A Past Genetic Bottleneck from Argentine Beans and a Selective Sweep Led to the Race Chile of the Common Bean (<i>Phaseolus vulgaris</i> L.)
The domestication process of the common bean gave rise to six different races which come from the two ancestral genetic pools, the Mesoamerican (Durango, Jalisco, and Mesoamerica races) and the Andean (New Granada, Peru, and Chile races). In this study, a collection of 281 common bean landraces from...
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2024-04-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/25/7/4081 |
| _version_ | 1797212408045895680 |
|---|---|
| author | Osvin Arriagada Bárbara Arévalo Igor Pacheco Andrés R. Schwember Lee A. Meisel Herman Silva Katherine Márquez Andrea Plaza Ricardo Pérez-Diáz José Pico-Mendoza Ricardo A. Cabeza Gerardo Tapia Camila Fuentes Yohaily Rodríguez-Alvarez Basilio Carrasco |
| author_facet | Osvin Arriagada Bárbara Arévalo Igor Pacheco Andrés R. Schwember Lee A. Meisel Herman Silva Katherine Márquez Andrea Plaza Ricardo Pérez-Diáz José Pico-Mendoza Ricardo A. Cabeza Gerardo Tapia Camila Fuentes Yohaily Rodríguez-Alvarez Basilio Carrasco |
| author_sort | Osvin Arriagada |
| collection | DOAJ |
| description | The domestication process of the common bean gave rise to six different races which come from the two ancestral genetic pools, the Mesoamerican (Durango, Jalisco, and Mesoamerica races) and the Andean (New Granada, Peru, and Chile races). In this study, a collection of 281 common bean landraces from Chile was analyzed using a 12K-SNP microarray. Additionally, 401 accessions representing the rest of the five common bean races were analyzed. A total of 2543 SNPs allowed us to differentiate a genetic group of 165 accessions that corresponds to the race Chile, 90 of which were classified as pure accessions, such as the bean types ‘Tórtola’, ‘Sapito’, ‘Coscorrón’, and ‘Frutilla’. Our genetic analysis indicates that the race Chile has a close relationship with accessions from Argentina, suggesting that nomadic ancestral peoples introduced the bean seed to Chile. Previous archaeological and genetic studies support this hypothesis. Additionally, the low genetic diversity (π = 0.053; uHe = 0.53) and the negative value of Tajima’ D (D = −1.371) indicate that the race Chile suffered a bottleneck and a selective sweep after its introduction, supporting the hypothesis that a small group of Argentine bean genotypes led to the race Chile. A total of 235 genes were identified within haplotype blocks detected exclusively in the race Chile, most of them involved in signal transduction, supporting the hypothesis that intracellular signaling pathways play a fundamental role in the adaptation of organisms to changes in the environment. To date, our findings are the most complete investigation associated with the origin of the race Chile of common bean. |
| first_indexed | 2024-04-24T10:41:54Z |
| format | Article |
| id | doaj.art-0fbcab1ae5614521825211c610e83e61 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-04-24T10:41:54Z |
| publishDate | 2024-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-0fbcab1ae5614521825211c610e83e612024-04-12T13:20:36ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672024-04-01257408110.3390/ijms25074081A Past Genetic Bottleneck from Argentine Beans and a Selective Sweep Led to the Race Chile of the Common Bean (<i>Phaseolus vulgaris</i> L.)Osvin Arriagada0Bárbara Arévalo1Igor Pacheco2Andrés R. Schwember3Lee A. Meisel4Herman Silva5Katherine Márquez6Andrea Plaza7Ricardo Pérez-Diáz8José Pico-Mendoza9Ricardo A. Cabeza10Gerardo Tapia11Camila Fuentes12Yohaily Rodríguez-Alvarez13Basilio Carrasco14Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, ChileCentro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, ChileInstituto de Nutrición y Tecnología de los Alimentos (INTA), El Líbano 5524, Santiago 7830490, ChileDepartamento de Ciencias Vegetales, Facultad de Agronomía y Sistemas Naturales, Pontificia Universidad Católica de Chile, Santiago 7820436, ChileInstituto de Nutrición y Tecnología de los Alimentos (INTA), El Líbano 5524, Santiago 7830490, ChileLaboratorio de Genómica Funcional & Bioinformática, Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Chile, Av. Santa Rosa 11315, Santiago 8820808, ChileCentro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, ChileCentro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, ChileCentro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, ChileFacultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Portoviejo 130105, EcuadorLaboratorio de Nutrición Vegetal, Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, ChileUnidad de Recursos Genéticos, Instituto de Investigaciones Agropecuarias (INIA Quilamapu), Chillán 3800062, ChileCentro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, ChileDepartamento de Ciencias Vegetales, Facultad de Agronomía y Sistemas Naturales, Pontificia Universidad Católica de Chile, Santiago 7820436, ChileCentro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, ChileThe domestication process of the common bean gave rise to six different races which come from the two ancestral genetic pools, the Mesoamerican (Durango, Jalisco, and Mesoamerica races) and the Andean (New Granada, Peru, and Chile races). In this study, a collection of 281 common bean landraces from Chile was analyzed using a 12K-SNP microarray. Additionally, 401 accessions representing the rest of the five common bean races were analyzed. A total of 2543 SNPs allowed us to differentiate a genetic group of 165 accessions that corresponds to the race Chile, 90 of which were classified as pure accessions, such as the bean types ‘Tórtola’, ‘Sapito’, ‘Coscorrón’, and ‘Frutilla’. Our genetic analysis indicates that the race Chile has a close relationship with accessions from Argentina, suggesting that nomadic ancestral peoples introduced the bean seed to Chile. Previous archaeological and genetic studies support this hypothesis. Additionally, the low genetic diversity (π = 0.053; uHe = 0.53) and the negative value of Tajima’ D (D = −1.371) indicate that the race Chile suffered a bottleneck and a selective sweep after its introduction, supporting the hypothesis that a small group of Argentine bean genotypes led to the race Chile. A total of 235 genes were identified within haplotype blocks detected exclusively in the race Chile, most of them involved in signal transduction, supporting the hypothesis that intracellular signaling pathways play a fundamental role in the adaptation of organisms to changes in the environment. To date, our findings are the most complete investigation associated with the origin of the race Chile of common bean.https://www.mdpi.com/1422-0067/25/7/4081Andean poolcommon beangenetic diversitygenetic structurerace Chile |
| spellingShingle | Osvin Arriagada Bárbara Arévalo Igor Pacheco Andrés R. Schwember Lee A. Meisel Herman Silva Katherine Márquez Andrea Plaza Ricardo Pérez-Diáz José Pico-Mendoza Ricardo A. Cabeza Gerardo Tapia Camila Fuentes Yohaily Rodríguez-Alvarez Basilio Carrasco A Past Genetic Bottleneck from Argentine Beans and a Selective Sweep Led to the Race Chile of the Common Bean (<i>Phaseolus vulgaris</i> L.) International Journal of Molecular Sciences Andean pool common bean genetic diversity genetic structure race Chile |
| title | A Past Genetic Bottleneck from Argentine Beans and a Selective Sweep Led to the Race Chile of the Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_full | A Past Genetic Bottleneck from Argentine Beans and a Selective Sweep Led to the Race Chile of the Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_fullStr | A Past Genetic Bottleneck from Argentine Beans and a Selective Sweep Led to the Race Chile of the Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_full_unstemmed | A Past Genetic Bottleneck from Argentine Beans and a Selective Sweep Led to the Race Chile of the Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_short | A Past Genetic Bottleneck from Argentine Beans and a Selective Sweep Led to the Race Chile of the Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_sort | past genetic bottleneck from argentine beans and a selective sweep led to the race chile of the common bean i phaseolus vulgaris i l |
| topic | Andean pool common bean genetic diversity genetic structure race Chile |
| url | https://www.mdpi.com/1422-0067/25/7/4081 |
| work_keys_str_mv | AT osvinarriagada apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT barbaraarevalo apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT igorpacheco apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT andresrschwember apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT leeameisel apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT hermansilva apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT katherinemarquez apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT andreaplaza apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT ricardoperezdiaz apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT josepicomendoza apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT ricardoacabeza apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT gerardotapia apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT camilafuentes apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT yohailyrodriguezalvarez apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT basiliocarrasco apastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT osvinarriagada pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT barbaraarevalo pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT igorpacheco pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT andresrschwember pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT leeameisel pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT hermansilva pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT katherinemarquez pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT andreaplaza pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT ricardoperezdiaz pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT josepicomendoza pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT ricardoacabeza pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT gerardotapia pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT camilafuentes pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT yohailyrodriguezalvarez pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil AT basiliocarrasco pastgeneticbottleneckfromargentinebeansandaselectivesweepledtotheracechileofthecommonbeaniphaseolusvulgarisil |