Development of a Large Set of Microsatellite Markers in Zapote Mamey (Pouteria sapota (Jacq.) H.E. Moore & Stearn) and Their Potential Use in the Study of the Species
Pouteria sapota is known for its edible fruits that contain unique carotenoids, as well as for its fungitoxic, anti-inflammatory and anti-oxidant activity. However, its genetics is mostly unknown, including aspects about its genetic diversity and domestication process. We did high-throughput sequenc...
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| Format: | Article |
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MDPI AG
2015-06-01
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| Series: | Molecules |
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| Online Access: | http://www.mdpi.com/1420-3049/20/6/11400 |
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| author | Renée S. Arias Jaime Martínez-Castillo Victor S. Sobolev Nasib H. Blancarte-Jasso Sheron A. Simpson Linda L. Ballard Mary V. Duke Xiaofen F. Liu Brian M. Irish Brian E. Scheffler |
| author_facet | Renée S. Arias Jaime Martínez-Castillo Victor S. Sobolev Nasib H. Blancarte-Jasso Sheron A. Simpson Linda L. Ballard Mary V. Duke Xiaofen F. Liu Brian M. Irish Brian E. Scheffler |
| author_sort | Renée S. Arias |
| collection | DOAJ |
| description | Pouteria sapota is known for its edible fruits that contain unique carotenoids, as well as for its fungitoxic, anti-inflammatory and anti-oxidant activity. However, its genetics is mostly unknown, including aspects about its genetic diversity and domestication process. We did high-throughput sequencing of microsatellite-enriched libraries of P. sapota, generated 5223 contig DNA sequences, 1.8 Mbp, developed 368 microsatellites markers and tested them on 29 individuals from 10 populations (seven wild, three cultivated) from Mexico, its putative domestication center. Gene ontology BLAST analysis of the DNA sequences containing microsatellites showed potential association to physiological functions. Genetic diversity was slightly higher in cultivated than in the wild gene pool (HE = 0.41 and HE = 0.35, respectively), although modified Garza–Williamson Index and Bottleneck software showed evidence for a reduction in genetic diversity for the cultivated one. Neighbor Joining, 3D Principal Coordinates Analysis and assignment tests grouped most individuals according to their geographic origin but no clear separation was observed between wild or cultivated gene pools due to, perhaps, the existence of several admixed populations. The developed microsatellites have a great potential in genetic population and domestication studies of P. sapota but additional sampling will be necessary to better understand how the domestication process has impacted the genetic diversity of this fruit crop. |
| first_indexed | 2024-12-23T14:56:17Z |
| format | Article |
| id | doaj.art-04482a9399694026be08259567b6b44a |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-12-23T14:56:17Z |
| publishDate | 2015-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-04482a9399694026be08259567b6b44a2022-12-21T17:42:45ZengMDPI AGMolecules1420-30492015-06-01206114001141710.3390/molecules200611400molecules200611400Development of a Large Set of Microsatellite Markers in Zapote Mamey (Pouteria sapota (Jacq.) H.E. Moore & Stearn) and Their Potential Use in the Study of the SpeciesRenée S. Arias0Jaime Martínez-Castillo1Victor S. Sobolev2Nasib H. Blancarte-Jasso3Sheron A. Simpson4Linda L. Ballard5Mary V. Duke6Xiaofen F. Liu7Brian M. Irish8Brian E. Scheffler9USDA-ARS National Peanut Research Laboratory, 1011 Forrester Dr. S.E., Dawson, GA 39842, USACentro de Investigación Científica de Yucatán A.C., Unidad de Recursos Naturales, Calle 43 No. 130, Colonia Chuburná de Hidalgo CP 97200, Mérida, MexicoUSDA-ARS National Peanut Research Laboratory, 1011 Forrester Dr. S.E., Dawson, GA 39842, USACentro de Investigación Científica de Yucatán A.C., Unidad de Recursos Naturales, Calle 43 No. 130, Colonia Chuburná de Hidalgo CP 97200, Mérida, MexicoUSDA-ARS Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd., Stoneville, MI 387761, USAUSDA-ARS Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd., Stoneville, MI 387761, USAUSDA-ARS Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd., Stoneville, MI 387761, USAUSDA-ARS Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd., Stoneville, MI 387761, USAUSDA-ARS Tropical Agriculture Research Station, 2200 Pedro Albizu Campos Ave, Mayaguez, PR 00680, USAUSDA-ARS Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd., Stoneville, MI 387761, USAPouteria sapota is known for its edible fruits that contain unique carotenoids, as well as for its fungitoxic, anti-inflammatory and anti-oxidant activity. However, its genetics is mostly unknown, including aspects about its genetic diversity and domestication process. We did high-throughput sequencing of microsatellite-enriched libraries of P. sapota, generated 5223 contig DNA sequences, 1.8 Mbp, developed 368 microsatellites markers and tested them on 29 individuals from 10 populations (seven wild, three cultivated) from Mexico, its putative domestication center. Gene ontology BLAST analysis of the DNA sequences containing microsatellites showed potential association to physiological functions. Genetic diversity was slightly higher in cultivated than in the wild gene pool (HE = 0.41 and HE = 0.35, respectively), although modified Garza–Williamson Index and Bottleneck software showed evidence for a reduction in genetic diversity for the cultivated one. Neighbor Joining, 3D Principal Coordinates Analysis and assignment tests grouped most individuals according to their geographic origin but no clear separation was observed between wild or cultivated gene pools due to, perhaps, the existence of several admixed populations. The developed microsatellites have a great potential in genetic population and domestication studies of P. sapota but additional sampling will be necessary to better understand how the domestication process has impacted the genetic diversity of this fruit crop.http://www.mdpi.com/1420-3049/20/6/11400blast analysisfounder effectgenetic diversitygermplasmdomesticationMexicoSSR markersgenetic structure |
| spellingShingle | Renée S. Arias Jaime Martínez-Castillo Victor S. Sobolev Nasib H. Blancarte-Jasso Sheron A. Simpson Linda L. Ballard Mary V. Duke Xiaofen F. Liu Brian M. Irish Brian E. Scheffler Development of a Large Set of Microsatellite Markers in Zapote Mamey (Pouteria sapota (Jacq.) H.E. Moore & Stearn) and Their Potential Use in the Study of the Species Molecules blast analysis founder effect genetic diversity germplasm domestication Mexico SSR markers genetic structure |
| title | Development of a Large Set of Microsatellite Markers in Zapote Mamey (Pouteria sapota (Jacq.) H.E. Moore & Stearn) and Their Potential Use in the Study of the Species |
| title_full | Development of a Large Set of Microsatellite Markers in Zapote Mamey (Pouteria sapota (Jacq.) H.E. Moore & Stearn) and Their Potential Use in the Study of the Species |
| title_fullStr | Development of a Large Set of Microsatellite Markers in Zapote Mamey (Pouteria sapota (Jacq.) H.E. Moore & Stearn) and Their Potential Use in the Study of the Species |
| title_full_unstemmed | Development of a Large Set of Microsatellite Markers in Zapote Mamey (Pouteria sapota (Jacq.) H.E. Moore & Stearn) and Their Potential Use in the Study of the Species |
| title_short | Development of a Large Set of Microsatellite Markers in Zapote Mamey (Pouteria sapota (Jacq.) H.E. Moore & Stearn) and Their Potential Use in the Study of the Species |
| title_sort | development of a large set of microsatellite markers in zapote mamey pouteria sapota jacq h e moore amp stearn and their potential use in the study of the species |
| topic | blast analysis founder effect genetic diversity germplasm domestication Mexico SSR markers genetic structure |
| url | http://www.mdpi.com/1420-3049/20/6/11400 |
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