and a greater genome coverage when compared to the individual maps, but also serves as a valuable tool for estimating genetic positions of unmapped markers. In this study, a previously developed linkage map from the cross between two peach cultivars 'Zin Dai' and 'Crimson Lady' (ZC2) was improved by genotyping additional progenies. In addition, a peach consensus map was developed based on the combination of the improved ZC2 genetic linkage map with three existing high-density genetic maps of peach and a reference map of Prunus. A total of 1,476 SNPs representing 351 unique marker positions were mapped across eight linkage groups on the ZC2 genetic map. The ZC2 linkage map spans 483.3 cM with an average distance between markers of 1.38 cM/marker. The MergeMap and LPmerge tools were used for the construction of a consensus map based on markers shared across five genetic linkage maps. The consensus linkage map contains a total of 3,092 molecular markers, consisting of 2,975 SNPs, 116 SSRs and 1 morphological marker associated with slow ripening in peach (SR). The consensus map provides valuable information on marker order and genetic position for QTL identification in peach and other genetic studies within Prunus and Rosaceae.
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Affiliation(s)
- Cassia da Silva Linge
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
| | - Laima Antanaviciute
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
| | - Asma Abdelghafar
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
| | - Pere Arús
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas (CSIC)-IRTA–Universitat Autònoma de Barcelona (UAB)–University of Barcelona (UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Daniele Bassi
- Università degli Studi di Milano, Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Milan, Italy
| | - Laura Rossini
- Università degli Studi di Milano, Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Milan, Italy
| | - Stephen Ficklin
- Washington State University, Department of Horticulture, Pullman, WA, United States of America
| | - Ksenija Gasic
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
- * E-mail:
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19
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Cantín CM, Arús P, Eduardo I. Identification of a new allele of the Dw gene causing brachytic dwarfing in peach. BMC Res Notes 2018; 11:386. [PMID: 29898773 PMCID: PMC6000960 DOI: 10.1186/s13104-018-3490-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/05/2018] [Indexed: 12/04/2022] Open
Abstract
Objective Peach brachytic dwarfism determined by Dwarf gene (Dw) is an undesired trait segregating in some peach breeding programs. Recently, a single nucleotide polymorphism (SNP) mutation in the gibberellin insensitive dwarf 1 (GID1) peach gene causing brachytic dwarfism was described. In this research we wanted to validate this marker in an F2 population of the ‘Nectavantop’ peach cultivar (Nv) to include it as a marker assisted selection tool for peach breeding programs. Results The observed segregation of the trait was in agreement with that of a recessive gene, the individuals homozygous for the recessive allele (dwdw) presenting the dwarf genotype. Dw was mapped to the distal part of linkage group 6 as previously described. The SNP marker based on the causal mutation previously described did not segregate in Nv F2 population. The sequence of the GID1c gene in Nv revealed a second SNP in its coding sequence which cosegregated with the dwarf phenotype. This SNP was predicted by the SNAP2 software to cause a major functional change and was validated in the dwarf peach cultivar ‘Small sunning’. These results suggest the existence of at least two independent mutations of the Dw gene causing the peach brachytic dwarf phenotype. Electronic supplementary material The online version of this article (10.1186/s13104-018-3490-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Celia M Cantín
- IRTA, FruitCentre, Parc Científic i Tecnològic Agroalimentari de Lleida (PCiTAL), Edifici Fruitcentre, Parc de Gardeny, 25003, Lleida, Spain
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain.
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20
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López-Girona E, Zhang Y, Eduardo I, Mora JRH, Alexiou KG, Arús P, Aranzana MJ. A deletion affecting an LRR-RLK gene co-segregates with the fruit flat shape trait in peach. Sci Rep 2017; 7:6714. [PMID: 28751691 PMCID: PMC5532255 DOI: 10.1038/s41598-017-07022-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/20/2017] [Indexed: 01/01/2023] Open
Abstract
In peach, the flat phenotype is caused by a partially dominant allele in heterozygosis (Ss), fruits from homozygous trees (SS) abort a few weeks after fruit setting. Previous research has identified a SSR marker (UDP98-412) highly associated with the trait, found suitable for marker assisted selection (MAS). Here we report a ∼10 Kb deletion affecting the gene PRUPE.6G281100, 400 Kb upstream of UDP98-412, co-segregating with the trait. This gene is a leucine-rich repeat receptor-like kinase (LRR-RLK) orthologous to the Brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1) group. PCR markers suitable for MAS confirmed its strong association with the trait in a collection of 246 cultivars. They were used to evaluate the DNA from a round fruit derived from a somatic mutation of the flat variety 'UFO-4', revealing that the mutation affected the flat associated allele (S). Protein BLAST alignment identified significant hits with genes involved in different biological processes. Best protein hit occurred with AtRLP12, which may functionally complement CLAVATA2, a key regulator that controls the stem cell population size. RT-PCR analysis revealed the absence of transcription of the partially deleted allele. The data support PRUPE.6G281100 as a candidate gene for flat shape in peach.
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Affiliation(s)
- Elena López-Girona
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
| | - Yu Zhang
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Iban Eduardo
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
| | | | | | - Pere Arús
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
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21
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Hernández Mora JR, Micheletti D, Bink M, Van de Weg E, Cantín C, Nazzicari N, Caprera A, Dettori MT, Micali S, Banchi E, Campoy JA, Dirlewanger E, Lambert P, Pascal T, Troggio M, Bassi D, Rossini L, Verde I, Quilot-Turion B, Laurens F, Arús P, Aranzana MJ. Integrated QTL detection for key breeding traits in multiple peach progenies. BMC Genomics 2017; 18:404. [PMID: 28583082 PMCID: PMC5460339 DOI: 10.1186/s12864-017-3783-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/10/2017] [Indexed: 01/23/2023] Open
Abstract
Background Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability. Results Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A total of 1467 plants from these progenies were genotyped with a 9 k SNP array. Forty-seven QTLs were identified, 22 coinciding with major genes and QTLs that have been consistently found in the same populations when studied individually and 25 were new. A substantial part of the QTLs observed (47%) would not have been detected in crosses between only commercial materials, showing the high value of exotic lines as a source of novel alleles for the commercial gene pool. Our strategy also provided estimations on the narrow sense heritability of each character, and the estimation of the QTL genotypes of each parent for the different QTLs and their breeding value. Conclusions The integrated strategy used provides a broader and more accurate picture of the variability available for peach breeding with the identification of many new QTLs, information on the sources of the alleles of interest and the breeding values of the potential donors of such valuable alleles. These results are first-hand information for breeders and a step forward towards the implementation of DNA-informed strategies to facilitate selection of new cultivars with improved productivity and quality. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3783-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José R Hernández Mora
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193, Barcelona, Spain
| | - Diego Micheletti
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | - Marco Bink
- Hendrix Genetics Research, Technology & Services B.V., P.O. Box 114, 5830AC, Boxmeer, The Netherlands
| | - Eric Van de Weg
- Plant Breeding, Wageningen University and Research Droevendaalsesteeg 1, P.O. Box 386, 6700AJ, Wageningen, The Netherlands
| | - Celia Cantín
- IRTA, FruitCentreParc Cientific i Tecnològic Agroalimentari de Lleida (PCiTAL), Lleida, Spain
| | - Nelson Nazzicari
- PTP Science Park, Via Einstein, 26900, Lodi, Italy.,Council for Agricultural Research and Economics (CREA) Research Centre for Fodder Crops and Dairy Productions, Lodi, Italy
| | | | - Maria Teresa Dettori
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria (CREA) - Centro di Ricerca per la Frutticoltura, 00134, Roma, Italy
| | - Sabrina Micali
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria (CREA) - Centro di Ricerca per la Frutticoltura, 00134, Roma, Italy
| | - Elisa Banchi
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | | | | | | | | | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | - Daniele Bassi
- Università degli Studi di Milano, DiSAA, Via Celoria 2, 20133, Milan, Italy
| | - Laura Rossini
- PTP Science Park, Via Einstein, 26900, Lodi, Italy.,Università degli Studi di Milano, DiSAA, Via Celoria 2, 20133, Milan, Italy
| | - Ignazio Verde
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria (CREA) - Centro di Ricerca per la Frutticoltura, 00134, Roma, Italy
| | | | | | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193, Barcelona, Spain
| | - Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193, Barcelona, Spain.
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22
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Biscarini F, Nazzicari N, Bink M, Arús P, Aranzana MJ, Verde I, Micali S, Pascal T, Quilot-Turion B, Lambert P, da Silva Linge C, Pacheco I, Bassi D, Stella A, Rossini L. Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies. BMC Genomics 2017; 18:432. [PMID: 28583089 PMCID: PMC5460546 DOI: 10.1186/s12864-017-3781-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/10/2017] [Indexed: 11/16/2022] Open
Abstract
Background Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach. Results A repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented. The analysis included 1147 individuals derived from both commercial and non-commercial peach or peach-related accessions. Considered traits were average fruit weight (FW), sugar content (SC) and titratable acidity (TA). Plants were genotyped with the 9K IPSC array, grown in three countries (France, Italy, Spain) and phenotyped for 3–5 years. An analysis of imputation accuracy of missing genotypic data was conducted using the software Beagle, showing that two of the eleven populations were highly sensitive to increasing levels of missing data. The regression model produced, for each trait and each population, estimates of heritability (FW:0.35, SC:0.48, TA:0.53, on average) and repeatability (FW:0.56, SC:0.63, TA:0.62, on average). Predictive ability was estimated in a five-fold cross validation scheme within population as the correlation of true and predicted phenotypes. Results differed by populations and traits, but predictive abilities were in general high (FW:0.60, SC:0.72, TA:0.65, on average). Conclusions This study assessed the feasibility of Genomic Selection in peach for highly polygenic traits linked to yield and fruit quality. The accuracy of imputing missing genotypes was as high as 96%, and the genomic predictive ability was on average 0.65, but could be as high as 0.84 for fruit weight or 0.83 for titratable acidity. The estimated repeatability may prove very useful in the management of the typical long cycles involved in peach productions. All together, these results are very promising for the application of genomic selection to peach breeding programmes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3781-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Filippo Biscarini
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy.,IBBA-CNR, Via Edoardo Bassini, 15, Milan, 20133, Italy
| | - Nelson Nazzicari
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy.,Council for Agricultural Research and Economics (CREA) Research Centre for Fodder Crops and Dairy Productions, Lodi, Italy
| | - Marco Bink
- Wageningen UR Biometris, Wageningen, The Netherlands.,Present Address: Hendrix Genetics Research, Technology & Services B.V., P.O. Box 114, Boxmeer NL, 5830AC, The Netherlands
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Centro di Ricerca per la Frutticoltura (CREA-FRU), Via di Fioranello 52, Roma, Italy
| | - Sabrina Micali
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Centro di Ricerca per la Frutticoltura (CREA-FRU), Via di Fioranello 52, Roma, Italy
| | | | | | - Patrick Lambert
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milano, Italy
| | | | - Igor Pacheco
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milano, Italy.,Institute of Nutrition and Food Technology - INTA, Universidad de Chile, Av El Líbano 5524, Santiago, Chile
| | - Daniele Bassi
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milano, Italy
| | - Alessandra Stella
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy.,IBBA-CNR, Via Edoardo Bassini, 15, Milan, 20133, Italy
| | - Laura Rossini
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy. .,Università degli Studi di Milano - DiSAA, Via Celoria 2, Milano, Italy.
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23
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Di Guardo M, Micheletti D, Bianco L, Koehorst-van Putten HJJ, Longhi S, Costa F, Aranzana MJ, Velasco R, Arús P, Troggio M, van de Weg EW. ASSIsT: an automatic SNP scoring tool for in- and outbreeding species. Bioinformatics 2015; 31:3873-4. [PMID: 26249809 PMCID: PMC4653386 DOI: 10.1093/bioinformatics/btv446] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/25/2015] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio (GS). ASSIsT builds on GS-derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker-trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux. AVAILABILITY AND IMPLEMENTATION The software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/. CONTACT eric.vandeweg@wur.nl.
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Affiliation(s)
- Mario Di Guardo
- Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy, Graduate School Experimental Plant Sciences, Wageningen University, 6700 AJ Wageningen, The Netherlands and
| | - Diego Micheletti
- Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy, Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands
| | - Luca Bianco
- Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | | | - Sara Longhi
- Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands
| | - Fabrizio Costa
- Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Maria J Aranzana
- IRTA, Centre de Recerca en Agrigenómica CSIC-IRTA-UAB, Beellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenómica CSIC-IRTA-UAB, Beellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
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24
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Urrutia M, Bonet J, Arús P, Monfort A. A near-isogenic line (NIL) collection in diploid strawberry and its use in the genetic analysis of morphologic, phenotypic and nutritional characters. Theor Appl Genet 2015; 128:1261-1275. [PMID: 25841354 DOI: 10.1007/s00122-015-2503-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 03/20/2015] [Indexed: 06/04/2023]
Abstract
First near-isogenic line collection in diploid strawberry, a tool for morphologic, phenotypic and nutritional QTL analysis. Diploid strawberry (Fragaria vesca), with a small genome, has a high degree of synteny with the octoploid cultivated strawberry (F. × ananassa), so can be used as a simplified model for genetic analysis of the octoploid species. Agronomically interesting traits are usually inherited quantitatively and they need to be studied in large segregating progenies well characterized with molecular markers. Near-isogenic lines (NILs) are tools to dissect quantitative characters and identify some of their components as Mendelian traits. NILs are fixed homozygous lines that share the same genetic background from a recurrent parent with a single introgression region from a donor parent. Here, we developed the first NIL collection in Fragaria, with F. vesca cv. Reine des Vallées as the recurrent parent and F. bucharica as the donor parent. A collection of 39 NILs was identified using a set of single sequence repeat markers. The NILs had an average introgression of 32 cM (6 % of genome) and were phenotyped over several years in two locations. This collection segregates for agronomic characters, such as flowering, germination, fruit size and shape, and nutritional content. At least 16 QTLs for morphological and reproductive traits, such as round fruits and vegetative propagation, and seven for nutritional traits such as sugar composition and total polyphenol content, were identified. The NIL collection of F. vesca can significantly facilitate understanding of the genetics of many traits and provide insight into the more complex F. × ananassa genome.
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Affiliation(s)
- María Urrutia
- IRTA, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Bellaterra, Barcelona, Spain
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25
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Micheletti D, Dettori MT, Micali S, Aramini V, Pacheco I, Da Silva Linge C, Foschi S, Banchi E, Barreneche T, Quilot-Turion B, Lambert P, Pascal T, Iglesias I, Carbó J, Wang LR, Ma RJ, Li XW, Gao ZS, Nazzicari N, Troggio M, Bassi D, Rossini L, Verde I, Laurens F, Arús P, Aranzana MJ. Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm. PLoS One 2015; 10:e0136803. [PMID: 26352671 PMCID: PMC4564248 DOI: 10.1371/journal.pone.0136803] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 08/07/2015] [Indexed: 12/24/2022] Open
Abstract
Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.
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Affiliation(s)
- Diego Micheletti
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Maria Teresa Dettori
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy
| | - Sabrina Micali
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy
| | - Valeria Aramini
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy
| | - Igor Pacheco
- Università degli Studi di Milano, DiSAA, Milan, Italy
| | | | | | - Elisa Banchi
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige (TN), Italy
| | - Teresa Barreneche
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d’Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d’Ornon, France
| | | | | | - Thierry Pascal
- INRA UR1052 GAFL, Domaine Saint Maurice, Montfavet, France
| | - Ignasi Iglesias
- IRTA, Estació Experimental de Lleida, Parc de Gardeny, Edifici Fruitcentre, Lleida, Spain
| | - Joaquim Carbó
- IRTA, Estacio Experimental Mas Badia, La Tallada d'Empordà, Girona, Spain
| | - Li-rong Wang
- Zhenzhou Fruit Research Institute, CAAS, Zhengzhou, China
| | - Rui-juan Ma
- Horticultural Institute, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiong-wei Li
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Zhong-shan Gao
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | | | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige (TN), Italy
| | - Daniele Bassi
- Università degli Studi di Milano, DiSAA, Milan, Italy
| | - Laura Rossini
- Università degli Studi di Milano, DiSAA, Milan, Italy
- Parco Tecnologico Padano, Lodi, Italy
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy
| | - François Laurens
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- * E-mail:
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Donoso JM, Eduardo I, Picañol R, Batlle I, Howad W, Aranzana MJ, Arús P. High-density mapping suggests cytoplasmic male sterility with two restorer genes in almond × peach progenies. Hortic Res 2015; 2:15016. [PMID: 26504569 PMCID: PMC4595988 DOI: 10.1038/hortres.2015.16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/09/2015] [Indexed: 05/18/2023]
Abstract
Peach (Prunus persica) and almond (Prunus dulcis) are two sexually compatible species that produce fertile offspring. Almond, a highly polymorphic species, is a potential source of new genes for peach that has a strongly eroded gene pool. Here we describe the genetics of a male sterile phenotype that segregated in two almond ('Texas') × peach ('Earlygold') progenies: an F2 (T×E) and a backcross one (T1E) to the 'Earlygold' parent. High-density maps were developed using a 9k peach SNP chip and 135 simple-sequence repeats. Three highly syntenic and collinear maps were obtained: one for the F2 (T×E) and two for the backcross, T1E (for the hybrid) and E (for 'Earlygold'). A major reduction of recombination was observed in the interspecific maps (T×E and T1E) compared to the intraspecific parent (E). The E map also had extensive monomorphic genomic regions suggesting the presence of large DNA fragments identical by descent. Our data for the male sterility character were consistent with the existence of cytoplasmic male sterility, where individuals having the almond cytoplasm required the almond allele in at least one of two independent restorer genes, Rf1 and Rf2, to be fertile. The restorer genes were located in a 3.4 Mbp fragment of linkage group 2 (Rf1) and 1.4 Mbp of linkage group 6 (Rf2). Both fragments contained several genes coding for pentatricopeptide proteins, demonstrated to be responsible for restoring fertility in other species. The implications of these results for using almond as a source of novel variability in peach are discussed.
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Affiliation(s)
- José Manuel Donoso
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Roger Picañol
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Ignasi Batlle
- IRTA. Centre de Mas de Bover. Crta. De Reus – El Morell Km 3.8. 43120 Constantί, Tarragona, Spain
| | - Werner Howad
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - María José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
- E-mail:
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27
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Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J, Vendramin E, Meisel LA, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A, Cipriani G, Dondini L, Ficklin S, Goodstein DM, Xuan P, Del Fabbro C, Aramini V, Copetti D, Gonzalez S, Horner DS, Falchi R, Lucas S, Mica E, Maldonado J, Lazzari B, Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P, Arús P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M, Rokhsar DS. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 2013; 45:487-94. [PMID: 23525075 DOI: 10.1038/ng.2586] [Citation(s) in RCA: 578] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 02/22/2013] [Indexed: 11/09/2022]
Abstract
Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.
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Affiliation(s)
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- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA)-Centro di Ricerca per la Frutticoltura, Rome, Italy.
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Lahaye M, Falourd X, Quemener B, Ralet MC, Howad W, Dirlewanger E, Arús P. Cell wall polysaccharide chemistry of peach genotypes with contrasted textures and other fruit traits. J Agric Food Chem 2012; 60:6594-605. [PMID: 22697314 DOI: 10.1021/jf301494j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cell wall composition, pectin, and hemicellulose fine structure variation were assessed in peach and related genotypes with contrasted texture and fruit shape. Cell walls were prepared from four commercial peaches, eight genotypes from the Jalousia × Fantasia peach cross, and six genotypes from the Earlygold peach × Texas almond cross. Sugar composition was determined chemically while fine structure of homogalacturonan pectin and xyloglucan hemicellulose were assessed by coupling pectin lyase and glucanase degradation, respectively, with MALDI-TOF MS analysis of the degradation products. The results indicate clear compositional and structural differences between the parents and their related genotypes on the basis of pectin versus cellulose/hemicellulose content and on the fine structure of homogalacturonan and xyloglucan. A relation between methyl- and acetyl-esterification of pectin with fruit shape is revealed in the Fantasia × Jalousia peach genotypes.
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Affiliation(s)
- Marc Lahaye
- INRA, UR1268 Biopolymères Interactions Assemblages, Nantes, France.
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29
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Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin E, Main D, Aramini V, Blas AL, Mockler TC, Bryant DW, Wilhelm L, Troggio M, Sosinski B, Aranzana MJ, Arús P, Iezzoni A, Morgante M, Peace C. Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One 2012; 7:e35668. [PMID: 22536421 PMCID: PMC3334984 DOI: 10.1371/journal.pone.0035668] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/19/2012] [Indexed: 01/14/2023] Open
Abstract
Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs. The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species.
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Affiliation(s)
- Ignazio Verde
- Fruit Tree Research Center, Rome, Italy
- * E-mail: (IV); (CP)
| | - Nahla Bassil
- United States Department of Agriculture-Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | | | - Barbara Gilmore
- United States Department of Agriculture-Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | | | - Ksenija Gasic
- School of Agricultural, Forest and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Diego Micheletti
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Umesh R. Rosyara
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | | | | | - Dorrie Main
- Department of Horticulture & Landscape Architecture, Washington State University, Pullman, Washington, United States of America
| | | | - Andrea L. Blas
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Todd C. Mockler
- The Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Douglas W. Bryant
- The Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Intuitive Genomics, Inc., St. Louis, Missouri, United States of America
| | - Larry Wilhelm
- Oregon Health Sciences University, Portland, Oregon, United States of America
| | - Michela Troggio
- The Istituto Agrario di San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Italy
| | - Bryon Sosinski
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Cameron Peace
- Department of Horticulture & Landscape Architecture, Washington State University, Pullman, Washington, United States of America
- * E-mail: (IV); (CP)
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Jung S, Cestaro A, Troggio M, Main D, Zheng P, Cho I, Folta KM, Sosinski B, Abbott A, Celton JM, Arús P, Shulaev V, Verde I, Morgante M, Rokhsar D, Velasco R, Sargent DJ. Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. BMC Genomics 2012; 13:129. [PMID: 22475018 PMCID: PMC3368713 DOI: 10.1186/1471-2164-13-129] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 04/04/2012] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes. RESULTS Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes. CONCLUSION Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae.
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Affiliation(s)
- Sook Jung
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA
| | - Alessandro Cestaro
- Istituto Agrario San Michele all'Adige, Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Michela Troggio
- Istituto Agrario San Michele all'Adige, Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Dorrie Main
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA
| | - Ping Zheng
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA
| | - Ilhyung Cho
- Computer Science, Saginaw Valley State University, University Center, MI 48710, USA
| | - Kevin M Folta
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA
| | - Bryon Sosinski
- Department of Horticultural Science, North Carolina State University, Campus Box 7609, Raleigh, NC 27695, USA
| | - Albert Abbott
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Jean-Marc Celton
- UMR Génétique et Horticulture (GenHort), INRA/Agrocampus-ouest/Université d'Angers, Centre Angers-Nantes, 42 rue Georges Morel -, BP 60057, 49071 Beaucouzé cedex, France
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Vladimir Shulaev
- Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, Texas, USA
| | - Ignazio Verde
- CRA - Fruit Tree Research Center, Via di Fioranello, 52, 00134 Rome, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico L. Danieli, via Linussio, 51, 33100 Udine, Italy
| | - Daniel Rokhsar
- DOE Joint Genomics Institute, 2800 Mitchell Dr, Walnut Creek, CA, USA
| | - Riccardo Velasco
- Istituto Agrario San Michele all'Adige, Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Daniel James Sargent
- Istituto Agrario San Michele all'Adige, Via E. Mach 1, 38010 San Michele all'Adige, Italy
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Illa E, Sargent DJ, Lopez Girona E, Bushakra J, Cestaro A, Crowhurst R, Pindo M, Cabrera A, van der Knaap E, Iezzoni A, Gardiner S, Velasco R, Arús P, Chagné D, Troggio M. Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evol Biol 2011; 11:9. [PMID: 21226921 PMCID: PMC3033827 DOI: 10.1186/1471-2148-11-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 01/12/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. RESULTS We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. CONCLUSIONS A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae.
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Affiliation(s)
- Eudald Illa
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348 Cabrils (Barcelona), Spain
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Aranzana MJ, Abbassi EK, Howad W, Arús P. Genetic variation, population structure and linkage disequilibrium in peach commercial varieties. BMC Genet 2010; 11:69. [PMID: 20646280 PMCID: PMC2915947 DOI: 10.1186/1471-2156-11-69] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2010] [Accepted: 07/20/2010] [Indexed: 12/16/2022] Open
Abstract
Background Peach [Prunus persica (L.) Batsch] is one of the most economically important fruit crops that, due to its genetic and biological characteristics (small genome size, taxonomic proximity to other important species and short juvenile period), has become a model plant in genomic studies of fruit trees. Our aim was an in-depth study of the extent, distribution and structure of peach genetic variation in North American and European commercial varieties as well as old Spanish varieties and several founders used in the early USA peach breeding programmes. For this we genotyped 224 peach cultivars using 50 SSRs evenly distributed along the 8 linkage groups of the Prunus reference map. Results Genetic distance analysis based on SSRs divided the peach cultivars in three main groups based mainly on their fruit characteristics: melting flesh peaches, melting flesh nectarines and non-melting varieties. Whereas non-melting flesh peaches had a higher number of alleles than melting peaches and nectarines, they were more homozygous. With some exceptions ('Admiral Dewey', 'Early Crawford' and 'Chinese Cling'), the founder US cultivars clustered together with the commercial melting peaches, indicating that their germplasm is well represented in modern cultivars. Population structure analysis showed a similar subdivision of the sample into subpopulations. Linkage disequilibrium (LD) analysis in three unstructured, or barely structured, subpopulations revealed a high level of LD conservation in peach extending up to 13-15 cM. Conclusions Using a much larger set of SSRs, our results confirm previous observations on peach variability and population structure and provide additional tools for breeding and breeders' rights enforcement. SSR data are also used for the estimation of marker mutation rates and allow pedigree inferences, particularly with founder genotypes of the currently grown cultivars, which are useful to understand the evolution of peach as a crop. Results on LD conservation can be explained by the self-pollinating nature of peach cultivated germplasm and by a bottleneck that occurred at the beginning of modern breeding practices. High LD suggests that the development of whole-genome scanning approaches is suitable for genetic studies of agronomically important traits in peach.
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Affiliation(s)
- Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348 Cabrils, Barcelona, Spain
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Abstract
BACKGROUND Cucumis melo (melon) belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has high intra-specific genetic variation, morphologic diversity and a small genome size (450 Mb), which make this species suitable for a great variety of molecular and genetic studies that can lead to the development of tools for breeding varieties of the species. A number of genetic and genomic resources have already been developed, such as several genetic maps and BAC genomic libraries. These tools are essential for the construction of a physical map, a valuable resource for map-based cloning, comparative genomics and assembly of whole genome sequencing data. However, no physical map of any Cucurbitaceae has yet been developed. A project has recently been started to sequence the complete melon genome following a whole-genome shotgun strategy, which makes use of massive sequencing data. A BAC-based melon physical map will be a useful tool to help assemble and refine the draft genome data that is being produced. RESULTS A melon physical map was constructed using a 5.7 x BAC library and a genetic map previously developed in our laboratories. High-information-content fingerprinting (HICF) was carried out on 23,040 BAC clones, digesting with five restriction enzymes and SNaPshot labeling, followed by contig assembly with FPC software. The physical map has 1,355 contigs and 441 singletons, with an estimated physical length of 407 Mb (0.9 x coverage of the genome) and the longest contig being 3.2 Mb. The anchoring of 845 BAC clones to 178 genetic markers (100 RFLPs, 76 SNPs and 2 SSRs) also allowed the genetic positioning of 183 physical map contigs/singletons, representing 55 Mb (12%) of the melon genome, to individual chromosomal loci. The melon FPC database is available for download at http://melonomics.upv.es/static/files/public/physical_map/. CONCLUSIONS Here we report the construction of the first physical map of a Cucurbitaceae species described so far. The physical map was integrated with the genetic map so that a number of physical contigs, representing 12% of the melon genome, could be anchored to known genetic positions. The data presented is already helping to improve the quality of the melon genomic sequence available as a result of a project currently being carried out in Spain, adopting a whole genome shotgun approach based on 454 sequencing data.
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Affiliation(s)
- Víctor M González
- Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Jordi Girona, 18-26, 08034 Barcelona, Spain
| | - Jordi Garcia-Mas
- Plant Genetics Department, IRTA, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Carretera de Cabrils Km 2, 08348 Barcelona, Spain
| | - Pere Arús
- Plant Genetics Department, IRTA, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Carretera de Cabrils Km 2, 08348 Barcelona, Spain
| | - Pere Puigdomènech
- Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Jordi Girona, 18-26, 08034 Barcelona, Spain
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Bonet J, Girona EL, Sargent DJ, Muñoz-Torres MC, Monfort A, Abbott AG, Arús P, Simpson DW, Davik J. The development and characterisation of a bacterial artificial chromosome library for Fragaria vesca. BMC Res Notes 2009; 2:188. [PMID: 19772672 PMCID: PMC2754993 DOI: 10.1186/1756-0500-2-188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 09/23/2009] [Indexed: 11/30/2022] Open
Abstract
Background The cultivated strawberry Fragaria ×ananassa is one of the most economically-important soft-fruit species. Few structural genomic resources have been reported for Fragaria and there exists an urgent need for the development of physical mapping resources for the genus. The first stage in the development of a physical map for Fragaria is the construction and characterisation of a high molecular weight bacterial artificial chromosome (BAC) library. Methods A BAC library, consisting of 18,432 clones was constructed from Fragaria vesca f. semperflorens accession 'Ali Baba'. BAC DNA from individual library clones was pooled to create a PCR-based screening assay for the library, whereby individual clones could be identified with just 34 PCR reactions. These pools were used to screen the BAC library and anchor individual clones to the diploid Fragaria reference map (FV×FN). Findings Clones from the BAC library developed contained an average insert size of 85 kb, representing over seven genome equivalents. The pools and superpools developed were used to identify a set of BAC clones containing 70 molecular markers previously mapped to the diploid Fragaria FV×FN reference map. The number of positive colonies identified for each marker suggests the library represents between 4× and 10× coverage of the diploid Fragaria genome, which is in accordance with the estimate of library coverage based on average insert size. Conclusion This BAC library will be used for the construction of a physical map for F. vesca and the superpools will permit physical anchoring of molecular markers using PCR.
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Affiliation(s)
- Julio Bonet
- IRTA. Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, 38348 Cabrils, Spain.
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Deleu W, Esteras C, Roig C, González-To M, Fernández-Silva I, Gonzalez-Ibeas D, Blanca J, Aranda MA, Arús P, Nuez F, Monforte AJ, Picó MB, Garcia-Mas J. A set of EST-SNPs for map saturation and cultivar identification in melon. BMC Plant Biol 2009; 9:90. [PMID: 19604363 PMCID: PMC2722630 DOI: 10.1186/1471-2229-9-90] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 07/15/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND There are few genomic tools available in melon (Cucumis melo L.), a member of the Cucurbitaceae, despite its importance as a crop. Among these tools, genetic maps have been constructed mainly using marker types such as simple sequence repeats (SSR), restriction fragment length polymorphisms (RFLP) and amplified fragment length polymorphisms (AFLP) in different mapping populations. There is a growing need for saturating the genetic map with single nucleotide polymorphisms (SNP), more amenable for high throughput analysis, especially if these markers are located in gene coding regions, to provide functional markers. Expressed sequence tags (ESTs) from melon are available in public databases, and resequencing ESTs or validating SNPs detected in silico are excellent ways to discover SNPs. RESULTS EST-based SNPs were discovered after resequencing ESTs between the parental lines of the PI 161375 (SC) x 'Piel de sapo' (PS) genetic map or using in silico SNP information from EST databases. In total 200 EST-based SNPs were mapped in the melon genetic map using a bin-mapping strategy, increasing the map density to 2.35 cM/marker. A subset of 45 SNPs was used to study variation in a panel of 48 melon accessions covering a wide range of the genetic diversity of the species. SNP analysis correctly reflected the genetic relationships compared with other marker systems, being able to distinguish all the accessions and cultivars. CONCLUSION This is the first example of a genetic map in a cucurbit species that includes a major set of SNP markers discovered using ESTs. The PI 161375 x 'Piel de sapo' melon genetic map has around 700 markers, of which more than 500 are gene-based markers (SNP, RFLP and SSR). This genetic map will be a central tool for the construction of the melon physical map, the step prior to sequencing the complete genome. Using the set of SNP markers, it was possible to define the genetic relationships within a collection of forty-eight melon accessions as efficiently as with SSR markers, and these markers may also be useful for cultivar identification in Occidental melon varieties.
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Affiliation(s)
- Wim Deleu
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348 Cabrils (Barcelona), Spain
| | - Cristina Esteras
- COMAV-UPV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Cristina Roig
- COMAV-UPV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Mireia González-To
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348 Cabrils (Barcelona), Spain
| | - Iria Fernández-Silva
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348 Cabrils (Barcelona), Spain
| | - Daniel Gonzalez-Ibeas
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS)- CSIC, Apdo. correos 164, 30100 Espinardo (Murcia), Spain
| | - José Blanca
- COMAV-UPV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Miguel A Aranda
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS)- CSIC, Apdo. correos 164, 30100 Espinardo (Murcia), Spain
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348 Cabrils (Barcelona), Spain
| | - Fernando Nuez
- COMAV-UPV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Antonio J Monforte
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348 Cabrils (Barcelona), Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP) UPV-CSIC, Ciudad Politécnica de la Innovación Edificio 8E, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Maria Belén Picó
- COMAV-UPV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Jordi Garcia-Mas
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348 Cabrils (Barcelona), Spain
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Dirlewanger E, Cardinet G, Boudehri K, Renaud C, Monllor S, Illa E, Howad W, Arús P, Croset C, Poëssel J, Maucourt M, Deborde C, Moing A. DETECTION OF QTLS CONTROLLING MAJOR FRUIT QUALITY COMPONENTS IN PEACH WITHIN THE EUROPEAN PROJECT ISAFRUIT. ACTA ACUST UNITED AC 2009. [DOI: 10.17660/actahortic.2009.814.90] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Fernandez-Silva I, Eduardo I, Blanca J, Esteras C, Picó B, Nuez F, Arús P, Garcia-Mas J, Monforte AJ. Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.). Theor Appl Genet 2008; 118:139-50. [PMID: 18806992 DOI: 10.1007/s00122-008-0883-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 08/23/2008] [Indexed: 05/03/2023]
Abstract
We report the development of 158 primer pairs flanking SSR motifs in genomic (gSSR) and EST (EST-SSR) melon sequences, all yielding polymorphic bands in melon germplasm, except one that was polymorphic only in Cucurbita species. A similar polymorphism level was found among EST-SSRs and gSSRs, between dimeric and trimeric EST-SSRs, and between EST-SSRs placed in the open reading frame or any of the 5'- or 3'-untranslated regions. Correlation between SSR length and polymorphism was only found for dinucleotide EST-SSRs located within the untranslated regions, but not for trinucleotide EST-SSRs. Transferability of EST-SSRs to Cucurbita species was assayed and 12.7% of the primer pairs amplified at least in one species, although only 5.4% were polymorphic. A set of 14 double haploid lines from the cross between the cultivar "Piel de Sapo" and the accession PI161375 were selected for the bin mapping approach in melon. One hundred and twenty-one SSR markers were newly mapped. The position of 46 SSR loci was also verified by genotyping the complete population. A final bin-map was constructed including 80 RFLPs, 212 SSRs, 3 SNPs and the Nsv locus, distributed in 122 bins with an average bin length of 10.2 cM and a maximum bin length of 33 cM. Map density was 4.2 cM/marker or 5.9 cM/SSR.
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Affiliation(s)
- I Fernandez-Silva
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB (CRAG), Carretera de Cabrils, Km 2, 08348, Cabrils, Barcelona, Spain
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Chen L, Zhang S, Illa E, Song L, Wu S, Howad W, Arús P, van de Weg E, Chen K, Gao Z. Genomic characterization of putative allergen genes in peach/almond and their synteny with apple. BMC Genomics 2008; 9:543. [PMID: 19014629 PMCID: PMC2621206 DOI: 10.1186/1471-2164-9-543] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Accepted: 11/17/2008] [Indexed: 01/15/2023] Open
Abstract
Background Fruits from several species of the Rosaceae family are reported to cause allergic reactions in certain populations. The allergens identified belong to mainly four protein families: pathogenesis related 10 proteins, thaumatin-like proteins, lipid transfer proteins and profilins. These families of putative allergen genes in apple (Mal d 1 to 4) have been mapped on linkage maps and subsequent genetic study on allelic diversity and hypoallergenic traits has been carried out recently. In peach (Prunus persica), these allergen gene families are denoted as Pru p 1 to 4 and for almond (Prunus dulcis)Pru du 1 to 4. Genetic analysis using current molecular tools may be helpful to establish the cause of allergenicity differences observed among different peach cultivars. This study was to characterize putative peach allergen genes for their genomic sequences and linkage map positions, and to compare them with previously characterized homologous genes in apple (Malus domestica). Results Eight Pru p/du 1 genes were identified, four of which were new. All the Pru p/du 1 genes were mapped in a single bin on the top of linkage group 1 (G1). Five Pru p/du 2 genes were mapped on four different linkage groups, two very similar Pru p/du 2.01 genes (A and B) were on G3, Pru p/du 2.02 on G7,Pru p/du 2.03 on G8 and Pru p/du 2.04 on G1. There were differences in the intron and exon structure in these Pru p/du 2 genes and in their amino acid composition. Three Pru p/du 3 genes (3.01–3.03) containing an intron and a mini exon of 10 nt were mapped in a cluster on G6. Two Pru p/du 4 genes (Pru p/du 4.01 and 4.02) were located on G1 and G7, respectively. The Pru p/du 1 cluster on G1 aligned to the Mal d 1 clusters on LG16; Pru p/du 2.01A and B on G3 to Mal d 2.01A and B on LG9; the Pru p/du 3 cluster on G6 to Mal d 3.01 on LG12; Pru p/du 4.01 on G1 to Mal d 4.03 on LG2; and Pru p/du 4.02 on G7 to Mal d 4.02 on LG2. Conclusion A total of 18 putative peach/almond allergen genes have been mapped on five linkage groups. Their positions confirm the high macro-synteny between peach/almond and apple. The insight gained will help to identify key genes causing differences in allergenicity among different cultivars of peach and other Prunus species.
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Affiliation(s)
- Lin Chen
- Institute of Fruit Science, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Biotechnology, Zhejiang University, Hangzhou, 310029, PR China.
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Fernández-Silva I, Moreno E, Eduardo I, Arús P, Alvarez JM, Monforte AJ. On the genetic control of heterosis for fruit shape in melon (Cucumis melo L.). ACTA ACUST UNITED AC 2008; 100:229-35. [PMID: 18815117 DOI: 10.1093/jhered/esn075] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The objective of the present work is to study the genetic basis of heterosis for fruit shape (FS) in melon observed in a cross between the Spanish cultivar "Piel de Sapo" (PS) and the Korean accession PI 161375 (Songwang Charmi [SC]) using a set of near-isogenic lines (NILs) with contrasting phenotypes for FS, each carrying a single chromosomal introgression from SC within the genetic background of PS. We investigated the FS of homozygous NILs, hybrids NIL x PS, and all 2-way crosses between NILs to test the main heterosis hypotheses (dominance, overdominance, and epistatic interactions). Gene action of alleles of quantitative trait loci inducing fruit enlargement was dominance, whereas those inducing rounder fruit were additive or recessive. Only minor epistatic interactions were found. Therefore, the most plausible explanation for FS heterosis in this cross is in agreement with the dominance complementation hypothesis. Over 70% of the hybrid heterosis could be achieved by combining just 2 loci, indicating that the genetic control of FS heterosis in this cross is relatively simple. FS is proposed as a reproductive trait in melon because of the high correlation to the number of seeds produced along the fruit longitudinal axis.
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Affiliation(s)
- Iria Fernández-Silva
- Departament de Genètica Vegetal, IRTA, Centre de Recerca en Agrigenómica, Ctra de Cabrils, Km 2, E-08348 Cabrils, Spain
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Shulaev V, Korban SS, Sosinski B, Abbott AG, Aldwinckle HS, Folta KM, Iezzoni A, Main D, Arús P, Dandekar AM, Lewers K, Brown SK, Davis TM, Gardiner SE, Potter D, Veilleux RE. Multiple models for Rosaceae genomics. Plant Physiol 2008; 147:985-1003. [PMID: 18487361 PMCID: PMC2442536 DOI: 10.1104/pp.107.115618] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Accepted: 05/13/2008] [Indexed: 05/19/2023]
Abstract
The plant family Rosaceae consists of over 100 genera and 3,000 species that include many important fruit, nut, ornamental, and wood crops. Members of this family provide high-value nutritional foods and contribute desirable aesthetic and industrial products. Most rosaceous crops have been enhanced by human intervention through sexual hybridization, asexual propagation, and genetic improvement since ancient times, 4,000 to 5,000 B.C. Modern breeding programs have contributed to the selection and release of numerous cultivars having significant economic impact on the U.S. and world markets. In recent years, the Rosaceae community, both in the United States and internationally, has benefited from newfound organization and collaboration that have hastened progress in developing genetic and genomic resources for representative crops such as apple (Malus spp.), peach (Prunus spp.), and strawberry (Fragaria spp.). These resources, including expressed sequence tags, bacterial artificial chromosome libraries, physical and genetic maps, and molecular markers, combined with genetic transformation protocols and bioinformatics tools, have rendered various rosaceous crops highly amenable to comparative and functional genomics studies. This report serves as a synopsis of the resources and initiatives of the Rosaceae community, recent developments in Rosaceae genomics, and plans to apply newly accumulated knowledge and resources toward breeding and crop improvement.
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Vilanova S, Sargent DJ, Arús P, Monfort A. Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry). BMC Plant Biol 2008. [PMID: 18564412 DOI: 10.1186/1471-22229-8-67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND The Rosaceae encompass a large number of economically-important diploid and polyploid fruit and ornamental species in many different genera. The basic chromosome numbers of these genera are x = 7, 8 and 9 and all have compact and relatively similar genome sizes. Comparative mapping between distantly-related genera has been performed to a limited extent in the Rosaceae including a comparison between Malus (subfamily Maloideae) and Prunus (subfamily Prunoideae); however no data has been published to date comparing Malus or Prunus to a member of the subfamily Rosoideae. In this paper we compare the genome of Fragaria, a member of the Rosoideae, to Prunus, a member of the Prunoideae. RESULTS The diploid genomes of Prunus (2n = 2x = 16) and Fragaria (2n = 2x = 14) were compared through the mapping of 71 anchor markers - 40 restriction fragment length polymorphisms (RFLPs), 29 indels or single nucleotide polymorphisms (SNPs) derived from expressed sequence tags (ESTs) and two simple-sequence repeats (SSRs) - on the reference maps of both genera. These markers provided good coverage of the Prunus (78%) and Fragaria (78%) genomes, with maximum gaps and average densities of 22 cM and 7.3 cM/marker in Prunus and 32 cM and 8.0 cM/marker in Fragaria. CONCLUSION Our results indicate a clear pattern of synteny, with most markers of each chromosome of one of these species mapping to one or two chromosomes of the other. A large number of rearrangements (36), most of which produced by inversions (27) and the rest (9) by translocations or fission/fusion events could also be inferred. We have provided the first framework for the comparison of the position of genes or DNA sequences of these two economically valuable and yet distantly-related genera of the Rosaceae.
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Affiliation(s)
- Santiago Vilanova
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, 08348 Cabrils, Spain.
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Vilanova S, Sargent DJ, Arús P, Monfort A. Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry). BMC Plant Biol 2008; 8:67. [PMID: 18564412 PMCID: PMC2442709 DOI: 10.1186/1471-2229-8-67] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 06/18/2008] [Indexed: 05/19/2023]
Abstract
BACKGROUND The Rosaceae encompass a large number of economically-important diploid and polyploid fruit and ornamental species in many different genera. The basic chromosome numbers of these genera are x = 7, 8 and 9 and all have compact and relatively similar genome sizes. Comparative mapping between distantly-related genera has been performed to a limited extent in the Rosaceae including a comparison between Malus (subfamily Maloideae) and Prunus (subfamily Prunoideae); however no data has been published to date comparing Malus or Prunus to a member of the subfamily Rosoideae. In this paper we compare the genome of Fragaria, a member of the Rosoideae, to Prunus, a member of the Prunoideae. RESULTS The diploid genomes of Prunus (2n = 2x = 16) and Fragaria (2n = 2x = 14) were compared through the mapping of 71 anchor markers - 40 restriction fragment length polymorphisms (RFLPs), 29 indels or single nucleotide polymorphisms (SNPs) derived from expressed sequence tags (ESTs) and two simple-sequence repeats (SSRs) - on the reference maps of both genera. These markers provided good coverage of the Prunus (78%) and Fragaria (78%) genomes, with maximum gaps and average densities of 22 cM and 7.3 cM/marker in Prunus and 32 cM and 8.0 cM/marker in Fragaria. CONCLUSION Our results indicate a clear pattern of synteny, with most markers of each chromosome of one of these species mapping to one or two chromosomes of the other. A large number of rearrangements (36), most of which produced by inversions (27) and the rest (9) by translocations or fission/fusion events could also be inferred. We have provided the first framework for the comparison of the position of genes or DNA sequences of these two economically valuable and yet distantly-related genera of the Rosaceae.
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Affiliation(s)
- Santiago Vilanova
- IRTA. Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, 08348 Cabrils, Spain
- Universidad Politécnica de Valencia, Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Spain
| | | | - Pere Arús
- IRTA. Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, 08348 Cabrils, Spain
| | - Amparo Monfort
- IRTA. Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, 08348 Cabrils, Spain
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Sargent DJ, Cipriani G, Vilanova S, Gil-Ariza D, Arús P, Simpson DW, Tobutt KR, Monfort A. The development of a bin mapping population and the selective mapping of 103 markers in the diploid Fragaria reference map. Genome 2008; 51:120-7. [PMID: 18356946 DOI: 10.1139/g07-107] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have identified a set of plants (the bin set) to permit "selective" or "bin" mapping using the diploid strawberry mapping population FV x FN, derived from the F2 cross F. vesca 815 x F. nubicola 601, which has been used to develop the Fragaria reference map. The bin set consists of 8 plants: the F. vesca 815 parent, the F1 hybrid individual, and 6 seedlings of the F2 population. This bin set divides the 578 cM of the diploid Fragaria genome into 46 bins, the largest mapping bin being 26 cM in length and the average bin size being 12.6 cM. To validate the FV x FN bin set, we used it to locate 103 loci into bins on the FV x FN map. These loci comprised 61 previously described SSRs, 38 new SSRs developed in this investigation from Fragaria x ananassa genomic DNA, EST and gene sequences, and 4 ripening-related genes developed for Prunus. The 103 markers were located to bins on all 7 linkage groups of the Fragaria map and a new mapping bin was identified with the novel markers, demonstrating that the map covers the majority of the diploid Fragaria genome and that the 6 bin-set seedlings selected were appropriate for bin mapping using this progeny.
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Affiliation(s)
- D J Sargent
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK
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Gonzalez-Ibeas D, Blanca J, Roig C, González-To M, Picó B, Truniger V, Gómez P, Deleu W, Caño-Delgado A, Arús P, Nuez F, Garcia-Mas J, Puigdomènech P, Aranda MA. MELOGEN: an EST database for melon functional genomics. BMC Genomics 2007; 8:306. [PMID: 17767721 PMCID: PMC2034596 DOI: 10.1186/1471-2164-8-306] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 09/03/2007] [Indexed: 11/22/2022] Open
Abstract
Background Melon (Cucumis melo L.) is one of the most important fleshy fruits for fresh consumption. Despite this, few genomic resources exist for this species. To facilitate the discovery of genes involved in essential traits, such as fruit development, fruit maturation and disease resistance, and to speed up the process of breeding new and better adapted melon varieties, we have produced a large collection of expressed sequence tags (ESTs) from eight normalized cDNA libraries from different tissues in different physiological conditions. Results We determined over 30,000 ESTs that were clustered into 16,637 non-redundant sequences or unigenes, comprising 6,023 tentative consensus sequences (contigs) and 10,614 unclustered sequences (singletons). Many potential molecular markers were identified in the melon dataset: 1,052 potential simple sequence repeats (SSRs) and 356 single nucleotide polymorphisms (SNPs) were found. Sixty-nine percent of the melon unigenes showed a significant similarity with proteins in databases. Functional classification of the unigenes was carried out following the Gene Ontology scheme. In total, 9,402 unigenes were mapped to one or more ontology. Remarkably, the distributions of melon and Arabidopsis unigenes followed similar tendencies, suggesting that the melon dataset is representative of the whole melon transcriptome. Bioinformatic analyses primarily focused on potential precursors of melon micro RNAs (miRNAs) in the melon dataset, but many other genes potentially controlling disease resistance and fruit quality traits were also identified. Patterns of transcript accumulation were characterised by Real-Time-qPCR for 20 of these genes. Conclusion The collection of ESTs characterised here represents a substantial increase on the genetic information available for melon. A database (MELOGEN) which contains all EST sequences, contig images and several tools for analysis and data mining has been created. This set of sequences constitutes also the basis for an oligo-based microarray for melon that is being used in experiments to further analyse the melon transcriptome.
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Affiliation(s)
- Daniel Gonzalez-Ibeas
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS)- CSIC, Apdo. correos 164, 30100 Espinardo (Murcia), Spain
| | - José Blanca
- Departamento de Biotecnología, Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain
| | - Cristina Roig
- Departamento de Biotecnología, Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain
| | - Mireia González-To
- Departament de Genètica Vegetal, Centre de Recerca en Agrigenòmica CSIC-IRTA, Carretera de Cabrils Km2, 08348 Cabrils (Barcelona), Spain
| | - Belén Picó
- Departamento de Biotecnología, Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain
| | - Verónica Truniger
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS)- CSIC, Apdo. correos 164, 30100 Espinardo (Murcia), Spain
| | - Pedro Gómez
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS)- CSIC, Apdo. correos 164, 30100 Espinardo (Murcia), Spain
| | - Wim Deleu
- Departament de Genètica Vegetal, Centre de Recerca en Agrigenòmica CSIC-IRTA, Carretera de Cabrils Km2, 08348 Cabrils (Barcelona), Spain
| | - Ana Caño-Delgado
- Departament de Genètica Molecular, Centre de Recerca en Agrigenòmica CSIC-IRTA, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Pere Arús
- Departament de Genètica Vegetal, Centre de Recerca en Agrigenòmica CSIC-IRTA, Carretera de Cabrils Km2, 08348 Cabrils (Barcelona), Spain
| | - Fernando Nuez
- Departamento de Biotecnología, Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain
| | - Jordi Garcia-Mas
- Departament de Genètica Vegetal, Centre de Recerca en Agrigenòmica CSIC-IRTA, Carretera de Cabrils Km2, 08348 Cabrils (Barcelona), Spain
| | - Pere Puigdomènech
- Departament de Genètica Molecular, Centre de Recerca en Agrigenòmica CSIC-IRTA, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Miguel A Aranda
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS)- CSIC, Apdo. correos 164, 30100 Espinardo (Murcia), Spain
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Deleu W, González V, Monfort A, Bendahmane A, Puigdomènech P, Arús P, Garcia-Mas J. Structure of two melon regions reveals high microsynteny with sequenced plant species. Mol Genet Genomics 2007; 278:611-22. [PMID: 17665215 DOI: 10.1007/s00438-007-0277-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Revised: 07/04/2007] [Accepted: 07/06/2007] [Indexed: 01/23/2023]
Abstract
In this study, two melon bacterial artificial chromosome (BAC) clones have been sequenced and annotated. BAC 1-21-10 spans 92 kb and contains the nsv locus conferring resistance to the Melon Necrotic Spot Virus (MNSV) in melon linkage group 11. BAC 13J4 spans 98 kb and belongs to a BAC contig containing resistance gene homologues, extending a previous sequenced region of 117 kb in linkage group 4. Both regions have microsyntenic relationships to the model plant species Arabidopsis thaliana, and to Medicago truncatula and Populus trichocarpa. The network of synteny found between melon and each of the sequenced genomes reflects the polyploid structure of Arabidopsis, Populus, and Medicago genomes due to whole genome duplications (WGD). A detailed analysis revealed that both melon regions have a lower relative syntenic quality with Arabidopsis (eurosid II) than when compared to Populus and Medicago (eurosid I). Although phylogenetically Cucurbitales seem to be closer to Fabales than to Malphigiales, synteny was higher between both melon regions and Populus. Presented data imply that the recently completed Populus genome sequence could preferentially be used to obtain positional information in melon, based on microsynteny.
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Affiliation(s)
- Wim Deleu
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km2, 08348 Cabrils, Barcelona, Spain
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Sargent DJ, Clarke J, Simpson DW, Tobutt KR, Arús P, Monfort A, Vilanova S, Denoyes-Rothan B, Rousseau M, Folta KM, Bassil NV, Battey NH. An enhanced microsatellite map of diploid Fragaria. Theor Appl Genet 2006; 112:1349-59. [PMID: 16505996 DOI: 10.1007/s00122-006-0237-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Accepted: 02/05/2006] [Indexed: 05/03/2023]
Abstract
A total of 45 microsatellites (SSRs) were developed for mapping in Fragaria. They included 31 newly isolated codominant genomic SSRs from F. nubicola and a further 14 SSRs, derived from an expressed sequence tagged library (EST-SSRs) of the cultivated strawberry, F. x ananassa. These, and an additional 64 previously characterised but unmapped SSRs and EST-SSRs, were scored in the diploid Fragaria interspecific F2 mapping population (FVxFN) derived from a cross between F. vesca 815 and F. nubicola 601. The cosegregation data of these 109 SSRs, and of 73 previously mapped molecular markers, were used to elaborate an enhanced linkage map. The map is composed of 182 molecular markers (175 microsatellites, six gene specific markers and one sequence-characterised amplified region) and spans 424 cM over seven linkage groups. The average marker spacing is 2.3 cM/marker and the map now contains just eight gaps longer than 10 cM. The transferability of the new SSR markers to the cultivated strawberry was demonstrated using eight cultivars. Because of the transferable nature of these markers, the map produced will provide a useful reference framework for the development of linkage maps of the cultivated strawberry and for the development of other key resources for Fragaria such as a physical map. In addition, the map now provides a framework upon which to place transferable markers, such as genes of known function, for comparative mapping purposes within Rosaceae.
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Affiliation(s)
- D J Sargent
- East Malling Research (EMR), New Road, East Malling, Kent, ME19 6BJ, UK.
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Jung S, Main D, Staton M, Cho I, Zhebentyayeva T, Arús P, Abbott A. Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes. BMC Genomics 2006; 7:81. [PMID: 16615871 PMCID: PMC1479338 DOI: 10.1186/1471-2164-7-81] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 04/14/2006] [Indexed: 11/18/2022] Open
Abstract
Background Due to the lack of availability of large genomic sequences for peach or other Prunus species, the degree of synteny conservation between the Prunus species and Arabidopsis has not been systematically assessed. Using the recently available peach EST sequences that are anchored to Prunus genetic maps and to peach physical map, we analyzed the extent of conserved synteny between the Prunus and the Arabidopsis genomes. The reconstructed pseudo-ancestral Arabidopsis genome, existed prior to the proposed recent polyploidy event, was also utilized in our analysis to further elucidate the evolutionary relationship. Results We analyzed the synteny conservation between the Prunus and the Arabidopsis genomes by comparing 475 peach ESTs that are anchored to Prunus genetic maps and their Arabidopsis homologs detected by sequence similarity. Microsyntenic regions were detected between all five Arabidopsis chromosomes and seven of the eight linkage groups of the Prunus reference map. An additional 1097 peach ESTs that are anchored to 431 BAC contigs of the peach physical map and their Arabidopsis homologs were also analyzed. Microsyntenic regions were detected in 77 BAC contigs. The syntenic regions from both data sets were short and contained only a couple of conserved gene pairs. The synteny between peach and Arabidopsis was fragmentary; all the Prunus linkage groups containing syntenic regions matched to more than two different Arabidopsis chromosomes, and most BAC contigs with multiple conserved syntenic regions corresponded to multiple Arabidopsis chromosomes. Using the same peach EST datasets and their Arabidopsis homologs, we also detected conserved syntenic regions in the pseudo-ancestral Arabidopsis genome. In many cases, the gene order and content of peach regions was more conserved in the ancestral genome than in the present Arabidopsis region. Statistical significance of each syntenic group was calculated using simulated Arabidopsis genome. Conclusion We report here the result of the first extensive analysis of the conserved microsynteny using DNA sequences across the Prunus genome and their Arabidopsis homologs. Our study also illustrates that both the ancestral and present Arabidopsis genomes can provide a useful resource for marker saturation and candidate gene search, as well as elucidating evolutionary relationships between species.
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Affiliation(s)
- Sook Jung
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Dorrie Main
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA
| | - Margaret Staton
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Ilhyung Cho
- Department of Computer Science, Saginaw Valley State University, University Center, MI 48710, USA
| | | | - Pere Arús
- Departament de Genètica Vegetal, Laboratori de Genètica Molecular Vegetal. CSIC-IRTA,08348 Cabrils, Spain
| | - Albert Abbott
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
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Eduardo I, Arús P, Monforte AJ. Development of a genomic library of near isogenic lines (NILs) in melon (Cucumis melo L.) from the exotic accession PI161375. Theor Appl Genet 2005; 112:139-48. [PMID: 16208502 DOI: 10.1007/s00122-005-0116-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2005] [Accepted: 09/14/2005] [Indexed: 05/04/2023]
Abstract
A doubled haploid line (DHL) population of melon derived from a cross between the Korean cultivar "Songwhan Charmi" accession PI161375 (SC), included in the horticultural group conomon, and the Spanish cultivar "Piel de Sapo" (PS), included in the horticultural group inodorus, was used to develop a collection of near isogenic lines (NILs). These parental lines represent very different melon cultivar groups, with important differences at fruit, plant, disease response and molecular level. This cross is one of the most polymorphic ones within melon germplasm. Selected DHLs were backcrossed to PS and further backcrossing and selfing was performed, monitoring introgressions from SC using molecular markers covering the melon genetic map. A final collection of 57 NILs was obtained, containing a unique independent introgression from SC in the PS genetic background. The introgressions within the collection cover at least 85% of the SC genome with an average introgression size of 41 cM, corresponding to 3.4% of the SC genome. The average resolution for mapping genes or quantitative trait loci is 18.90 cM. This set of NILs is a potentially powerful tool for the study of quantitative trait locus involved in melon fruit quality and other important complex traits, and the introduction of new genetic variability in modern cultivars from exotic sources. The NILs can also be used as pre-competitive breeding lines in melon breeding projects.
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Affiliation(s)
- Iban Eduardo
- Departament de Genètica Vegetal, Laboratori de Genètica Molecular Vegetal CSIC-IRTA, Carretera de Cabrils s/n, 08348 Cabrils, Barcelona, Spain
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Morales M, Orjeda G, Nieto C, van Leeuwen H, Monfort A, Charpentier M, Caboche M, Arús P, Puigdomènech P, Aranda MA, Dogimont C, Bendahmane A, Garcia-Mas J. A physical map covering the nsv locus that confers resistance to Melon necrotic spot virus in melon (Cucumis melo L.). Theor Appl Genet 2005; 111:914-22. [PMID: 16052354 DOI: 10.1007/s00122-005-0019-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Accepted: 06/14/2005] [Indexed: 05/03/2023]
Abstract
Melon necrotic spot virus (MNSV) is a member of the genus Carmovirus, which produces severe yield losses in melon and cucumber crops. The nsv gene is the only known natural source of resistance against MNSV in melon, and confers protection against all widespread strains of this virus. nsv has been previously mapped in melon linkage group 11, in a region spanning 5.9 cM, saturated with RAPD and AFLP markers. To identify the nsv gene by positional cloning, we started construction of a high-resolution map for this locus. On the basis of the two mapping populations, F(2) and BC1, which share the same resistant parent PI 161375 (nsv/nsv), and using more than 3,000 offspring, a high-resolution genetic map has been constructed in the region around the nsv locus, spanning 3.2 cM between CAPS markers M 29 and M 132. The availability of two melon BAC libraries allowed for screening and the identification of new markers closer to the resistance gene, by means of BAC-end sequencing and mapping. We constructed a BAC contig in this region and identified the marker 52 K 20 sp 6, which co-segregates with nsv in 408 F(2) and 2.727 BC1 individuals in both mapping populations. We also identified a single 100 kb BAC that physically contains the resistance gene and covers a genetic distance of 0.73 cM between both BAC ends. These are the basis for the isolation of the nsv recessive-resistance gene.
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Affiliation(s)
- Mónica Morales
- Departament de Genètica Vegetal, Laboratori de Genètica Molecular Vegetal CSIC-IRTA, carretera de Cabrils s/n, 08348 Cabrils (Barcelona), Spain
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Howad W, Yamamoto T, Dirlewanger E, Testolin R, Cosson P, Cipriani G, Monforte AJ, Georgi L, Abbott AG, Arús P. Mapping with a few plants: using selective mapping for microsatellite saturation of the Prunus reference map. Genetics 2005; 171:1305-9. [PMID: 16118196 PMCID: PMC1456826 DOI: 10.1534/genetics.105.043661] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The concept of selective (or bin) mapping is used here for the first time, using as an example the Prunus reference map constructed with an almond x peach F2 population. On the basis of this map, a set of six plants that jointly defined 65 possible different genotypes for the codominant markers mapped on it was selected. Sixty-three of these joint genotypes corresponded to a single chromosomal region (a bin) of the Prunus genome, and the two remaining corresponded to two bins each. The 67 bins defined by these six plants had a 7.8-cM average length and a maximum individual length of 24.7 cM. Using a unit of analysis composed of these six plants, their F1 hybrid parent, and one of the parents of the hybrid, we mapped 264 microsatellite (or simple-sequence repeat, SSR) markers from 401 different microsatellite primer pairs. Bin mapping proved to be a fast and economic strategy that could be used for further map saturation, the addition of valuable markers (such as those based on microsatellites or ESTs), and giving a wider scope to, and a more efficient use of, reference mapping populations.
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Affiliation(s)
- Werner Howad
- Departament de Genètica Vegetal, Laboratori de Genètica Molecular Vegetal, CSIC-IRTA, 08348 Cabrils (Barcelona), Spain
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