Simple Sequence Repeat Markers Reveal Genetic Diversity and Population Structure of Bolivian Wild and Cultivated Tomatoes (<i>Solanum lycopersicum</i> L.)
The western part of South America is a centre of diversity for tomatoes, but genetic diversity studies are lacking for parts of that region, including Bolivia. We used 11 simple sequence repeat (SSR) markers (including seven novel markers) to evaluate genetic diversity and population structure of 28...
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MDPI AG
2022-08-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/9/1505 |
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| author | Evelyn E. Villanueva-Gutierrez Eva Johansson Maria Luisa Prieto-Linde Alberto Centellas Quezada Marie E. Olsson Mulatu Geleta |
| author_facet | Evelyn E. Villanueva-Gutierrez Eva Johansson Maria Luisa Prieto-Linde Alberto Centellas Quezada Marie E. Olsson Mulatu Geleta |
| author_sort | Evelyn E. Villanueva-Gutierrez |
| collection | DOAJ |
| description | The western part of South America is a centre of diversity for tomatoes, but genetic diversity studies are lacking for parts of that region, including Bolivia. We used 11 simple sequence repeat (SSR) markers (including seven novel markers) to evaluate genetic diversity and population structure of 28 accessions (four modern cultivars, four advanced lines, nine landraces, 11 wild populations), and to compare their genetic variation against phenotypic traits, geographical origin and altitude. In total, 33 alleles were detected across all loci, with 2–5 alleles per locus. The top three informative SSRs were SLM6-11, LE20592 and TomSatX11-1, with polymorphism information content (PIC) of 0.65, 0.55 and 0.49, respectively. The genetic diversity of Bolivian tomatoes was low, as shown by mean expected heterozygosity (He) of 0.07. Analysis of molecular variance (AMOVA) revealed that 77.3% of the total variation was due to variation between accessions. Significant genetic differentiation was found for geographical origin, cultivation status, fruit shape, fruit size and growth type, each explaining 16–23% of the total variation. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) tree and principal coordinate analysis (PCoA) scatter plot both revealed differentiation between accessions with determinate flowers and accessions with indeterminate flowers, regardless of cultivation status. The genetic profiles of the accessions suggest that the Bolivian tomato gene pool comprises both strictly self-pollinating and open-pollinating genotypes. |
| first_indexed | 2024-03-09T23:57:11Z |
| format | Article |
| id | doaj.art-29901aaf8b3941ebac32be0e5645d0f4 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T23:57:11Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-29901aaf8b3941ebac32be0e5645d0f42023-11-23T16:23:13ZengMDPI AGGenes2073-44252022-08-01139150510.3390/genes13091505Simple Sequence Repeat Markers Reveal Genetic Diversity and Population Structure of Bolivian Wild and Cultivated Tomatoes (<i>Solanum lycopersicum</i> L.)Evelyn E. Villanueva-Gutierrez0Eva Johansson1Maria Luisa Prieto-Linde2Alberto Centellas Quezada3Marie E. Olsson4Mulatu Geleta5Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-234 22 Lomma, SwedenDepartment of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-234 22 Lomma, SwedenDepartment of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-234 22 Lomma, SwedenDepartmento de Fitotecnia, Facultad de Ciencias Agricolas, Pecuarias y Forestales “Dr. Martín Cárdenas”, Universidad Mayor de San Simón, Cochabamba P.O. Box 4894, BoliviaDepartment of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-234 22 Lomma, SwedenDepartment of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-234 22 Lomma, SwedenThe western part of South America is a centre of diversity for tomatoes, but genetic diversity studies are lacking for parts of that region, including Bolivia. We used 11 simple sequence repeat (SSR) markers (including seven novel markers) to evaluate genetic diversity and population structure of 28 accessions (four modern cultivars, four advanced lines, nine landraces, 11 wild populations), and to compare their genetic variation against phenotypic traits, geographical origin and altitude. In total, 33 alleles were detected across all loci, with 2–5 alleles per locus. The top three informative SSRs were SLM6-11, LE20592 and TomSatX11-1, with polymorphism information content (PIC) of 0.65, 0.55 and 0.49, respectively. The genetic diversity of Bolivian tomatoes was low, as shown by mean expected heterozygosity (He) of 0.07. Analysis of molecular variance (AMOVA) revealed that 77.3% of the total variation was due to variation between accessions. Significant genetic differentiation was found for geographical origin, cultivation status, fruit shape, fruit size and growth type, each explaining 16–23% of the total variation. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) tree and principal coordinate analysis (PCoA) scatter plot both revealed differentiation between accessions with determinate flowers and accessions with indeterminate flowers, regardless of cultivation status. The genetic profiles of the accessions suggest that the Bolivian tomato gene pool comprises both strictly self-pollinating and open-pollinating genotypes.https://www.mdpi.com/2073-4425/13/9/1505core germplasmAMOVAUPGMAlandracesadvanced linesmodern cultivars |
| spellingShingle | Evelyn E. Villanueva-Gutierrez Eva Johansson Maria Luisa Prieto-Linde Alberto Centellas Quezada Marie E. Olsson Mulatu Geleta Simple Sequence Repeat Markers Reveal Genetic Diversity and Population Structure of Bolivian Wild and Cultivated Tomatoes (<i>Solanum lycopersicum</i> L.) Genes core germplasm AMOVA UPGMA landraces advanced lines modern cultivars |
| title | Simple Sequence Repeat Markers Reveal Genetic Diversity and Population Structure of Bolivian Wild and Cultivated Tomatoes (<i>Solanum lycopersicum</i> L.) |
| title_full | Simple Sequence Repeat Markers Reveal Genetic Diversity and Population Structure of Bolivian Wild and Cultivated Tomatoes (<i>Solanum lycopersicum</i> L.) |
| title_fullStr | Simple Sequence Repeat Markers Reveal Genetic Diversity and Population Structure of Bolivian Wild and Cultivated Tomatoes (<i>Solanum lycopersicum</i> L.) |
| title_full_unstemmed | Simple Sequence Repeat Markers Reveal Genetic Diversity and Population Structure of Bolivian Wild and Cultivated Tomatoes (<i>Solanum lycopersicum</i> L.) |
| title_short | Simple Sequence Repeat Markers Reveal Genetic Diversity and Population Structure of Bolivian Wild and Cultivated Tomatoes (<i>Solanum lycopersicum</i> L.) |
| title_sort | simple sequence repeat markers reveal genetic diversity and population structure of bolivian wild and cultivated tomatoes i solanum lycopersicum i l |
| topic | core germplasm AMOVA UPGMA landraces advanced lines modern cultivars |
| url | https://www.mdpi.com/2073-4425/13/9/1505 |
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