Phenomic and Genomic Characterization of a Mutant Platform in Cucurbita pepo
The Cucurbita pepo genome comprises 263 Mb and 34,240 gene models organized in 20 different chromosomes. To improve our understanding of gene function we have generated an EMS mutant platform, consisting of 3,751 independent M2 families. The quality of the collection has been evaluated based on phen...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-08-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2018.01049/full |
| _version_ | 1824005200104390656 |
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| author | Alicia García Encarni Aguado Genis Parra Susana Manzano Cecilia Martínez Zoraida Megías Gustavo Cebrián Jonathan Romero Sergi Beltrán Dolores Garrido Manuel Jamilena |
| author_facet | Alicia García Encarni Aguado Genis Parra Susana Manzano Cecilia Martínez Zoraida Megías Gustavo Cebrián Jonathan Romero Sergi Beltrán Dolores Garrido Manuel Jamilena |
| author_sort | Alicia García |
| collection | DOAJ |
| description | The Cucurbita pepo genome comprises 263 Mb and 34,240 gene models organized in 20 different chromosomes. To improve our understanding of gene function we have generated an EMS mutant platform, consisting of 3,751 independent M2 families. The quality of the collection has been evaluated based on phenotyping and whole-genome re-sequencing (WGS) results. The phenotypic evaluation of the whole platform at seedling stage has demonstrated that the rate of variation for easily observable traits is more than 10%. The percentage of families with albino or chlorotic seedlings exceeded 3%, similar or higher to that found in other EMS collections of cucurbit crops. A rapid screening of the library for triple ethylene response in etiolated seedlings allowed the identification of four ethylene-insensitive mutants, that were found to be semidominant (ein1, ein2, and ein3) or dominant (EIN4). By evaluating 4 adult plants from 300 independent families more than 28% of apparent mutations were found for vegetative and reproductive traits, including plant vigor, leaf size and shape, sex expression and sex determination, and fruit set and development. Two pools of genomic DNA derived from 20 plants of two mutant families were subjected to WGS by using NGS methodology, estimating the density, spectrum, distribution and impact of EMS induced mutation. The number of EMS mutations in the genomes of families L1 and L2 was 1,704 and 859, respectively, which represents a density of 11.8 and 6 mutations per Mb, respectively. As expected, the predominant EMS induced mutations were C > T and G > A transitions (80.3% in L1, and 61% L2), that were found to be randomly distributed along the 20 chromosomes of C. pepo. The mutations were mostly affecting intergenic regions, but 7.9 and 6% of the identified EMS mutations in L1 and L2, respectively, were located in the exome, and 0.4 and 0.2% had a moderate and high putative impact on gene functions. These results provide information regarding the potential use of the obtained mutant platform in the discovery of novel alleles for both functional genomics and Cucurbita breeding by using direct- or reverse-genetic approaches. |
| first_indexed | 2024-12-18T20:06:28Z |
| format | Article |
| id | doaj.art-081d6cc54cbf45fa8c6d76010a68358f |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-18T20:06:28Z |
| publishDate | 2018-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-081d6cc54cbf45fa8c6d76010a68358f2022-12-21T20:54:44ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-08-01910.3389/fpls.2018.01049376580Phenomic and Genomic Characterization of a Mutant Platform in Cucurbita pepoAlicia García0Encarni Aguado1Genis Parra2Susana Manzano3Cecilia Martínez4Zoraida Megías5Gustavo Cebrián6Jonathan Romero7Sergi Beltrán8Dolores Garrido9Manuel Jamilena10Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, SpainDepartment of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, SpainCentro Nacional de Análisis Genómico, Barcelona, SpainDepartment of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, SpainDepartment of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, SpainDepartment of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, SpainDepartment of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, SpainDepartment of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, SpainCentro Nacional de Análisis Genómico, Barcelona, SpainDepartamento de Fisiología Vegetal, Facultad de Ciencias, Universidad de Granada, Granada, SpainDepartment of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, SpainThe Cucurbita pepo genome comprises 263 Mb and 34,240 gene models organized in 20 different chromosomes. To improve our understanding of gene function we have generated an EMS mutant platform, consisting of 3,751 independent M2 families. The quality of the collection has been evaluated based on phenotyping and whole-genome re-sequencing (WGS) results. The phenotypic evaluation of the whole platform at seedling stage has demonstrated that the rate of variation for easily observable traits is more than 10%. The percentage of families with albino or chlorotic seedlings exceeded 3%, similar or higher to that found in other EMS collections of cucurbit crops. A rapid screening of the library for triple ethylene response in etiolated seedlings allowed the identification of four ethylene-insensitive mutants, that were found to be semidominant (ein1, ein2, and ein3) or dominant (EIN4). By evaluating 4 adult plants from 300 independent families more than 28% of apparent mutations were found for vegetative and reproductive traits, including plant vigor, leaf size and shape, sex expression and sex determination, and fruit set and development. Two pools of genomic DNA derived from 20 plants of two mutant families were subjected to WGS by using NGS methodology, estimating the density, spectrum, distribution and impact of EMS induced mutation. The number of EMS mutations in the genomes of families L1 and L2 was 1,704 and 859, respectively, which represents a density of 11.8 and 6 mutations per Mb, respectively. As expected, the predominant EMS induced mutations were C > T and G > A transitions (80.3% in L1, and 61% L2), that were found to be randomly distributed along the 20 chromosomes of C. pepo. The mutations were mostly affecting intergenic regions, but 7.9 and 6% of the identified EMS mutations in L1 and L2, respectively, were located in the exome, and 0.4 and 0.2% had a moderate and high putative impact on gene functions. These results provide information regarding the potential use of the obtained mutant platform in the discovery of novel alleles for both functional genomics and Cucurbita breeding by using direct- or reverse-genetic approaches.https://www.frontiersin.org/article/10.3389/fpls.2018.01049/fullCucurbita pepoEMSmutant platformWGShigh-throughput screeningethylene |
| spellingShingle | Alicia García Encarni Aguado Genis Parra Susana Manzano Cecilia Martínez Zoraida Megías Gustavo Cebrián Jonathan Romero Sergi Beltrán Dolores Garrido Manuel Jamilena Phenomic and Genomic Characterization of a Mutant Platform in Cucurbita pepo Frontiers in Plant Science Cucurbita pepo EMS mutant platform WGS high-throughput screening ethylene |
| title | Phenomic and Genomic Characterization of a Mutant Platform in Cucurbita pepo |
| title_full | Phenomic and Genomic Characterization of a Mutant Platform in Cucurbita pepo |
| title_fullStr | Phenomic and Genomic Characterization of a Mutant Platform in Cucurbita pepo |
| title_full_unstemmed | Phenomic and Genomic Characterization of a Mutant Platform in Cucurbita pepo |
| title_short | Phenomic and Genomic Characterization of a Mutant Platform in Cucurbita pepo |
| title_sort | phenomic and genomic characterization of a mutant platform in cucurbita pepo |
| topic | Cucurbita pepo EMS mutant platform WGS high-throughput screening ethylene |
| url | https://www.frontiersin.org/article/10.3389/fpls.2018.01049/full |
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