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Mayobre C, Santo Domingo M, Özkan EN, Fernández-Borbolla A, Ruiz-Lasierra J, Garcia-Mas J, Pujol M. Genetic regulation of volatile production in two melon introgression line collections with contrasting ripening behavior. HORTICULTURE RESEARCH 2024; 11:uhae020. [PMID: 38469382 PMCID: PMC10925849 DOI: 10.1093/hr/uhae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/10/2024] [Indexed: 03/13/2024]
Abstract
The importance of melon aroma in determining fruit quality has been highlighted in recent years. The fruit volatile profile is influenced by the type of fruit ripening. Non-climacteric fruits contain predominantly aldehydes, while climacteric fruits mainly produce esters. Several genes have been described to participate in volatile organic compounds (VOCs) biosynthesis pathways, but knowledge in this area is still incomplete. In this work we analysed the volatile profile of two reciprocal Introgression Line (IL) collections generated from a cross between 'Piel de Sapo' (PS) and 'Védrantais' (VED) melons, differing in their aroma profile and ripening behaviour. SPME GC-MS was performed to identify genes responsible for VOCs formation. More than 1000 QTLs for many volatiles were detected taken together both populations. Introgressions on chromosomes 3, 5, 6, 7 and 8 modified ester-aldehyde balance and were correlated to ripening changes in both genetic backgrounds. Some previously identified QTLs for fruit ripening might be involved in these phenotypes, such as ETHQV8.1 on chromosome 8 and ETHQV6.3 on chromosome 6. PS alleles on chromosomes 2, 6, 10 and 11 were found to increase ester content when introgressed in VED melons. Terpenes showed to be affected by several genomic regions not related to ripening. In addition, several candidate genes have been hypothesized to be responsible for some of the QTLs detected. The analysis of volatile compounds in two reciprocal IL collections has increased our understanding of the relationship between ripening and aroma and offers valuable plant material to improve food quality in melon breeding programs.
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Affiliation(s)
- Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Elif Nur Özkan
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Andrés Fernández-Borbolla
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Javier Ruiz-Lasierra
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
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Campos M, Gonzalo MJ, Díaz A, Picó B, Gómez-Guillamón ML, Monforte AJ, Esteras C. A Novel Introgression Line Library Derived from a Wild Melon Gives Insights into the Genetics of Melon Domestication, Uncovering New Genetic Variability Useful for Breeding. Int J Mol Sci 2023; 24:10099. [PMID: 37373247 DOI: 10.3390/ijms241210099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/06/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
A collection of 30 melon introgression lines (ILs) was developed from the wild accession Ames 24297 (TRI) into 'Piel de Sapo' (PS) genetic background. Each IL carried an average of 1.4 introgressions from TRI, and the introgressions represented 91.4% of the TRI genome. Twenty-two ILs, representing 75% of the TRI genome, were evaluated in greenhouse (Algarrobo and Meliana) and field (Alcàsser) trials, mainly to study traits related to domestication syndrome such as fruit weight (FW) and flesh content (FFP), as well as other fruit quality traits as fruit shape (FS), flesh firmness (FF), soluble solid concentration (SSC), rind color and abscission layer. The IL collection showed an impressive variation in size-related traits, with FW ranging from 800 to 4100 g, reflecting the strong effect of the wild genome on these traits. Most of the ILs produced smaller fruits compared with PS; however, unexpectedly, the IL TRI05-2 produced bigger fruits, likely due to new epistatic interacions with the PS genetic background. In contrast, the genotypic effect for FS was smaller, and few QTLs with notable effects were detected. Interestingly, variability was also observed for FFP, FF and SSC, rind color and abscission layer formation. Genes in these introgressions are candidates for having been involved in melon domestication and diversification as well. These results confirm that the TRI IL collection is a very powerful tool for mapping traits of agronomic interest in melon, allowing the confirmation of previously reported QTLs and the identification of new ones to better understand the domestication process of this crop.
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Affiliation(s)
- Manuel Campos
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Maria José Gonzalo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Aurora Díaz
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
- Departamento de Ciencia Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda, Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Belén Picó
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Maria Luisa Gómez-Guillamón
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' (IHSM, CSIC-UMA), Algarrobo-Costa, 29750 Málaga, Spain
| | - Antonio José Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Cristina Esteras
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
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Thorough Characterization of ETHQB3.5, a QTL Involved in Melon Fruit Climacteric Behavior and Aroma Volatile Composition. Foods 2023; 12:foods12020376. [PMID: 36673468 PMCID: PMC9858179 DOI: 10.3390/foods12020376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
The effect of the QTL involved in climacteric ripening ETHQB3.5 on the fruit VOC composition was studied using a set of Near-Isogenic Lines (NILs) containing overlapping introgressions from the Korean accession PI 16375 on the chromosome 3 in the climacteric 'Piel de Sapo' (PS) genetic background. ETHQB3.5 was mapped in an interval of 1.24 Mb that contained a NAC transcription factor. NIL fruits also showed differences in VOC composition belonging to acetate esters, non-acetate esters, and sulfur-derived families. Cosegregation of VOC composition (23 out of 48 total QTLs were mapped) and climacteric ripening was observed, suggesting a pleiotropic effect of ETHQB3.5. On the other hand, other VOCs (mainly alkanes, aldehydes, and ketones) showed a pattern of variation independent of ETHQB3.5 effects, indicating the presence of other genes controlling non-climacteric ripening VOCs. Network correlation analysis and hierarchical clustering found groups of highly correlated compounds and confirmed the involvement of the climacteric differences in compound classes and VOC differences. The modification of melon VOCs may be achieved with or without interfering with its physiological behavior, but it is likely that high relative concentrations of some type of ethylene-dependent esters could be achieved in climacteric cultivars.
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Sharma K, Iruegas-Bocardo F, Abdurahman A, Alcalá-Briseño RI, Garrett KA, Goss EM, Ngundo G, Kreuze J, Atieno E, Munguti F. Ralstonia Strains from Potato-Growing Regions of Kenya Reveal Two Phylotypes and Epidemic Clonality of Phylotype II Sequevar 1 Strains. PHYTOPATHOLOGY 2022; 112:1640-1650. [PMID: 35522048 DOI: 10.1094/phyto-08-21-0339-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bacterial wilt, caused by the Ralstonia solanacearum species complex (RSSC), is the most destructive potato disease in Kenya. Studies were conducted to (i) determine the molecular diversity of RSSC strains associated with bacterial wilt of potato in Kenya, (ii) generate an RSSC distribution map for epidemiological inference, and (iii) determine whether phylotype II sequevar 1 strains exhibit epidemic clonality. Surveys were conducted in 2018 and 2019, in which tubers from wilting potato plants and stem samples of potential alternative hosts were collected for pathogen isolation. The pathogen was phylotyped by multiplex PCR and 536 RSSC strains typed at a sequevar level. Two RSSC phylotypes were identified, phylotype II (98.4%, n = 506 [sequevar 1 (n = 505) and sequevar 2 (n = 1)]) and phylotype I (1.6%, n = 30 [sequevar 13 (n = 9) and a new sequevar (n = 21)]). The phylotype II sequevar 1 strains were haplotyped using multilocus tandem repeat sequence typing (TRST) schemes. The TRST scheme identified 51 TRST profiles within the phylotype II sequevar 1 strains with a modest diversity index (HGDI = 0.87), confirming the epidemic clonality of RSSC phylotype II sequevar 1 strains in Kenya. A minimum spanning tree and mapping of the TRST profiles revealed that TRST27 '8-5-12-7-5' is the primary founder of the clonal complex of RSSC phylotype II sequevar 1 and is widely distributed via latently infected seed tubers. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Kalpana Sharma
- Consultative Group for International Agricultural Research (CGIAR) Research Program on Roots, Tubers and Bananas (RTB), Centro Internacional de la Papa, Nairobi, Kenya, Lima, Peru
- International Potato Center (CIP), Sub-Saharan Africa Regional Office, Nairobi, Kenya
| | | | - Abdulwahab Abdurahman
- Consultative Group for International Agricultural Research (CGIAR) Research Program on Roots, Tubers and Bananas (RTB), Centro Internacional de la Papa, Nairobi, Kenya, Lima, Peru
- International Potato Center (CIP), Sub-Saharan Africa Regional Office, Nairobi, Kenya
| | - Ricardo I Alcalá-Briseño
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
- Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
| | - Karen A Garrett
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
- Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
| | - Erica M Goss
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - George Ngundo
- Kenya Plant Health Inspectorate Service (KEPHIS), Plant Quarantine and Biosecurity Station (PQBS), Nairobi, Kenya
| | - Jan Kreuze
- Consultative Group for International Agricultural Research (CGIAR) Research Program on Roots, Tubers and Bananas (RTB), Centro Internacional de la Papa, Nairobi, Kenya, Lima, Peru
- International Potato Center (CIP), Crop and Systems Sciences Division, Lima, Peru
| | - Elly Atieno
- Consultative Group for International Agricultural Research (CGIAR) Research Program on Roots, Tubers and Bananas (RTB), Centro Internacional de la Papa, Nairobi, Kenya, Lima, Peru
- International Potato Center (CIP), Sub-Saharan Africa Regional Office, Nairobi, Kenya
| | - Florence Munguti
- Kenya Plant Health Inspectorate Service (KEPHIS), Plant Quarantine and Biosecurity Station (PQBS), Nairobi, Kenya
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Martínez-Martínez C, Gonzalo MJ, Sipowicz P, Campos M, Martínez-Fernández I, Leida C, Zouine M, Alexiou KG, Garcia-Mas J, Gómez MD, Tornero P, Pérez-Amador MÁ, Esteras C, Picó B, Romero C, Monforte AJ. A cryptic variation in a member of the Ovate Family Proteins is underlying the melon fruit shape QTL fsqs8.1. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:785-801. [PMID: 34821982 PMCID: PMC8942903 DOI: 10.1007/s00122-021-03998-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/08/2021] [Indexed: 06/01/2023]
Abstract
The gene underlying the melon fruit shape QTL fsqs8.1 is a member of the Ovate Family Proteins. Variation in fruit morphology is caused by changes in gene expression likely due to a cryptic structural variation in this locus. Melon cultivars have a wide range of fruit morphologies. Quantitative trait loci (QTL) have been identified underlying such diversity. This research focuses on the fruit shape QTL fsqs8.1, previously detected in a cross between the accession PI 124112 (CALC, producing elongated fruit) and the cultivar 'Piel de Sapo' (PS, producing oval fruit). The CALC fsqs8.1 allele induced round fruit shape, being responsible for the transgressive segregation for this trait observed in that population. In fact, the introgression line CALC8-1, carrying the fsqs8.1 locus from CALC into the PS genetic background, produced perfect round fruit. Following a map-based cloning approach, we found that the gene underlying fsqs8.1 is a member of the Ovate Family Proteins (OFP), CmOFP13, likely a homologue of AtOFP1 and SlOFP20 from Arabidopsis thaliana and tomato, respectively. The induction of the round shape was due to the higher expression of the CALC allele at the early ovary development stage. The fsqs8.1 locus showed an important structural variation, being CmOFP13 surrounded by two deletions in the CALC genome. The deletions are present at very low frequency in melon germplasm. Deletions and single nucleotide polymorphisms in the fsqs8.1 locus could not be not associated with variation in fruit shape among different melon accessions, what indicates that other genetic factors should be involved to induce the CALC fsqs8.1 allele effects. Therefore, fsqs8.1 is an example of a cryptic variation that alters gene expression, likely due to structural variation, resulting in phenotypic changes in melon fruit morphology.
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Affiliation(s)
- Cecilia Martínez-Martínez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
- Universidad de Almería, Almería, Spain
| | - Maria José Gonzalo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Pablo Sipowicz
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
- Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
| | - Manuel Campos
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Irene Martínez-Fernández
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Carmen Leida
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Mohammed Zouine
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Konstantinos G Alexiou
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Bellaterra, Barcelona, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Bellaterra, Barcelona, Spain
| | - María Dolores Gómez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Pablo Tornero
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Miguel Ángel Pérez-Amador
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | | | - Belén Picó
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Carlos Romero
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Antonio J Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022, Valencia, Spain.
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Santo Domingo M, Areco L, Mayobre C, Valverde L, Martín-Hernández AM, Pujol M, Garcia-Mas J. Modulating climacteric intensity in melon through QTL stacking. HORTICULTURE RESEARCH 2022; 9:uhac131. [PMID: 35928400 PMCID: PMC9343914 DOI: 10.1093/hr/uhac131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/29/2022] [Indexed: 05/14/2023]
Abstract
Fruit ripening is one of the main processes affecting fruit quality and shelf life. In melon there are both climacteric and non-climacteric genotypes, making it a suitable species to study fruit ripening. In the current study, in order to fine tune ripening, we have pyramided three climacteric QTLs in the non-climacteric genotype "Piel de Sapo": ETHQB3.5, ETHQV6.3 and ETHQV8.1. The results showed that the three QTLs interact epistatically, affecting ethylene production and ripening-related traits such as aroma profile. Each individual QTL has a specific role in the ethylene production profile. ETHQB3.5 accelerates the ethylene peak, ETHQV6.3 advances the ethylene production and ETHQV8.1 enhances the effect of the other two QTLs. Regarding aroma, the three QTLs independently activated the production of esters changing the aroma profile of the fruits, with no significant effects in fruit firmness, soluble solid content and fruit size. Understanding the interaction and the effect of different ripening QTLs offers a powerful knowledge for candidate gene identification as well as for melon breeding programs, where fruit ripening is one of the main objectives.
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Affiliation(s)
- Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Lorena Areco
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Laura Valverde
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Ana Montserrat Martín-Hernández
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agoralimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
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Liu B, Santo Domingo M, Mayobre C, Martín-Hernández AM, Pujol M, Garcia-Mas J. Knock-Out of CmNAC-NOR Affects Melon Climacteric Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2022; 13:878037. [PMID: 35755703 PMCID: PMC9226586 DOI: 10.3389/fpls.2022.878037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/23/2022] [Indexed: 05/14/2023]
Abstract
Fruit ripening is an important process that affects fruit quality. A QTL in melon, ETHQV6.3, involved in climacteric ripening regulation, has been found to be encoded by CmNAC-NOR, a homologue of the tomato NOR gene. To further investigate CmNAC-NOR function, we obtained two CRISPR/Cas9-mediated mutants (nor-3 and nor-1) in the climacteric Védrantais background. nor-3, containing a 3-bp deletion altering the NAC domain A, resulted in ~8 days delay in ripening without affecting fruit quality. In contrast, the 1-bp deletion in nor-1 resulted in a fully disrupted NAC domain, which completely blocked climacteric ripening. The nor-1 fruits did not produce ethylene, no abscission layer was formed and there was no external color change. Additionally, volatile components were dramatically altered, seeds were not well developed and flesh firmness was also altered. There was a delay in fruit ripening with the nor-1 allele in heterozygosis of ~20 days. Our results provide new information regarding the function of CmNAC-NOR in melon fruit ripening, suggesting that it is a potential target for modulating shelf life in commercial climacteric melon varieties.
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Affiliation(s)
- Bin Liu
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Ana Montserrat Martín-Hernández
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
- *Correspondence: Marta Pujol,
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
- Jordi Garcia-Mas,
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Pereira L, Santo Domingo M, Argyris J, Mayobre C, Valverde L, Martín-Hernández AM, Pujol M, Garcia-Mas J. A novel introgression line collection to unravel the genetics of climacteric ripening and fruit quality in melon. Sci Rep 2021; 11:11364. [PMID: 34059766 PMCID: PMC8166866 DOI: 10.1038/s41598-021-90783-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/18/2021] [Indexed: 11/09/2022] Open
Abstract
Introgression lines are valuable germplasm for scientists and breeders, since they ease genetic studies such as QTL interactions and positional cloning as well as the introduction of favorable alleles into elite varieties. We developed a novel introgression line collection in melon using two commercial European varieties with different ripening behavior, the climacteric cantalupensis 'Védrantais' as recurrent parent and the non-climacteric inodorus 'Piel de Sapo' as donor parent. The collection contains 34 introgression lines, covering 99% of the donor genome. The mean introgression size is 18.16 Mb and ~ 3 lines were obtained per chromosome, on average. The high segregation of these lines for multiple fruit quality traits allowed us to identify 27 QTLs that modified sugar content, altered fruit morphology or were involved in climacteric ripening. In addition, we confirmed the genomic location of five major genes previously described, which control mainly fruit appearance, such as mottled rind and external color. Most of the QTLs had been reported before in other populations sharing parental lines, while three QTLs (EAROQP11.3, ECDQP11.2 and FIRQP4.1) were newly detected in our work. These introgression lines would be useful to perform additional genetic studies, as fine mapping and gene pyramiding, especially for important complex traits such as fruit weight and climacteric ripening.
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Affiliation(s)
- Lara Pereira
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Jason Argyris
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain.,Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Laura Valverde
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Ana Montserrat Martín-Hernández
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain.,Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain. .,Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain.
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain. .,Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain.
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9
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Zarid M, García-Carpintero V, Esteras C, Esteva J, Bueso MC, Cañizares J, Picó MB, Monforte AJ, Fernández-Trujillo JP. Transcriptomic analysis of a near-isogenic line of melon with high fruit flesh firmness during ripening. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:754-777. [PMID: 32713003 DOI: 10.1002/jsfa.10688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 07/16/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND A near-isogenic line (NIL) of melon (SC10-2) with introgression in linkage group X was studied from harvest (at firm-ripe stage of maturity) until day 18 of postharvest storage at 20.5 °C together with its parental control ('Piel de Sapo', PS). RESULTS SC10-2 showed higher flesh firmness and whole fruit hardness but lower juiciness than its parental. SC10-2 showed a decrease in respiration rate accompanied by a decrease in ethylene production during ripening, both of which fell to a greater extent than in PS. The introgression affected 11 volatile organic compounds (VOCs), the levels of which during ripening were generally higher in SC10-2 than in PS. Transcriptomic analysis from RNA-Seq revealed differentially expressed genes (DEGs) associated with the effects studied. For example, 909 DEGs were exclusive to the introgression, and only 23 DEGs were exclusive to postharvest ripening time. Major functions of the DEGs associated with introgression or ripening time were identified by cluster analysis. About 37 genes directly and/or indirectly affected the delay in ripening of SC10-2 compared with PS in general and, more particularly, the physiological and quality traits measured and, probably, the differential non-climacteric response. Of the former genes, we studied in more detail at least five that mapped in the introgression in linkage group (LG) X, and 32 outside it. CONCLUSION There is an apparent control of textural changes, VOCs and fruit ripening by an expression quantitative trait locus located in LG X together with a direct control on them due to genes presented in the introgression (CmTrpD, CmNADH1, CmTCP15, CmGDSL esterase/lipase, and CmHK4-like) and CmNAC18. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Mohamed Zarid
- Department of Agronomical Engineering, Regional Campus of International Excellence 'Campus Mare Nostrum' (CMN), Technical University of Cartagena (UPCT), Cartagena, Spain
| | - Victor García-Carpintero
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Ciudad Politécnica de la Innovación, Universitat Politècnica de València (UPV), Valencia, Spain
| | - Cristina Esteras
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Ciudad Politécnica de la Innovación, Universitat Politècnica de València (UPV), Valencia, Spain
| | - Juan Esteva
- Department of Agronomical Engineering, Regional Campus of International Excellence 'Campus Mare Nostrum' (CMN), Technical University of Cartagena (UPCT), Cartagena, Spain
| | - María C Bueso
- Department of Applied Mathematics and Statistics, CMN, UPCT, Cartagena, Spain
| | - Joaquín Cañizares
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Ciudad Politécnica de la Innovación, Universitat Politècnica de València (UPV), Valencia, Spain
| | - María B Picó
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Ciudad Politécnica de la Innovación, Universitat Politècnica de València (UPV), Valencia, Spain
| | - Antonio J Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC/Universidad Politécnica de Valencia (UPV), Ciudad Politécnica de la Innovación, Valencia, Spain
| | - J Pablo Fernández-Trujillo
- Department of Agronomical Engineering, Regional Campus of International Excellence 'Campus Mare Nostrum' (CMN), Technical University of Cartagena (UPCT), Cartagena, Spain
- Institute of Plant Biotechnology, CMN, UPCT, Cartagena, Spain
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10
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Performance of a Set of Eggplant (Solanum melongena) Lines With Introgressions From Its Wild Relative S. incanum Under Open Field and Screenhouse Conditions and Detection of QTLs. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10040467] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Introgression lines (ILs) of eggplant (Solanum melongena) represent a resource of high value for breeding and the genetic analysis of important traits. We have conducted a phenotypic evaluation in two environments (open field and screenhouse) of 16 ILs from the first set of eggplant ILs developed so far. Each of the ILs carries a single marker-defined chromosomal segment from the wild eggplant relative S. incanum (accession MM577) in the genetic background of S. melongena (accession AN-S-26). Seventeen agronomic traits were scored to test the performance of ILs compared to the recurrent parent and of identifying QTLs for the investigated traits. Significant morphological differences were found between parents, and the hybrid was heterotic for vigour-related traits. Despite the presence of large introgressed fragments from a wild exotic parent, individual ILs did not display differences with respect to the recipient parent for most traits, although significant genotype × environment interaction (G × E ) was detected for most traits. Heritability values for the agronomic traits were generally low to moderate. A total of ten stable QTLs scattered across seven chromosomes was detected. For five QTLs, the S. incanum introgression was associated with higher mean values for plant- and flower-related traits, including vigour prickliness and stigma length. For one flower- and four fruit-related-trait QTLs, including flower peduncle and fruit pedicel lengths and fruit weight, the S. incanum introgression was associated with lower mean values for fruit-related traits. Evidence of synteny to other previously reported in eggplant populations was found for three of the fruit-related QTLs. The other seven stable QTLs are new, demonstrating that eggplant ILs are of great interest for eggplant breeding under different environments.
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11
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Moing A, Allwood JW, Aharoni A, Baker J, Beale MH, Ben-Dor S, Biais B, Brigante F, Burger Y, Deborde C, Erban A, Faigenboim A, Gur A, Goodacre R, Hansen TH, Jacob D, Katzir N, Kopka J, Lewinsohn E, Maucourt M, Meir S, Miller S, Mumm R, Oren E, Paris HS, Rogachev I, Rolin D, Saar U, Schjoerring JK, Tadmor Y, Tzuri G, de Vos RC, Ward JL, Yeselson E, Hall RD, Schaffer AA. Comparative Metabolomics and Molecular Phylogenetics of Melon ( Cucumis melo, Cucurbitaceae) Biodiversity. Metabolites 2020; 10:metabo10030121. [PMID: 32213984 PMCID: PMC7143154 DOI: 10.3390/metabo10030121] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 01/04/2023] Open
Abstract
The broad variability of Cucumis melo (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within C. melo, we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotyping-by-sequencing (GBS) provided over 20,000 single-nucleotide polymorphisms (SNPs). Metabolomics data of the mature fruit flesh and rind provided over 80,000 metabolomic and elemental features via an orchestra of six complementary metabolomic platforms. These technologies probed polar, semi-polar, and non-polar metabolite fractions as well as a set of mineral elements and included both flavor- and taste-relevant volatile and non-volatile metabolites. Together these results enabled an estimate of "metabolomic/elemental distance" and its correlation with the genetic GBS distance of melon accessions. This study indicates that extensive and non-targeted metabolomics/elemental characterization produced classifications that strongly, but not completely, reflect the current and extensive genetic classification. Certain melon Groups, such as Inodorous, clustered in parallel with the genetic classifications while other genome to metabolome/element associations proved less clear. We suggest that the combined genomic, metabolic, and element data reflect the extensive sexual compatibility among melon accessions and the breeding history that has, for example, targeted metabolic quality traits, such as taste and flavor.
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Affiliation(s)
- Annick Moing
- INRAE, Univ. Bordeaux, UMR1332 Fruit Biology and Pathology, Bordeaux Metabolome Facility MetaboHUB, Centre INRAE de Nouvelle Aquitaine - Bordeaux, 33140 Villenave d’Ornon, France; (A.M.); (B.B.); (C.D.); (D.J.); (M.M.); (D.R.)
| | - J. William Allwood
- The James Hutton Institute, Environmental & Biochemical Sciences, Invergowrie, Dundee, DD2 5DA Scotland, UK;
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (A.A.); (S.M.); (S.B.-D.)
| | - John Baker
- Rothamsted Research, Harpenden, Herts AL5 2JQ, UK; (J.B.); (M.H.B.); (S.M.); (J.L.W.)
| | - Michael H. Beale
- Rothamsted Research, Harpenden, Herts AL5 2JQ, UK; (J.B.); (M.H.B.); (S.M.); (J.L.W.)
| | - Shifra Ben-Dor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (A.A.); (S.M.); (S.B.-D.)
| | - Benoît Biais
- INRAE, Univ. Bordeaux, UMR1332 Fruit Biology and Pathology, Bordeaux Metabolome Facility MetaboHUB, Centre INRAE de Nouvelle Aquitaine - Bordeaux, 33140 Villenave d’Ornon, France; (A.M.); (B.B.); (C.D.); (D.J.); (M.M.); (D.R.)
| | - Federico Brigante
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; (F.B.); (A.E.); (J.K.)
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Dto. Química Orgánica, Córdoba 5000, Argentina
- CONICET, ICYTAC (Instituto de Ciencia y Tecnologia de Alimentos Córdoba), Córdoba 5000, Argentina
| | - Yosef Burger
- Institute of Plant Science, Agricultural Research Organization—Volcani Center, Rishon LeZiyyon 7515101, Israel; (Y.B.); (A.F.); (E.Y.)
| | - Catherine Deborde
- INRAE, Univ. Bordeaux, UMR1332 Fruit Biology and Pathology, Bordeaux Metabolome Facility MetaboHUB, Centre INRAE de Nouvelle Aquitaine - Bordeaux, 33140 Villenave d’Ornon, France; (A.M.); (B.B.); (C.D.); (D.J.); (M.M.); (D.R.)
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; (F.B.); (A.E.); (J.K.)
| | - Adi Faigenboim
- Institute of Plant Science, Agricultural Research Organization—Volcani Center, Rishon LeZiyyon 7515101, Israel; (Y.B.); (A.F.); (E.Y.)
| | - Amit Gur
- Newe Ya‘ar Research Center, Agricultural Research Organization, P. O. Box 1021, Ramat Yishay 3009500, Israel; (A.G.); (N.K.); (E.L.); (E.O.); (H.S.P.); (U.S.); (Y.T.); (G.T.)
| | - Royston Goodacre
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK;
| | - Thomas H. Hansen
- Department of Plant and Environmental Sciences & Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark; (T.H.H.); (J.K.S.)
| | - Daniel Jacob
- INRAE, Univ. Bordeaux, UMR1332 Fruit Biology and Pathology, Bordeaux Metabolome Facility MetaboHUB, Centre INRAE de Nouvelle Aquitaine - Bordeaux, 33140 Villenave d’Ornon, France; (A.M.); (B.B.); (C.D.); (D.J.); (M.M.); (D.R.)
| | - Nurit Katzir
- Newe Ya‘ar Research Center, Agricultural Research Organization, P. O. Box 1021, Ramat Yishay 3009500, Israel; (A.G.); (N.K.); (E.L.); (E.O.); (H.S.P.); (U.S.); (Y.T.); (G.T.)
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; (F.B.); (A.E.); (J.K.)
| | - Efraim Lewinsohn
- Newe Ya‘ar Research Center, Agricultural Research Organization, P. O. Box 1021, Ramat Yishay 3009500, Israel; (A.G.); (N.K.); (E.L.); (E.O.); (H.S.P.); (U.S.); (Y.T.); (G.T.)
| | - Mickael Maucourt
- INRAE, Univ. Bordeaux, UMR1332 Fruit Biology and Pathology, Bordeaux Metabolome Facility MetaboHUB, Centre INRAE de Nouvelle Aquitaine - Bordeaux, 33140 Villenave d’Ornon, France; (A.M.); (B.B.); (C.D.); (D.J.); (M.M.); (D.R.)
| | - Sagit Meir
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (A.A.); (S.M.); (S.B.-D.)
| | - Sonia Miller
- Rothamsted Research, Harpenden, Herts AL5 2JQ, UK; (J.B.); (M.H.B.); (S.M.); (J.L.W.)
| | - Roland Mumm
- Business Unit Bioscience, Wageningen University & Research, Post Box 16, 6700AA, Wageningen, Netherlands; (R.M.); (R.D.H.)
| | - Elad Oren
- Newe Ya‘ar Research Center, Agricultural Research Organization, P. O. Box 1021, Ramat Yishay 3009500, Israel; (A.G.); (N.K.); (E.L.); (E.O.); (H.S.P.); (U.S.); (Y.T.); (G.T.)
| | - Harry S. Paris
- Newe Ya‘ar Research Center, Agricultural Research Organization, P. O. Box 1021, Ramat Yishay 3009500, Israel; (A.G.); (N.K.); (E.L.); (E.O.); (H.S.P.); (U.S.); (Y.T.); (G.T.)
| | - Ilana Rogachev
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (A.A.); (S.M.); (S.B.-D.)
| | - Dominique Rolin
- INRAE, Univ. Bordeaux, UMR1332 Fruit Biology and Pathology, Bordeaux Metabolome Facility MetaboHUB, Centre INRAE de Nouvelle Aquitaine - Bordeaux, 33140 Villenave d’Ornon, France; (A.M.); (B.B.); (C.D.); (D.J.); (M.M.); (D.R.)
| | - Uzi Saar
- Newe Ya‘ar Research Center, Agricultural Research Organization, P. O. Box 1021, Ramat Yishay 3009500, Israel; (A.G.); (N.K.); (E.L.); (E.O.); (H.S.P.); (U.S.); (Y.T.); (G.T.)
| | - Jan K. Schjoerring
- Department of Plant and Environmental Sciences & Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark; (T.H.H.); (J.K.S.)
| | - Yaakov Tadmor
- Newe Ya‘ar Research Center, Agricultural Research Organization, P. O. Box 1021, Ramat Yishay 3009500, Israel; (A.G.); (N.K.); (E.L.); (E.O.); (H.S.P.); (U.S.); (Y.T.); (G.T.)
| | - Galil Tzuri
- Newe Ya‘ar Research Center, Agricultural Research Organization, P. O. Box 1021, Ramat Yishay 3009500, Israel; (A.G.); (N.K.); (E.L.); (E.O.); (H.S.P.); (U.S.); (Y.T.); (G.T.)
| | - Ric C.H. de Vos
- Business Unit Bioscience, Wageningen University & Research, Post Box 16, 6700AA, Wageningen, Netherlands; (R.M.); (R.D.H.)
| | - Jane L. Ward
- Rothamsted Research, Harpenden, Herts AL5 2JQ, UK; (J.B.); (M.H.B.); (S.M.); (J.L.W.)
| | - Elena Yeselson
- Institute of Plant Science, Agricultural Research Organization—Volcani Center, Rishon LeZiyyon 7515101, Israel; (Y.B.); (A.F.); (E.Y.)
| | - Robert D. Hall
- Business Unit Bioscience, Wageningen University & Research, Post Box 16, 6700AA, Wageningen, Netherlands; (R.M.); (R.D.H.)
- Department of Plant Physiology, Wageningen University & Research, Laboratory of Plant Physiology, Post Box 16, 6700AA, Wageningen, Netherlands
| | - Arthur A. Schaffer
- Institute of Plant Science, Agricultural Research Organization—Volcani Center, Rishon LeZiyyon 7515101, Israel; (Y.B.); (A.F.); (E.Y.)
- Correspondence: ; Tel.: + 972(3)9683646
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12
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Pan Y, Wang Y, McGregor C, Liu S, Luan F, Gao M, Weng Y. Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1-21. [PMID: 31768603 DOI: 10.1007/s00122-019-03481-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 11/11/2019] [Indexed: 05/28/2023]
Abstract
The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes CsSUN25-26-27a and CsTRM5 in cucumber, CmOFP1a in melon, and ClSUN25-26-27a in watermelon. In cucurbits, the andromonoecy (for 1-aminocyclopropane-1-carboxylate synthase) and the carpel number (for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.
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Affiliation(s)
- Yupeng Pan
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yuhui Wang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Cecilia McGregor
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Shi Liu
- College of Horticulture and, Landscape Architecture at Northeast Agricultural University, Harbin, 150030, China
| | - Feishi Luan
- College of Horticulture and, Landscape Architecture at Northeast Agricultural University, Harbin, 150030, China
| | - Meiling Gao
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Yiqun Weng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, 1575 Linden Dr., Madison, WI, 53706, USA.
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13
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Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S. Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1-25. [PMID: 30483819 DOI: 10.1007/s00122-018-3219-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/24/2018] [Indexed: 05/27/2023]
Abstract
CSSLs are a complete library of introgression lines with chromosomal segments of usually a distant genotype in an adapted background and are valuable genetic resources for basic and applied research on improvement of complex traits. Chromosome segment substitution lines (CSSLs) are genetic stocks representing the complete genome of any genotype in the background of a cultivar as overlapping segments. Ideally, each CSSL has a single chromosome segment from the donor with a maximum recurrent parent genome recovered in the background. CSSL development program requires population-wide backcross breeding and genome-wide marker-assisted selection followed by selfing. Each line in a CSSL library has a specific marker-defined large donor segment. CSSLs are evaluated for any target phenotype to identify lines significantly different from the parental line. These CSSLs are then used to map quantitative trait loci (QTLs) or causal genes. CSSLs are valuable prebreeding tools for broadening the genetic base of existing cultivars and harnessing the genetic diversity from the wild- and distant-related species. These are resources for genetic map construction, mapping QTLs, genes or gene interactions and their functional analysis for crop improvement. In the last two decades, the utility of CSSLs in identification of novel genomic regions and QTL hot spots influencing a wide range of traits has been well demonstrated in food and commercial crops. This review presents an overview of how CSSLs are developed, their status in major crops and their use in genomic studies and gene discovery.
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Affiliation(s)
- Divya Balakrishnan
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Malathi Surapaneni
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sukumar Mesapogu
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sarla Neelamraju
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India.
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14
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Argyris JM, Díaz A, Ruggieri V, Fernández M, Jahrmann T, Gibon Y, Picó B, Martín-Hernández AM, Monforte AJ, Garcia-Mas J. QTL Analyses in Multiple Populations Employed for the Fine Mapping and Identification of Candidate Genes at a Locus Affecting Sugar Accumulation in Melon ( Cucumis melo L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1679. [PMID: 29018473 PMCID: PMC5623194 DOI: 10.3389/fpls.2017.01679] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/12/2017] [Indexed: 05/24/2023]
Abstract
Sugar content is the major determinant of both fruit quality and consumer acceptance in melon (Cucumis melo L), and is a primary target for crop improvement. Near-isogenic lines (NILs) derived from the intraspecific cross between a "Piel de Sapo" (PS) type and the exotic cultivar "Songwhan Charmi" (SC), and several populations generated from the cross of PS × Ames 24294 ("Trigonus"), a wild melon, were used to identify QTL related to sugar and organic acid composition. Seventy-eight QTL were detected across several locations and different years, with three important clusters related to sugar content located on chromosomes 4, 5, and 7. Two PS × SC NILs (SC5-1 and SC5-2) sharing a common genomic interval of 1.7 Mb at the top of chromosome 5 contained QTL reducing soluble solids content (SSC) and sucrose content by an average of 29 and 68%, respectively. This cluster collocated with QTL affecting sugar content identified in other studies in lines developed from the PS × SC cross and supported the presence of a stable consensus locus involved in sugar accumulation that we named SUCQSC5.1. QTL reducing soluble solids and sucrose content identified in the "Trigonus" mapping populations, as well as QTL identified in previous studies from other ssp. agrestis sources, collocated with SUCQSC5.1, suggesting that they may be allelic and implying a role in domestication. In subNILs derived from the PS × SC5-1 cross, SUCQSC5.1 reduced SSC and sucrose content by an average of 18 and 34%, respectively, and was fine-mapped to a 56.1 kb interval containing four genes. Expression analysis of the candidate genes in mature fruit showed differences between the subNILs with PS alleles that were "high" sugar and SC alleles of "low" sugar phenotypes for MELO3C014519, encoding a putative BEL1-like homeodomain protein. Sequence differences in the gene predicted to affect protein function were restricted to SC and other ssp. agrestis cultivar groups. These results provide the basis for further investigation of genes affecting sugar accumulation in melon.
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Affiliation(s)
- Jason M. Argyris
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries, Barcelona, Spain
| | - Aurora Díaz
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Valentino Ruggieri
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries, Barcelona, Spain
| | | | | | - Yves Gibon
- UMR1332 Biologie du Fruit et Pathologie, Plateforme Métabolome Bordeaux, INRA, University of Bordeaux, Villenave d'Ornon, France
| | - Belén Picó
- Institute for the Conservation and Breeding of the Agricultural Biodiversity, Universitat Politècnica de València (COMAV-UPV), Valencia, Spain
| | - Ana M. Martín-Hernández
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries, Barcelona, Spain
| | - Antonio J. Monforte
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries, Barcelona, Spain
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Gramazio P, Prohens J, Plazas M, Mangino G, Herraiz FJ, Vilanova S. Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background. FRONTIERS IN PLANT SCIENCE 2017; 8:1477. [PMID: 28912788 PMCID: PMC5582342 DOI: 10.3389/fpls.2017.01477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/09/2017] [Indexed: 05/29/2023]
Abstract
Advanced backcrosses (ABs) and introgression lines (ILs) of eggplant (Solanum melongena) can speed up genetics and genomics studies and breeding in this crop. We have developed the first full set of ABs and ILs in eggplant using Solanum incanum, a wild eggplant that has a relatively high tolerance to drought, as a donor parent. The development of these ABs and IL eggplant populations had a low efficiency in the early stages, because of the lack of molecular markers and genomic tools. However, this dramatically improved after performing genotyping-by-sequencing in the first round of selfing, followed by high-resolution-melting single nucleotide polymorphism genotyping in subsequent selection steps. A set of 73 selected ABs covered 99% of the S. incanum genome, while 25 fixed immortal ILs, each carrying a single introgressed fragment in homozygosis, altogether spanned 61.7% of the S. incanum genome. The introgressed size fragment in the ILs contained between 0.1 and 10.9% of the S. incanum genome, with a mean value of 4.3%. Sixty-eight candidate genes involved in drought tolerance were identified in the set of ILs. This first set of ABs and ILs of eggplant will be extremely useful for the genetic dissection of traits of interest for eggplant, and represents an elite material for introduction into the breeding pipelines for developing new eggplant cultivars adapted to the challenges posed by the climate-change scenario.
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Affiliation(s)
- Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Mariola Plazas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politècnica de ValènciaValencia, Spain
| | - Giulio Mangino
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Francisco J. Herraiz
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
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16
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Ríos P, Argyris J, Vegas J, Leida C, Kenigswald M, Tzuri G, Troadec C, Bendahmane A, Katzir N, Picó B, Monforte AJ, Garcia-Mas J. ETHQV6.3 is involved in melon climacteric fruit ripening and is encoded by a NAC domain transcription factor. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:671-683. [PMID: 28493311 DOI: 10.1111/tpj.13596] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/27/2017] [Accepted: 05/02/2017] [Indexed: 05/05/2023]
Abstract
Fruit ripening is divided into climacteric and non-climacteric types depending on the presence or absence of a transient rise in respiration rate and the production of autocatalytic ethylene. Melon is ideal for the study of fruit ripening, as both climacteric and non-climacteric varieties exist. Two introgressions of the non-climacteric accession PI 161375, encompassed in the QTLs ETHQB3.5 and ETHQV6.3, into the non-climacteric 'Piel de Sapo' background are able to induce climacteric ripening independently. We report that the gene underlying ETHQV6.3 is MELO3C016540 (CmNAC-NOR), encoding a NAC (NAM, ATAF1,2, CUC2) transcription factor that is closely related to the tomato NOR (non-ripening) gene. CmNAC-NOR was functionally validated through the identification of two TILLING lines carrying non-synonymous mutations in the conserved NAC domain region. In an otherwise highly climacteric genetic background, both mutations provoked a significant delay in the onset of fruit ripening and in the biosynthesis of ethylene. The PI 161375 allele of ETHQV6.3 is similar to that of climacteric lines of the cantalupensis type and, when introgressed into the non-climacteric 'Piel de Sapo', partially restores its climacteric ripening capacity. CmNAC-NOR is expressed in fruit flesh of both climacteric and non-climacteric lines, suggesting that the causal mutation may not be acting at the transcriptional level. The use of a comparative genetic approach in a species with both climacteric and non-climacteric ripening is a powerful strategy to dissect the complex mechanisms regulating the onset of fruit ripening.
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Affiliation(s)
- Pablo Ríos
- IRTA, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Jason Argyris
- IRTA, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Juan Vegas
- IRTA, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Carmen Leida
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Merav Kenigswald
- Department of Vegetable Research, Agricultural Research Organization (ARO), Newe Ya'ar Research Center, Ramat Yishay, Israel
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Galil Tzuri
- Department of Vegetable Research, Agricultural Research Organization (ARO), Newe Ya'ar Research Center, Ramat Yishay, Israel
| | - Christelle Troadec
- Institute of Plant Sciences Paris-Saclay (IPS2), INRA, CNRS, University of Paris-Sud, University of Evry, University Paris-Diderot, Sorbone Paris-Cité, University of Paris-Saclay, Orsay, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), INRA, CNRS, University of Paris-Sud, University of Evry, University Paris-Diderot, Sorbone Paris-Cité, University of Paris-Saclay, Orsay, France
| | - Nurit Katzir
- Department of Vegetable Research, Agricultural Research Organization (ARO), Newe Ya'ar Research Center, Ramat Yishay, Israel
| | - Belén Picó
- Institute for the Conservation and Breeding of the Agricultural Biodiversity, COMAV-UPV, Universitat Politècnica de València, Valencia, Spain
| | - Antonio J Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
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17
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Pereira L, Pujol M, Garcia-Mas J, Phillips MA. Non-invasive quantification of ethylene in attached fruit headspace at 1 p.p.b. by gas chromatography-mass spectrometry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:172-183. [PMID: 28370685 DOI: 10.1111/tpj.13545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/01/2017] [Accepted: 03/17/2017] [Indexed: 05/05/2023]
Abstract
Ethylene is a gaseous plant hormone involved in defense, adaptations to environmental stress and fruit ripening. Its relevance to the latter makes its detection highly useful for physiologists interested in the onset of ripening. Produced as a sharp peak during the respiratory burst, ethylene is biologically active at tens of nl L-1 . Reliable quantification at such concentrations generally requires specialized instrumentation. Here we present a rapid, high-sensitivity method for detecting ethylene in attached fruit using a conventional gas chromatography-mass spectrometry (GC-MS) system and in situ headspace collection chambers. We apply this method to melon (Cucumis melo L.), a unique species consisting of climacteric and non-climacteric varieties, with a high variation in the climacteric phenotype among climacteric types. Using a population of recombinant inbred lines (RILs) derived from highly climacteric ('Védrantais', cantalupensis type) and non-climacteric ('Piel de Sapo', inodorus type) parental lines, we observed a significant variation for the intensity, onset and duration of the ethylene burst during fruit ripening. Our method does not require concentration, sampling times over 1 h or fruit harvest. We achieved a limit of detection of 0.41 ± 0.04 nl L-1 and a limit of quantification of 1.37 ± 0.13 nl L-1 with an analysis time per sample of 2.6 min. Validation of the analytical method indicated that linearity (>98%), precision (coefficient of variation ≤2%) and sensitivity compared favorably with dedicated optical sensors. This study adds to evidence of the characteristic climacteric ethylene burst as a complex trait whose intensity in our RIL population lies along a continuum in addition to two extremes.
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Affiliation(s)
- Lara Pereira
- IRTA, Center for Research in Agricultural Genomics (IRTA- CSIC- UAB-UB), Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Marta Pujol
- IRTA, Center for Research in Agricultural Genomics (IRTA- CSIC- UAB-UB), Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Jordi Garcia-Mas
- IRTA, Center for Research in Agricultural Genomics (IRTA- CSIC- UAB-UB), Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Michael A Phillips
- Department of Biology, University of Toronto-Mississauga, Mississauga, ON, L5L 1C6, Canada
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Cytogenetic and Molecular Characterization of B-Genome Introgression Lines of Brassica napus L. G3-GENES GENOMES GENETICS 2017; 7:77-86. [PMID: 27821632 PMCID: PMC5217125 DOI: 10.1534/g3.116.036442] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Brassica napus introgression lines (ILs), having B-genome segments from B. carinata, were assessed genetically for extent of introgression and phenotypically for siliqua shatter resistance. Introgression lines had 7-9% higher DNA content, were meiotically stable, and had almost normal pollen fertility/seed set. Segment introgressions were confirmed by fluorescent genomic in situ hybridization (fl-GISH), SSR analyses, and SNP studies. Genotyping with 48 B-genome specific SSRs detected substitutions from B3, B4, B6, and B7 chromosomes on 39 of the 69 ILs whereas SNP genotyping detected a total of 23 B-segments (≥3 Mb) from B4, B6, and B7 introgressed into 10 of the 19 (C1, C2, C3, C5, C6, C8, C9, A3, A9, A10) chromosomes in 17 ILs. The size of substitutions varied from 3.0 Mb on chromosome A9 (IL59) to 42.44 Mb on chromosome C2 (IL54), ranging from 7 to 83% of the recipient chromosome. Average siliqua strength in ILs was observed to be higher than that of B. napus parents (2.2-6.0 vs. 1.9-4.0 mJ) while siliqua strength in some of the lines was almost equal to that of the donor parent B. carinata (6.0 vs.7.2 mJ). These ILs, with large chunks of substituted B-genome, can prove to be a useful prebreeding resource for germplasm enhancement in B. napus, especially for siliqua shatter resistance.
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Barrantes W, López-Casado G, García-Martínez S, Alonso A, Rubio F, Ruiz JJ, Fernández-Muñoz R, Granell A, Monforte AJ. Exploring New Alleles Involved in Tomato Fruit Quality in an Introgression Line Library of Solanum pimpinellifolium. FRONTIERS IN PLANT SCIENCE 2016; 7:1172. [PMID: 27582742 PMCID: PMC4987366 DOI: 10.3389/fpls.2016.01172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/21/2016] [Indexed: 05/22/2023]
Abstract
We have studied a genomic library of introgression lines from the Solanum pimpinellifolium accession TO-937 into the genetic background of the "Moneymaker" cultivar in order to evaluate the accession's breeding potential. Overall, no deleterious phenotypes were observed, and the plants and fruits were phenotypically very similar to those of "Moneymaker," which confirms the feasibility of translating the current results into elite breeding programs. We identified chromosomal regions associated with traits that were both vegetative (plant vigor, trichome density) and fruit-related (morphology, organoleptic quality, color). A trichome-density locus was mapped on chromosome 10 that had not previously been associated with insect resistance, which indicates that the increment of trichomes by itself does not confer resistance. A large number of quantitative trait loci (QTLs) have been identified for fruit weight. Interestingly, fruit weight QTLs on chromosomes 1 and 10 showed a magnitude effect similar to that of QTLs previously defined as important in domestication and diversification. Low variability was observed for fruit-shape-related traits. We were, however, able to identify a QTL for shoulder height, although the effects were quite low, thus demonstrating the suitability of the current population for QTL detection. Regarding organoleptic traits, consistent QTLs were detected for soluble solid content (SSC). Interestingly, QTLs on chromosomes 2 and 9 increased SSC but did not affect fruit weight, making them quite promising for introduction in modern cultivars. Three ILs with introgressions on chromosomes 1, 2, and 10 increased the internal fruit color, making them candidates for increasing the color of modern cultivars. Comparing the QTL detection between this IL population and a recombinant inbred line population from the same cross, we found that QTL stability across generations depended on the trait, as it was very high for fruit weight but low for organoleptic traits. This difference in QTL stability may be due to a predominant additive gene action for QTLs involved in fruit weight, whereas epistatic and genetic background interactions are most likely important for the other traits.
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Affiliation(s)
- Walter Barrantes
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Polytechnic University of ValenciaValencia, Spain
- Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa RicaAlajuela, Costa Rica
| | - Gloria López-Casado
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas, University of MalagaAlgarrobo-Costa, Spain
| | - Santiago García-Martínez
- Departamento de Biología Aplicada, Escuela Politécnica Superior de Orihuela, Universidad Miguel HernándezOrihuela, Spain
| | - Aranzazu Alonso
- Departamento de Biología Aplicada, Escuela Politécnica Superior de Orihuela, Universidad Miguel HernándezOrihuela, Spain
| | - Fernando Rubio
- Departamento de Biología Aplicada, Escuela Politécnica Superior de Orihuela, Universidad Miguel HernándezOrihuela, Spain
| | - Juan J. Ruiz
- Departamento de Biología Aplicada, Escuela Politécnica Superior de Orihuela, Universidad Miguel HernándezOrihuela, Spain
| | - Rafael Fernández-Muñoz
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas, University of MalagaAlgarrobo-Costa, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Polytechnic University of ValenciaValencia, Spain
| | - Antonio J. Monforte
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Polytechnic University of ValenciaValencia, Spain
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20
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Perpiñá G, Esteras C, Gibon Y, Monforte AJ, Picó B. A new genomic library of melon introgression lines in a cantaloupe genetic background for dissecting desirable agronomical traits. BMC PLANT BIOLOGY 2016; 16:154. [PMID: 27390934 PMCID: PMC4938994 DOI: 10.1186/s12870-016-0842-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/28/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Genomic libraries of introgression lines (ILs) consist of collections of homozygous lines with a single chromosomal introgression from a donor genotype in a common, usually elite, genetic background, representing the whole donor genome in the full collection. Currently, the only available melon IL collection was generated using Piel de sapo (var. inodorus) as the recurrent background. ILs are not available in genetic backgrounds representing other important market class cultivars, such as the cantalupensis. The recent availability of genomic tools in melon, such as SNP collections and genetic maps, facilitates the development of such mapping populations. RESULTS We have developed a new genomic library of introgression lines from the Japanese cv. Ginsen Makuwa (var. makuwa) into the French Charentais-type cv. Vedrantais (var. cantalupensis) genetic background. In order to speed up the breeding program, we applied medium-throughput SNP genotyping with Sequenom MassARRAY technology in early backcross generations and High Resolution Melting in the final steps. The phenotyping of the backcross generations and of the final set of 27 ILs (averaging 1.3 introgressions/plant and covering nearly 100 % of the donor genome), in three environments, allowed the detection of stable QTLs for flowering and fruit quality traits, including some that affect fruit size in chromosomes 6 and 11, others that change fruit shape in chromosomes 7 and 11, others that change flesh color in chromosomes 2, 8 and 9, and still others that increase sucrose content and delay climacteric behavior in chromosomes 5 and 10. CONCLUSIONS A new melon IL collection in the Charentais genetic background has been developed. Genomic regions that consistently affect flowering and fruit quality traits have been identified, which demonstrates the suitability of this collection for dissecting complex traits in melon. Additionally, pre-breeding lines with new, commercially interesting phenotypes have been observed, including delayed climacteric ripening associated to higher sucrose levels, which is of great interest for Charentais cultivar breeding.
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Affiliation(s)
- Gorka Perpiñá
- />Instituto de Conservación y Mejora de la Agrodiversidad, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain
| | - Cristina Esteras
- />Instituto de Conservación y Mejora de la Agrodiversidad, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain
| | - Yves Gibon
- />UMR1332 Biologie du Fruit et Pathologie and Plateforme Métabolome, INRA-Bordeaux and Bordeaux University, 71 av. Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | - Antonio J. Monforte
- />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
| | - Belén Picó
- />Instituto de Conservación y Mejora de la Agrodiversidad, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain
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21
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Urrutia M, Schwab W, Hoffmann T, Monfort A. Genetic dissection of the (poly)phenol profile of diploid strawberry (Fragaria vesca) fruits using a NIL collection. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:151-168. [PMID: 26566833 DOI: 10.1016/j.plantsci.2015.07.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/24/2015] [Accepted: 07/25/2015] [Indexed: 05/18/2023]
Abstract
Over the last few years, diploid strawberry (Fragaria vesca) has been recognized as a model species for applied research of cultivated strawberry (Fragaria × ananassa) that is one of the most economically important crops. Berries, particularly strawberries, are known for their high antioxidant capacity due to a high concentration of (poly) phenolic compounds. Studies have already characterized the phenolic composition of fruits from sets of cultivated strawberries but the quantification of phenolics in a Fragaria mapping population has not been reported, yet. The metabolite profiling of a F. vesca near isogenic line (NIL) collection by LC-MS allowed the unambiguous identification of 22 (poly)-phenols, including anthocyanins, flavonols, flavan-3-ols, flavanones, hydroxycinnamic acid derivatives, and ellagic acid in the diploid strawberry fruit. The variability in the collection revealed that the genetic factor was more decisive than the environmental factor for the accumulation of 18 of the 24 compounds. Genotyping the NIL collection with the Axiom® IStraw90® SNPs array, we were able to map 76 stable QTLs controlling accumulation of the (poly)-phenolic compounds. They provide a powerful new tool to characterise candidate genes to increase the antioxidant capacity of fruits and produce healthier strawberries for consumers.
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Affiliation(s)
- Maria Urrutia
- IRTA, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Wilfried Schwab
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Thomas Hoffmann
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Amparo Monfort
- IRTA, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus UAB, 08193 Bellaterra, Barcelona, Spain.
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22
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Argyris JM, Pujol M, Martín-Hernández AM, Garcia-Mas J. Combined use of genetic and genomics resources to understand virus resistance and fruit quality traits in melon. PHYSIOLOGIA PLANTARUM 2015; 155:4-11. [PMID: 25594580 DOI: 10.1111/ppl.12323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/23/2014] [Indexed: 05/03/2023]
Abstract
The availability of the genome sequence of many crop species during the past few years has opened a new era in plant biology, allowing for the performance of massive genomic studies in plant species other than the classical models Arabidopsis and rice. One of these crop species is melon (Cucumis melo), a cucurbit of high economic value that has become an interesting model for the study of biological processes such as fruit ripening, sex determination and phloem transport. The recent availability of the melon genome sequence, together with a number of genetic and genomic resources, provides powerful tools that can be used to assist in the main melon breeding targets, namely disease resistance and fruit quality. In this review, we will describe recent data obtained combining the use of a melon near isogenic line (NIL) population and genomic resources to gain insight into agronomically important traits as fruit ripening, resistance to Cucumber Mosaic virus (CMV) and the accumulation of sugars in fruits.
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Affiliation(s)
- Jason M Argyris
- Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Marta Pujol
- Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Ana Montserrat Martín-Hernández
- Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Jordi Garcia-Mas
- Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
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23
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Sanseverino W, Hénaff E, Vives C, Pinosio S, Burgos-Paz W, Morgante M, Ramos-Onsins SE, Garcia-Mas J, Casacuberta JM. Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome. Mol Biol Evol 2015; 32:2760-74. [PMID: 26174143 DOI: 10.1093/molbev/msv152] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation (SV) and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding. Here, we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, SV, and transposon insertion polymorphisms. The variability found among seven melon varieties representing the species diversity and including wild accessions and highly breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed nonuniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding. We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly selected candidate regions. Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution.
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Affiliation(s)
- Walter Sanseverino
- Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Elizabeth Hénaff
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Cristina Vives
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Sara Pinosio
- Dipartimento di szience agrarie e ambientali, Università degli studi di Udine, Udine, Italy
| | - William Burgos-Paz
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Michele Morgante
- Dipartimento di szience agrarie e ambientali, Università degli studi di Udine, Udine, Italy
| | | | - Jordi Garcia-Mas
- Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
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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. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 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] [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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Saladié M, Cañizares J, Phillips MA, Rodriguez-Concepcion M, Larrigaudière C, Gibon Y, Stitt M, Lunn JE, Garcia-Mas J. Comparative transcriptional profiling analysis of developing melon (Cucumis melo L.) fruit from climacteric and non-climacteric varieties. BMC Genomics 2015; 16:440. [PMID: 26054931 PMCID: PMC4460886 DOI: 10.1186/s12864-015-1649-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 05/20/2015] [Indexed: 11/14/2022] Open
Abstract
Background In climacteric fruit-bearing species, the onset of fruit ripening is marked by a transient rise in respiration rate and autocatalytic ethylene production, followed by rapid deterioration in fruit quality. In non-climacteric species, there is no increase in respiration or ethylene production at the beginning or during fruit ripening. Melon is unusual in having climacteric and non-climacteric varieties, providing an interesting model system to compare both ripening types. Transcriptomic analysis of developing melon fruits from Védrantais and Dulce (climacteric) and Piel de sapo and PI 161375 (non-climacteric) varieties was performed to understand the molecular mechanisms that differentiate the two fruit ripening types. Results Fruits were harvested at 15, 25, 35 days after pollination and at fruit maturity. Transcript profiling was performed using an oligo-based microarray with 75 K probes. Genes linked to characteristic traits of fruit ripening were differentially expressed between climacteric and non-climacteric types, as well as several transcription factor genes and genes encoding enzymes involved in sucrose catabolism. The expression patterns of some genes in PI 161375 fruits were either intermediate between. Piel de sapo and the climacteric varieties, or more similar to the latter. PI 161375 fruits also accumulated some carotenoids, a characteristic trait of climacteric varieties. Conclusions Simultaneous changes in transcript abundance indicate that there is coordinated reprogramming of gene expression during fruit development and at the onset of ripening in both climacteric and non-climacteric fruits. The expression patterns of genes related to ethylene metabolism, carotenoid accumulation, cell wall integrity and transcriptional regulation varied between genotypes and was consistent with the differences in their fruit ripening characteristics. There were differences between climacteric and non-climacteric varieties in the expression of genes related to sugar metabolism suggesting that they may be potential determinants of sucrose content and post-harvest stability of sucrose levels in fruit. Several transcription factor genes were also identified that were differentially expressed in both types, implicating them in regulation of ripening behaviour. The intermediate nature of PI 161375 suggested that classification of melon fruit ripening behaviour into just two distinct types is an over-simplification, and that in reality there is a continuous spectrum of fruit ripening behaviour. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1649-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Montserrat Saladié
- IRTA, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain. .,Present address: School of Chemistry and Biochemistry, Biochemistry and Molecular Biology, The University of Western Australia, Crawley, WA, 6009, Australia.
| | - Joaquin Cañizares
- COMAV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universitat Politècnica de València (UPV), Camino de Vera s/n, Valencia, 46022, Spain.
| | - Michael A Phillips
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Manuel Rodriguez-Concepcion
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Christian Larrigaudière
- IRTA, Parc Científic i Tecnològic Agroalimentari, Parc de Gardeny, Edifici Fruitcentre, Lleida, 25003, Spain.
| | - Yves Gibon
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam, 14476, (OT) Golm, Germany. .,Present address: INRA Bordeaux, University of Bordeaux, UMR1332 Fruit Biology and Pathology, Villenave d'Ornon, F-33883, France.
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam, 14476, (OT) Golm, Germany.
| | - John Edward Lunn
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam, 14476, (OT) Golm, Germany.
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
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Leida C, Moser C, Esteras C, Sulpice R, Lunn JE, de Langen F, Monforte AJ, Picó B. Variability of candidate genes, genetic structure and association with sugar accumulation and climacteric behavior in a broad germplasm collection of melon (Cucumis melo L.). BMC Genet 2015; 16:28. [PMID: 25886993 PMCID: PMC4380257 DOI: 10.1186/s12863-015-0183-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/18/2015] [Indexed: 11/15/2022] Open
Abstract
Background A collection of 175 melon (Cucumis melo L.) accessions (including wild relatives, feral types, landraces, breeding lines and commercial cultivars) from 50 countries was selected to study the phenotypic variability for ripening behavior and sugar accumulation. The variability of single nucleotide polymorphisms (SNPs) at 53 selected candidate genes involved in sugar accumulation and fruit ripening processes was studied, as well as their association with phenotypic variation of related traits. Results The collection showed a strong genetic structure, defining seven groups plus a number of accessions that could not be associated to any of the groups (admixture), which fitted well with the botanical classification of melon varieties. The variability in candidate genes for ethylene, cell wall and sugar-related traits was high and similar to SNPs located in reference genes. Variability at ripening candidate genes had an important weight on the genetic stratification of melon germplasm, indicating that traditional farmers might have selected for ripening traits during cultivar diversification. A strong relationship was also found between the genetic structure and phenotypic diversity, which could hamper genetic association studies. Accessions belonging to the ameri group are the most appropriate for association analysis given the high phenotypic and molecular diversity within the group, and lack of genetic structure. The most remarkable association was found between sugar content and SNPs in LG III, where a hotspot of sugar content QTLs has previously been defined. By studying the differences in allelic variation of SNPs within horticultural groups with specific phenotypic features, we also detected differential variation in sugar-related candidates located in LGIX and LGX, and in ripening-related candidates located in LGII and X, all in regions with previously mapped QTLs for the corresponding traits. Conclusions In the current study we have found an important variability at both the phenotypic and candidate gene levels for ripening behavior and sugar accumulation in melon fruit. By combination of differences in allelic diversity and association analysis, we have identified several candidate genes that may be involved in the melon phenotypic diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0183-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carmen Leida
- Research and Innovation Center, Department Genomics and Biology of Fruit Crops, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele, Italy.
| | - Claudio Moser
- Research and Innovation Center, Department Genomics and Biology of Fruit Crops, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele, Italy.
| | - Cristina Esteras
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de Valencia, Camino de Vera s/n, 46022, Valencia, Spain.
| | - Ronan Sulpice
- Max-Planck-Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam, Germany. .,Plant Systems Biology Research Laboratory, Department of Botany and Plant Science, Plant and AgriBiosciences Research Centre, National University of Galway, University Road, Galway, Ireland.
| | - John E Lunn
- Max-Planck-Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam, Germany.
| | - Frank de Langen
- HMCLAUSE (Business Unit of Limagrain), Station de Mas Saint Pierre, La Galine, 13210, Saint-Rémy-de-Provence, France.
| | - Antonio J Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain.
| | - Belen Picó
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de Valencia, Camino de Vera s/n, 46022, Valencia, Spain.
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Argyris JM, Ruiz-Herrera A, Madriz-Masis P, Sanseverino W, Morata J, Pujol M, Ramos-Onsins SE, Garcia-Mas J. Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly. BMC Genomics 2015; 16:4. [PMID: 25612459 PMCID: PMC4316794 DOI: 10.1186/s12864-014-1196-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 12/22/2014] [Indexed: 01/01/2023] Open
Abstract
Background The genome of the melon (Cucumis melo L.) double-haploid line DHL92 was recently sequenced, with 87.5 and 80.8% of the scaffold assembly anchored and oriented to the 12 linkage groups, respectively. However, insufficient marker coverage and a lack of recombination left several large, gene rich scaffolds unanchored, and some anchored scaffolds unoriented. To improve the anchoring and orientation of the melon genome assembly, we used resequencing data between the parental lines of DHL92 to develop a new set of SNP markers from unanchored scaffolds. Results A high-resolution genetic map composed of 580 SNPs was used to anchor 354.8 Mb of sequence, contained in 141 scaffolds (average size 2.5 Mb) and corresponding to 98.2% of the scaffold assembly, to the 12 melon chromosomes. Over 325.4 Mb (90%) of the assembly was oriented. The genetic map revealed regions of segregation distortion favoring SC alleles as well as recombination suppression regions coinciding with putative centromere, 45S, and 5S rDNA sites. New chromosome-scale pseudomolecules were created by incorporating to the previous v3.5 version an additional 38.3 Mb of anchored sequence representing 1,837 predicted genes contained in 55 scaffolds. Using fluorescent in situ hybridization (FISH) with BACs that produced chromosome-specific signals, melon chromosomes that correspond to the twelve linkage groups were identified, and a standardized karyotype of melon inbred line T111 was developed. Conclusions By utilizing resequencing data and targeted SNP selection combined with a large F2 mapping population, we significantly improved the quantity of anchored and oriented melon scaffold genome assembly. Using genome information combined with FISH mapping provided the first cytogenetic map of an inodorus melon type. With these results it was possible to make inferences on melon chromosome structure by relating zones of recombination suppression to centromeres and 45S and 5S heterochromatic regions. This study represents the first steps towards the integration of the high-resolution genetic and cytogenetic maps with the genomic sequence in melon that will provide more information on genome organization and allow for the improvement of the melon genome draft sequence. Electronic supplementary material The online version of this article (doi:10.1186/s12864-014-1196-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jason M Argyris
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB, 08193, Barcelona, Spain. .,Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Campus UAB, 08193, Barcelona, Spain.
| | - Pablo Madriz-Masis
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
| | - Walter Sanseverino
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain. .,Present Address: Sequentia Biotech, Campus UAB - Edifici CRAG, Bellaterra - Cerdanyola del Vallès, 08193, Barcelona, Spain.
| | - Jordi Morata
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
| | - Marta Pujol
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
| | | | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
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Falke KC, Mahone GS, Bauer E, Haseneyer G, Miedaner T, Breuer F, Frisch M. Genome-wide prediction methods for detecting genetic effects of donor chromosome segments in introgression populations. BMC Genomics 2014; 15:782. [PMID: 25213628 PMCID: PMC4169839 DOI: 10.1186/1471-2164-15-782] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 08/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Introgression populations are used to make the genetic variation of unadapted germplasm or wild relatives of crops available for plant breeding. They consist of introgression lines that carry small chromosome segments from an exotic donor in the genetic background of an elite line. The goal of our study was to investigate the detection of favorable donor chromosome segments in introgression lines with statistical methods developed for genome-wide prediction. RESULTS Computer simulations showed that genome-wide prediction employing heteroscedastic marker variances had a greater power and a lower false positive rate compared with homoscedastic marker variances when the phenotypic difference between the donor and recipient lines was controlled by few genes. The simulations helped to interpret the analyses of glycosinolate and linolenic acid content in a rapeseed introgression population and plant height in a rye introgression population. These analyses support the superiority of genome-wide prediction approaches that use heteroscedastic marker variances. CONCLUSIONS We conclude that genome-wide prediction methods in combination with permutation tests can be employed for analysis of introgression populations. They are particularly useful when introgression lines carry several donor segments or when the donor segments of different introgression lines are overlapping.
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Affiliation(s)
- Karen Christin Falke
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, 35392 Giessen, Germany.
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Saladié M, Wright LP, Garcia-Mas J, Rodriguez-Concepcion M, Phillips MA. The 2-C-methylerythritol 4-phosphate pathway in melon is regulated by specialized isoforms for the first and last steps. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5077-92. [PMID: 25013119 PMCID: PMC4144782 DOI: 10.1093/jxb/eru275] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway provides the precursors for the biosynthesis of plastidial isoprenoids, which include the carotenoid pigments of many fruits. We have analysed the genes encoding the seven enzymes of the MEP pathway in melon (Cucumis melo L.) and determined that the first one, 1-deoxyxylulose 5-phosphate synthase (DXS), and the last one, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (HDR), are represented in the genome as a small gene family and paralogous pair, respectively. In the case of DXS, three genes encode functional DXS activities which fall into previously established type I (CmDXS1) and II (CmDXS2a and CmDXS2b) categories, while a fourth DXS-like gene belonging to the type III group did not encode a protein with DXS activity. Their expression patterns and phylogenies suggest that CmDXS1 is functionally specialized for developmental and photosynthetic processes, while CmDXS2a and CmDXS2b are induced in flowers and ripening fruit of orange- (but not white-) fleshed varieties, coinciding with β-carotene accumulation. This is the first instance connecting type II DXS genes to specialized isoprenoid biosynthesis in the fruit of an agronomically important species. Two HDR paralogues were shown to encode functional enzymes, although only CmHDR1 was highly expressed in the tissues and developmental stages tested. Phylogenetic analysis showed that in cucurbits such as melon, these HDR paralogues probably arose through individual gene duplications in a common angiosperm ancestor, mimicking a prior division in gymnosperms, while other flowering plants, including apple, soy, canola, and poplar, acquired HDR duplicates recently as homoeologues through large-scale genome duplications. We report the influence of gene duplication history on the regulation of the MEP pathway in melon and the role of specialized MEP-pathway isoforms in providing precursors for β-carotene production in orange-fleshed melon varieties.
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Affiliation(s)
- Montserrat Saladié
- Plant and Animal Genomics Programme, Institut de Recerca i Tecnologia Agroalimentàries and Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Louwrance P Wright
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans Knöll Street 8, 07745 Jena, Germany
| | - Jordi Garcia-Mas
- Plant and Animal Genomics Programme, Institut de Recerca i Tecnologia Agroalimentàries and Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Manuel Rodriguez-Concepcion
- Plant Metabolism and Metabolic Engineering Programme, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Michael A Phillips
- Plant Metabolism and Metabolic Engineering Programme, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
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Díaz A, Zarouri B, Fergany M, Eduardo I, Álvarez JM, Picó B, Monforte AJ. Mapping and introgression of QTL involved in fruit shape transgressive segregation into ‘piel de sapo’ melon (cucumis melo l.) [corrected]. PLoS One 2014; 9:e104188. [PMID: 25126852 PMCID: PMC4134209 DOI: 10.1371/journal.pone.0104188] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 07/10/2014] [Indexed: 11/19/2022] Open
Abstract
A mapping F2 population from the cross ‘Piel de Sapo’ × PI124112 was selectively genotyped to study the genetic control of morphological fruit traits by QTL (Quantitative Trait Loci) analysis. Ten QTL were identified, five for FL (Fruit Length), two for FD (Fruit Diameter) and three for FS (Fruit Shape). At least one robust QTL per character was found, flqs8.1 (LOD = 16.85, R2 = 34%), fdqs12.1 (LOD = 3.47, R2 = 11%) and fsqs8.1 (LOD = 14.85, R2 = 41%). flqs2.1 and fsqs2.1 cosegregate with gene a (andromonoecious), responsible for flower sex determination and with pleiotropic effects on FS. They display a positive additive effect (a) value, so the PI124112 allele causes an increase in FL and FS, producing more elongated fruits. Conversely, the negative a value for flqs8.1 and fsqs8.1 indicates a decrease in FL and FS, what results in rounder fruits, even if PI124112 produces very elongated melons. This is explained by a significant epistatic interaction between fsqs2.1 and fsqs8.1, where the effects of the alleles at locus a are attenuated by the additive PI124112 allele at fsqs8.1. Roundest fruits are produced by homozygous for PI124112 at fsqs8.1 that do not carry any dominant A allele at locus a (PiPiaa). A significant interaction between fsqs8.1 and fsqs12.1 was also detected, with the alleles at fsqs12.1 producing more elongated fruits. fsqs8.1 seems to be allelic to QTL discovered in other populations where the exotic alleles produce elongated fruits. This model has been validated in assays with backcross lines along 3 years and ultimately obtaining a fsqs8.1-NIL (Near Isogenic Line) in ‘Piel de Sapo’ background which yields round melons.
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Affiliation(s)
- Aurora Díaz
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- * E-mail: (AD); (AJM)
| | - Belkacem Zarouri
- Laboratorio de Biología Molecular. Dpto. Investigación Agroalimentaria. Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), Alcalá de Henares, Madrid, Spain
| | - Mohamed Fergany
- Centre de Recerca en Agrigenòmica (CRAG), IRTA-CSIC-UAB, Bellaterra, Cerdanyola del Vallès, Barcelona, Spain
| | - Iban Eduardo
- Centre de Recerca en Agrigenòmica (CRAG), IRTA-CSIC-UAB, Bellaterra, Cerdanyola del Vallès, Barcelona, Spain
| | - José M. Álvarez
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
| | - Belén Picó
- COMAV-UPV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universitad Politécnica de Valencia, Valencia, Spain
| | - Antonio J. Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- * E-mail: (AD); (AJM)
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Dos-Santos N, Bueso MC, Fernández-Trujillo JP. Aroma volatiles as biomarkers of textural differences at harvest in non-climacteric near-isogenic lines of melon. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.09.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Delgado-Goñi T, Campo S, Martín-Sitjar J, Cabañas ME, San Segundo B, Arús C. Assessment of a 1H high-resolution magic angle spinning NMR spectroscopy procedure for free sugars quantification in intact plant tissue. PLANTA 2013; 238:397-413. [PMID: 23824526 DOI: 10.1007/s00425-013-1924-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/14/2013] [Indexed: 06/02/2023]
Abstract
In most plants, sucrose is the primary product of photosynthesis, the transport form of assimilated carbon, and also one of the main factors determining sweetness in fresh fruits. Traditional methods for sugar quantification (mainly sucrose, glucose and fructose) require obtaining crude plant extracts, which sometimes involve substantial sample manipulation, making the process time-consuming and increasing the risk of sample degradation. Here, we describe and validate a fast method to determine sugar content in intact plant tissue by using high-resolution magic angle spinning nuclear magnetic resonance spectroscopy (HR-MAS NMR). The HR-MAS NMR method was used for quantifying sucrose, glucose and fructose in mesocarp tissues from melon fruits (Cucumis melo var. reticulatus and Cucumis melo var. cantalupensis). The resulting sugar content varied among individual melons, ranging from 1.4 to 7.3 g of sucrose, 0.4-2.5 g of glucose; and 0.73-2.83 g of fructose (values per 100 g fw). These values were in agreement with those described in the literature for melon fruit tissue, and no significant differences were found when comparing them with those obtained using the traditional, enzymatic procedure, on melon tissue extracts. The HR-MAS NMR method offers a fast (usually <30 min) and sensitive method for sugar quantification in intact plant tissues, it requires a small amount of tissue (typically 50 mg fw) and avoids the interferences and risks associated with obtaining plant extracts. Furthermore, this method might also allow the quantification of additional metabolites detectable in the plant tissue NMR spectrum.
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Affiliation(s)
- Teresa Delgado-Goñi
- Unitat de Biociències, Dept. Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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Vegas J, Garcia-Mas J, Monforte AJ. Interaction between QTLs induces an advance in ethylene biosynthesis during melon fruit ripening. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1531-44. [PMID: 23443139 DOI: 10.1007/s00122-013-2071-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 02/12/2013] [Indexed: 05/03/2023]
Abstract
The coexistence of both climacteric and non-climacteric genotypes and the availability of a set of genetic and genomic resources make melon a suitable model for genetic studies of fruit ripening. We have previously described a QTL, ETHQB3.5, which induces climacteric fruit ripening in the near-isogenic line (NIL) SC3-5 that harbors an introgression on linkage group (LG) III from the non-climacteric melon accession PI 161375 in the, also non-climacteric cultivar, "Piel de Sapo" genetic background. In the current study, a new major QTL, ETHQV6.3, on LG VI was detected on an additional introgression in the same NIL. These QTLs are capable, individually, of inducing climacteric ripening in the non-climacteric background, the effects of ETHQV6.3 being greater than that of ETHQB3.5. The QTLs interact epistatically, advancing the timing of ethylene biosynthesis during ripening and, therefore, the climacteric responses. ETHQV6.3 was fine-mapped to a 4.5 Mb physical region of the melon genome, probably in the centromeric region of LG VI. The results presented will be of value in the molecular identification of the gene underlying ETHQV6.3.
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Affiliation(s)
- Juan Vegas
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
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Corbacho J, Romojaro F, Pech JC, Latché A, Gomez-Jimenez MC. Transcriptomic events involved in melon mature-fruit abscission comprise the sequential induction of cell-wall degrading genes coupled to a stimulation of endo and exocytosis. PLoS One 2013; 8:e58363. [PMID: 23484021 PMCID: PMC3590154 DOI: 10.1371/journal.pone.0058363] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 02/03/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Mature-fruit abscission (MFA) in fleshy-fruit is a genetically controlled process with mechanisms that, contrary to immature-fruit abscission, has not been fully characterized. Here, we use pyrosequencing to characterize the transcriptomes of melon abscission zone (AZ) at three stages during AZ-cell separation in order to understand MFA control at an early stage of AZ-activation. PRINCIPAL FINDINGS The results show that by early induction of MFA, the melon AZ exhibits major gene induction, while by late induction of MFA, melon AZ shows major gene repression. Although some genes displayed similar regulation in both early and late induction of abscission, such as EXT1-EXT4, EGase1, IAA2, ERF1, AP2D15, FLC, MADS2, ERAF17, SAP5 and SCL13 genes, the majority had different expression patterns. This implies that time-specific events occur during MFA, and emphasizes the value of characterizing multiple time-specific abscission transcriptomes. Analysis of gene-expression from these AZs reveal that a sequential induction of cell-wall-degrading genes is associated with the upregulation of genes involved in endo and exocytosis, and a shift in plant-hormone metabolism and signaling genes during MFA. This is accompanied by transcriptional activity of small-GTPases and synthaxins together with tubulins, dynamins, V-type ATPases and kinesin-like proteins potentially involved in MFA signaling. Early events are potentially controlled by down-regulation of MADS-box, AP2/ERF and Aux/IAA transcription-factors, and up-regulation of homeobox, zinc finger, bZIP, and WRKY transcription-factors, while late events may be controlled by up-regulation of MYB transcription-factors. SIGNIFICANCE Overall, the data provide a comprehensive view on MFA in fleshy-fruit, identifying candidate genes and pathways associated with early induction of MFA. Our comprehensive gene-expression profile will be very useful for elucidating gene regulatory networks of the MFA in fleshy-fruit.
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Affiliation(s)
- Jorge Corbacho
- Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz, Spain
| | | | - Jean-Claude Pech
- UMR990 INRA/INP-ENSA Toulouse, Avenue de l'Agrobiopole, Castanet-Tolosan, France
| | - Alain Latché
- UMR990 INRA/INP-ENSA Toulouse, Avenue de l'Agrobiopole, Castanet-Tolosan, France
| | - Maria C. Gomez-Jimenez
- Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz, Spain
- * E-mail:
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Mahone GS, Frisch M, Miedaner T, Wilde P, Wortmann H, Falke KC. Identification of quantitative trait loci in rye introgression lines carrying multiple donor chromosome segments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:49-58. [PMID: 22926309 DOI: 10.1007/s00122-012-1958-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 07/21/2012] [Indexed: 06/01/2023]
Abstract
Introgression libraries can be used to make favorable genetic variation of exotic donor genotypes available in the genetic background of elite breeding material. Our objective was to employ a combination of the Dunnett test and a linear model analysis to identify favorable donor alleles in introgression lines (ILs) that carry long or multiple donor chromosome segments (DCS). We reanalyzed a dataset of two rye introgression libraries that consisted of ILs carrying on average about four donor segments. After identifying ILs that had a significantly better per se or testcross performance than the recipient line with the Dunnett test, the linear model analysis was in most instances able to clearly identify the donor regions that were responsible for the superior performance. The precise localization of the favorable DCS allowed a detailed analysis of pleiotropic effects and the study of the consistency of effects for per se and testcross performance. We conclude that in many cases the linear model analysis allows the assignment of donor effects to individual DCS even for ILs with long or multiple donor segments. This may considerably increase the efficiency of producing sub-ILs, because only such segments need to be isolated that are known to have a significant effect on the phenotype.
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Affiliation(s)
- Gregory S Mahone
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, 35392 Giessen, Germany
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Roig C, Fita A, Ríos G, Hammond JP, Nuez F, Picó B. Root transcriptional responses of two melon genotypes with contrasting resistance to Monosporascus cannonballus (Pollack et Uecker) infection. BMC Genomics 2012; 13:601. [PMID: 23134692 PMCID: PMC3542287 DOI: 10.1186/1471-2164-13-601] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 10/31/2012] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Monosporascus cannonballus is the main causal agent of melon vine decline disease. Several studies have been carried out mainly focused on the study of the penetration of this pathogen into melon roots, the evaluation of symptoms severity on infected roots, and screening assays for breeding programs. However, a detailed molecular view on the early interaction between M. cannonballus and melon roots in either susceptible or resistant genotypes is lacking. In the present study, we used a melon oligo-based microarray to investigate the gene expression responses of two melon genotypes, Cucumis melo 'Piel de sapo' ('PS') and C. melo 'Pat 81', with contrasting resistance to the disease. This study was carried out at 1 and 3 days after infection (DPI) by M. cannonballus. RESULTS Our results indicate a dissimilar behavior of the susceptible vs. the resistant genotypes from 1 to 3 DPI. 'PS' responded with a more rapid infection response than 'Pat 81' at 1 DPI. At 3 DPI the total number of differentially expressed genes identified in 'PS' declined from 451 to 359, while the total number of differentially expressed transcripts in 'Pat 81' increased from 187 to 849. Several deregulated transcripts coded for components of Ca2+ and jasmonic acid (JA) signalling pathways, as well as for other proteins related to defence mechanisms. Transcriptional differences in the activation of the JA-mediated response in 'Pat 81' compared to 'PS' suggested that JA response might be partially responsible for their observed differences in resistance. CONCLUSIONS As a result of this study we have identified for the first time a set of candidate genes involved in the root response to the infection of the pathogen causing melon vine decline. This information is useful for understanding the disease progression and resistance mechanisms few days after inoculation.
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Affiliation(s)
- Cristina Roig
- Institute for the Conservation and Breeding of the Agricultural Biodiversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022, Valencia, Spain
| | - Ana Fita
- Institute for the Conservation and Breeding of the Agricultural Biodiversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022, Valencia, Spain
| | - Gabino Ríos
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain
| | - John P Hammond
- School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
| | - Fernando Nuez
- Institute for the Conservation and Breeding of the Agricultural Biodiversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022, Valencia, Spain
| | - Belén Picó
- Institute for the Conservation and Breeding of the Agricultural Biodiversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022, Valencia, Spain
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Rodríguez-Moreno L, González VM, Benjak A, Martí MC, Puigdomènech P, Aranda MA, Garcia-Mas J. Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin. BMC Genomics 2011; 12:424. [PMID: 21854637 PMCID: PMC3175227 DOI: 10.1186/1471-2164-12-424] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 08/20/2011] [Indexed: 01/31/2023] Open
Abstract
Background The melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and genetic studies. Despite similar nuclear and chloroplast genome sizes, cucurbits show great variation when their mitochondrial genomes are compared. The melon possesses the largest plant mitochondrial genome, as much as eight times larger than that of other cucurbits. Results The nucleotide sequences of the melon chloroplast and mitochondrial genomes were determined. The chloroplast genome (156,017 bp) included 132 genes, with 98 single-copy genes dispersed between the small (SSC) and large (LSC) single-copy regions and 17 duplicated genes in the inverted repeat regions (IRa and IRb). A comparison of the cucumber and melon chloroplast genomes showed differences in only approximately 5% of nucleotides, mainly due to short indels and SNPs. Additionally, 2.74 Mb of mitochondrial sequence, accounting for 95% of the estimated mitochondrial genome size, were assembled into five scaffolds and four additional unscaffolded contigs. An 84% of the mitochondrial genome is contained in a single scaffold. The gene-coding region accounted for 1.7% (45,926 bp) of the total sequence, including 51 protein-coding genes, 4 conserved ORFs, 3 rRNA genes and 24 tRNA genes. Despite the differences observed in the mitochondrial genome sizes of cucurbit species, Citrullus lanatus (379 kb), Cucurbita pepo (983 kb) and Cucumis melo (2,740 kb) share 120 kb of sequence, including the predicted protein-coding regions. Nevertheless, melon contained a high number of repetitive sequences and a high content of DNA of nuclear origin, which represented 42% and 47% of the total sequence, respectively. Conclusions Whereas the size and gene organisation of chloroplast genomes are similar among the cucurbit species, mitochondrial genomes show a wide variety of sizes, with a non-conserved structure both in gene number and organisation, as well as in the features of the noncoding DNA. The transfer of nuclear DNA to the melon mitochondrial genome and the high proportion of repetitive DNA appear to explain the size of the largest mitochondrial genome reported so far.
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Affiliation(s)
- Luis Rodríguez-Moreno
- Departamento de Biología del Estrés y Patología Vegetal, Centro deEdafología y Biología Aplicada del Segura (CEBAS)-CSIC, 30100 Espinardo(Murcia), Spain
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Dos-Santos N, Jimenez-Araujo A, Rodriguez-Arcos R, Fernandez-Trujillo JP. Cell wall polysaccharides of near-isogenic lines of melon (Cucumis melo L.) and their inbred parentals which show differential flesh firmness or physiological behavior. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:7773-84. [PMID: 21608971 DOI: 10.1021/jf201155a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We characterized differences in cell wall material and polysaccharide structures, due to the quantitative trait loci associated with higher flesh firmness in a nonclimacteric near-isogenic line (NIL) SC7-2, and with the climacteric behavior of the NIL SC3-5-1, using their nonclimacteric inbred parentals, "Piel de Sapo" (PS) and PI 161375 (SC). PS was firmer and had a higher ripening index and greater hemicellulosic content than SC, with its lower wall material yield, and uronic acid, neutral sugar, cellulose and free sugar content and higher pectic content. SC3-5-1 showed lower uronic acid values, a higher soluble solid content, and similar flesh firmness to PS. SC3-5-1 yielded mainly high molecular weight polysaccharides in the imidazole-soluble fraction than PS. SC7-2 showed greater flesh firmness, a higher neutral sugar (especially galactose and mannose) and uronic acid content, together with a larger cellulose and α-cellulose residue than PS. SC7-2 also contained more polysaccharides of low molecular weight in the first pectic fraction and shifted toward higher molecular weights in the main peak of the 4 M potassium-soluble fraction compared with PS.
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Affiliation(s)
- Noelia Dos-Santos
- Department of Agricultural and Food Engineering, Technical University of Cartagena, Cartagena, Spain
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González VM, Benjak A, Hénaff EM, Mir G, Casacuberta JM, Garcia-Mas J, Puigdomènech P. Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy. BMC PLANT BIOLOGY 2010; 10:246. [PMID: 21073723 PMCID: PMC3095328 DOI: 10.1186/1471-2229-10-246] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 11/12/2010] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cucumis melo (melon) belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has a high intra-specific genetic variation, morphologic diversity and a small genome size (454 Mb), which make it suitable for a great variety of molecular and genetic studies. A number of genetic and genomic resources have already been developed, such as several genetic maps, BAC genomic libraries, a BAC-based physical map and EST collections. Sequence information would be invaluable to complete the picture of the melon genomic landscape, furthering our understanding of this species' evolution from its relatives and providing an important genetic tool. However, to this day there is little sequence data available, only a few melon genes and genomic regions are deposited in public databases. The development of massively parallel sequencing methods allows envisaging new strategies to obtain long fragments of genomic sequence at higher speed and lower cost than previous Sanger-based methods. RESULTS In order to gain insight into the structure of a significant portion of the melon genome we set out to perform massive sequencing of pools of BAC clones. For this, a set of 57 BAC clones from a double haploid line was sequenced in two pools with the 454 system using both shotgun and paired-end approaches. The final assembly consists of an estimated 95% of the actual size of the melon BAC clones, with most likely complete sequences for 50 of the BACs, and a total sequence coverage of 39x. The accuracy of the assembly was assessed by comparing the previously available Sanger sequence of one of the BACs against its 454 sequence, and the polymorphisms found involved only 1.7 differences every 10,000 bp that were localized in 15 homopolymeric regions and two dinucleotide tandem repeats. Overall, the study provides approximately 6.7 Mb or 1.5% of the melon genome. The analysis of this new data has allowed us to gain further insight into characteristics of the melon genome such as gene density, average protein length, or microsatellite and transposon content. The annotation of the BAC sequences revealed a high degree of collinearity and protein sequence identity between melon and its close relative Cucumis sativus (cucumber). Transposon content analysis of the syntenic regions suggests that transposition activity after the split of both cucurbit species has been low in cucumber but very high in melon. CONCLUSIONS The results presented here show that the strategy followed, which combines shotgun and BAC-end sequencing together with anchored marker information, is an excellent method for sequencing specific genomic regions, especially from relatively compact genomes such as that of melon. However, in agreement with other results, this map-based, BAC approach is confirmed to be an expensive way of sequencing a whole plant genome. Our results also provide a partial description of the melon genome's structure. Namely, our analysis shows that the melon genome is highly collinear with the smaller one of cucumber, the size difference being mainly due to the expansion of intergenic regions and proliferation of transposable elements.
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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
| | - Andrej Benjak
- IRTA, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Carretera de Cabrils Km 2, 08348 (Barcelona), Spain
| | - Elizabeth Marie Hénaff
- Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Jordi Girona, 18-26, 08034 Barcelona, Spain
| | - Gisela Mir
- IRTA, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Carretera de Cabrils Km 2, 08348 (Barcelona), Spain
| | - Josep M Casacuberta
- Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Jordi Girona, 18-26, 08034 Barcelona, Spain
| | - Jordi Garcia-Mas
- 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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González VM, Rodríguez-Moreno L, Centeno E, Benjak A, Garcia-Mas J, Puigdomènech P, Aranda MA. Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries. BMC Genomics 2010; 11:618. [PMID: 21054843 PMCID: PMC3091759 DOI: 10.1186/1471-2164-11-618] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 11/05/2010] [Indexed: 11/10/2022] Open
Abstract
Background Although melon (Cucumis melo L.) is an economically important fruit crop, no genome-wide sequence information is openly available at the current time. We therefore sequenced BAC-ends representing a total of 33,024 clones, half of them from a previously described melon BAC library generated with restriction endonucleases and the remainder from a new random-shear BAC library. Results We generated a total of 47,140 high-quality BAC-end sequences (BES), 91.7% of which were paired-BES. Both libraries were assembled independently and then cross-assembled to obtain a final set of 33,372 non-redundant, high-quality sequences. These were grouped into 6,411 contigs (4.5 Mb) and 26,961 non-assembled BES (14.4 Mb), representing ~4.2% of the melon genome. The sequences were used to screen genomic databases, identifying 7,198 simple sequence repeats (corresponding to one microsatellite every 2.6 kb) and 2,484 additional repeats of which 95.9% represented transposable elements. The sequences were also used to screen expressed sequence tag (EST) databases, revealing 11,372 BES that were homologous to ESTs. This suggests that ~30% of the melon genome consists of coding DNA. We observed regions of microsynteny between melon paired-BES and six other dicotyledonous plant genomes. Conclusion The analysis of nearly 50,000 BES from two complementary genomic libraries covered ~4.2% of the melon genome, providing insight into properties such as microsatellite and transposable element distribution, and the percentage of coding DNA. The observed synteny between melon paired-BES and six other plant genomes showed that useful comparative genomic data can be derived through large scale BAC-end sequencing by anchoring a small proportion of the melon genome to other sequenced genomes.
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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
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Fernandez-Silva I, Moreno E, Essafi A, Fergany M, Garcia-Mas J, Martín-Hernandez AM, Alvarez JM, Monforte AJ. Shaping melons: agronomic and genetic characterization of QTLs that modify melon fruit morphology. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:931-40. [PMID: 20506012 DOI: 10.1007/s00122-010-1361-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 05/12/2010] [Indexed: 05/03/2023]
Abstract
The consistency of quantitative trait locus (QTL) effects among genetic backgrounds is a key factor for introgressing QTLs from initial mapping experiments into applied breeding programs. We have selected four QTLs (fs6.4, fw4.3, fw4.4 and fw8.1) involved in melon fruit morphology that had previously been detected in a collection of introgression lines derived from the cross between a Spanish cultivar, "Piel de Sapo," and the Korean accession PI161375 (Songwan Charmi). Introgression lines harboring these QTLs were crossed with an array of melon inbred lines representative of the most important cultivar types. Hybrids of the introgression and inbred lines, with the appropriate controls, were evaluated in replicated agronomic trials. The effects of the QTLs were consistent among the different genetic backgrounds, demonstrating the utility of these QTLs for applied breeding programs in modifying melon fruit morphology. Three QTLs, fw4.4, fs6.4 and fs12.1 were subjected to further study in order to map them more accurately by substitution mapping using a new set of introgression lines with recombination events within the QTL chromosome region. The position of the QTLs was narrowed down to 36-5 cM, depending on the QTL. The results presented in the current study set the basis for the use of these QTLs in applied breeding programs and for the molecular characterization of the genes underlying them.
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Affiliation(s)
- Iria Fernandez-Silva
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348, Cabrils, Barcelona, Spain
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González VM, Garcia-Mas J, Arús P, Puigdomènech P. Generation of a BAC-based physical map of the melon genome. BMC Genomics 2010; 11:339. [PMID: 20509895 PMCID: PMC2894041 DOI: 10.1186/1471-2164-11-339] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 05/28/2010] [Indexed: 01/31/2023] Open
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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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 BIOLOGY 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] [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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Essafi A, Díaz-Pendón JA, Moriones E, Monforte AJ, Garcia-Mas J, Martín-Hernández AM. Dissection of the oligogenic resistance to Cucumber mosaic virus in the melon accession PI 161375. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:275-84. [PMID: 18825359 DOI: 10.1007/s00122-008-0897-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 09/12/2008] [Indexed: 05/03/2023]
Abstract
Resistance to Cucumber mosaic virus (CMV) in the exotic melon accession PI 161375, cultivar "Sonwang Charmi" (SC) had previously been described as oligogenic, recessive and quantitative, with a major QTL residing in linkage group XII (LGXII). We have used a collection of near isogenic lines (NILs) with introgressions of SC into the genome of the susceptible accession Piel de Sapo (PS) to further characterise this resistance. Infection of NILs carrying introgressions on LGXII showed that only NIL SC12-1 was resistant to CMV strains P9 and P104.82, but not to strains M6 and TL. Further mapping of this region showed that the resistance, named cmv1 maps in an area of 2.2 cM, between markers CMN61_44 and CMN21_55. Moreover, cmv1 confers total resistance to strains P9 and P104.82, indicating that in these cases it is not quantitative and that cmv1 is sufficient to confer full resistance to these CMV strains. Candidate gene mapping of ten translation initiation factors in the melon genome failed to find any of them in the interval between markers CMN61_44 and CMN21_55. All these results suggest that the resistance to CMV present in SC is oligogenic, where different loci confer resistance to different CMV strains, but not necessarily quantitative, since at least one of these genes (cmv1) confers total resistance, similar to that of the parental SC, and does not need the contribution of other loci.
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Affiliation(s)
- Ali Essafi
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils, Km 2, 08348, Cabrils, Barcelona, Spain
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Schmalenbach I, Körber N, Pillen K. Selecting a set of wild barley introgression lines and verification of QTL effects for resistance to powdery mildew and leaf rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:1093-1106. [PMID: 18663425 DOI: 10.1007/s00122-008-0847-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 07/05/2008] [Indexed: 05/26/2023]
Abstract
A set of 59 spring barley introgression lines (ILs) was developed from the advanced backcross population S42. The ILs were generated by three rounds of backcrossing, two to four subsequent selfings, and, in parallel, marker-assisted selection. Each line includes a single marker-defined chromosomal segment of the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum), whereas the remaining part of the genome is derived from the elite barley cultivar Scarlett (H. vulgare ssp. vulgare). Based on a map containing 98 SSR markers, the IL set covers so far 86.6% (1041.5 cM) of the donor genome. Each single line contains an average exotic introgression of 39.2 cM, representing 3.2% of the exotic genome. The utility of the developed IL set is illustrated by verification of QTLs controlling resistance to powdery mildew (Blumeria graminis f. sp. hordei L.) and leaf rust (Puccinia hordei L.) which were previously identified in the advanced backcross population S42. Altogether 57.1 and 75.0% of QTLs conferring resistance to powdery mildew and leaf rust, respectively, were verified by ILs. The strongest favorable effects were mapped to regions 1H, 0-85 cM and 4H, 125-170 cM, where susceptibility to powdery mildew and leaf rust was decreased by 66.1 and 34.7%, respectively, compared to the recurrent parent. In addition, three and one new QTLs were localized, respectively. A co-localization of two favorable QTLs was identified for line S42IL-138, which holds an introgressed segment in region 7H, 166-181. Here, a reduction effect was revealed for powdery mildew as well as for leaf rust severity. This line might be a valuable resource for transferring new resistance alleles into elite cultivars. In future, we aim to cover the complete exotic genome by selecting additional ILs. We intend to conduct further phenotype studies with the IL set in regard to the trait complexes agronomic performance, malting quality, biotic stress, and abiotic stress.
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Affiliation(s)
- Inga Schmalenbach
- Max-Planck-Institute for Plant Breeding Research, Barley Genetics Research Group, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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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] [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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47
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Falke KC, Susić Z, Hackauf B, Korzun V, Schondelmaier J, Wilde P, Wehling P, Wortmann H, Mank R, Rouppe van der Voort J, Maurer HP, Miedaner T, Geiger HH. Establishment of introgression libraries in hybrid rye (Secale cereale L.) from an Iranian primitive accession as a new tool for rye breeding and genomics. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:641-52. [PMID: 18535814 DOI: 10.1007/s00122-008-0808-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Accepted: 05/21/2008] [Indexed: 05/24/2023]
Abstract
Genetic diversity of elite breeding material can be increased by introgression of exotic germplasm to ensure long-term selection response. The objective of our study was to develop and characterize the first two rye introgression libraries generated by marker-assisted backcrossing and demonstrate their potential application for improving the baking quality of rye. Starting from a cross between inbred line L2053-N (recurrent parent) and a heterozygous Iranian primitive population Altevogt 14160 (donor) two backcross (BC) and three selfing generations were performed to establish introgression libraries A and B. Amplified fragment length polymorphisms (AFLP markers) and simple sequences repeats (SSRs) were employed to select and characterize candidate introgression lines (pre-ILs) from BC(1) to BC2S3. The two introgression libraries comprise each 40 BC2S3 pre-ILs. For analyzing the phenotypic effects of the exotic donor chromosome segment (DCS) we evaluated the per se performance for pentosan and starch content in replicated field trials at each of four locations in 2005 and 2006. Introgression library A and B cover 74 and 59% of the total donor genome, respectively. The pre-ILs contained mostly two to four homozygous DCS, with a mean length of 12.9 cM (A) and 10.0 cM (B). We detected eight (A) and nine (B) pre-ILs with a significant (P<0.05) higher pentosan content and two pre-ILs (B) with a significant (P<0.05) higher starch content than the elite recurrent parent. Thus, our results indicate that exotic genetic resources in rye carry favorable alleles for baking quality traits, which can be exploited for improving the elite breeding material by marker-assisted selection (MAS). These introgression libraries can substantially foster rye breeding programs and provide a promising opportunity to proceed towards functional genomics.
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Affiliation(s)
- K C Falke
- State Plant Breeding Institute, Universitaet Hohenheim, 70593 Stuttgart, Germany.
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van Berloo R. GGT 2.0: versatile software for visualization and analysis of genetic data. ACTA ACUST UNITED AC 2008; 99:232-6. [PMID: 18222930 DOI: 10.1093/jhered/esm109] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Ever since its first release in 1999, the free software package for visualization of molecular marker data, graphical genotype (GGT), has been constantly adapted and improved. The GGT package was developed in a plant-breeding context and thus focuses on plant genetic data but was not intended to be limited to plants only. The current version has many options for genetic analysis of populations including diversity analyses and simple association studies. A second release of the GGT package, GGT 2.0 (available through http://www.plantbreeding.wur.nl), is therefore presented in this paper. An overview of existing and new features that are available within GGT 2.0, and a case study in which GGT 2.0 is applied to analyze an existing set of plant genetic data, are presented and discussed.
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Affiliation(s)
- Ralph van Berloo
- Laboratory of Plant Breeding, Wageningen University, PO Box 386, Wageningen, The Netherlands.
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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] [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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Szalma SJ, Hostert BM, Ledeaux JR, Stuber CW, Holland JB. QTL mapping with near-isogenic lines in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:1211-28. [PMID: 17308934 DOI: 10.1007/s00122-007-0512-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 01/22/2007] [Indexed: 05/14/2023]
Abstract
A set of 89 near-isogenic lines (NILs) of maize was created using marker-assisted selection. Nineteen genomic regions, identified by restriction fragment length polymorphism loci and chosen to represent portions of all ten maize chromosomes, were introgressed by backcrossing three generations from donor line Tx303 into the B73 genetic background. NILs were genotyped at an additional 128 simple sequence repeat loci to estimate the size of introgressions and the amount of background introgression. Tx303 introgressions ranged in size from 10 to 150 cM, with an average of 60 cM. Across all NILs, 89% of the Tx303 genome is represented in targeted and background introgressions. The average proportion of background introgression was 2.5% (range 0-15%), significantly lower than the expected value of 9.4% for third backcross generation lines developed without marker-assisted selection. The NILs were grown in replicated field evaluations in two years to map QTLs for flowering time traits. A parallel experiment of testcrosses of each NIL to the unrelated inbred, Mo17, was conducted in the same environments to map QTLs in NIL testcross hybrids. QTLs affecting days to anthesis, days to silking, and anthesis-silk interval were detected in both inbreds and hybrids in both environments. The testing environments differed dramatically for drought stress, and different sets of QTLs were detected across environments. Furthermore, QTLs detected in inbreds were typically different from QTLs detected in hybrids, demonstrating the genetic complexity of flowering time. NILs can serve as a valuable genetic mapping resource for maize breeders and geneticists.
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Affiliation(s)
- S J Szalma
- USDA-ARS Plant Science Research Unit and Department of Crop Science, North Carolina State University, Raleigh, NC 27695, USA
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