Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (<i>Lupinus mutabilis</i>), with High Quality SNPs
<i>Lupinus mutabilis</i> Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the gene...
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MDPI AG
2023-03-01
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| author | Amelia Huaringa-Joaquin Carla L. Saldaña David Saravia Sady García-Bendezú Pedro Rodriguez-Grados Wilian Salazar Felix Camarena Pedro Injante Carlos I. Arbizu |
| author_facet | Amelia Huaringa-Joaquin Carla L. Saldaña David Saravia Sady García-Bendezú Pedro Rodriguez-Grados Wilian Salazar Felix Camarena Pedro Injante Carlos I. Arbizu |
| author_sort | Amelia Huaringa-Joaquin |
| collection | DOAJ |
| description | <i>Lupinus mutabilis</i> Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (F<sub>st</sub>) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative F<sub>is</sub> for both populations, demonstrating that, like other <i>Lupinus</i> species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume. |
| first_indexed | 2024-03-11T06:40:33Z |
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| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-11T06:40:33Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diversity |
| spelling | doaj.art-184513719feb41da8afef4a946dc68d52023-11-17T10:38:37ZengMDPI AGDiversity1424-28182023-03-0115343710.3390/d15030437Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (<i>Lupinus mutabilis</i>), with High Quality SNPsAmelia Huaringa-Joaquin0Carla L. Saldaña1David Saravia2Sady García-Bendezú3Pedro Rodriguez-Grados4Wilian Salazar5Felix Camarena6Pedro Injante7Carlos I. Arbizu8Departamento de Fitotecnia, Facultad de Agronomía, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima 15024, PeruDirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, PeruDepartamento de Fitotecnia, Facultad de Agronomía, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima 15024, PeruDepartamento de Suelos, Facultad de Agronomía, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima 15024, PeruFacultad de Ciencias, Universidad Nacional José Faustino Sánchez Carrión, Av. Mercedes Indacochea Nro. 609, Huacho 15136, PeruDirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, PeruDepartamento de Fitotecnia, Facultad de Agronomía, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima 15024, PeruDirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, PeruDirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru<i>Lupinus mutabilis</i> Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (F<sub>st</sub>) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative F<sub>is</sub> for both populations, demonstrating that, like other <i>Lupinus</i> species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.https://www.mdpi.com/1424-2818/15/3/437Fabaceaebioinformaticsmolecular markersneglected cropgenomics |
| spellingShingle | Amelia Huaringa-Joaquin Carla L. Saldaña David Saravia Sady García-Bendezú Pedro Rodriguez-Grados Wilian Salazar Felix Camarena Pedro Injante Carlos I. Arbizu Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (<i>Lupinus mutabilis</i>), with High Quality SNPs Diversity Fabaceae bioinformatics molecular markers neglected crop genomics |
| title | Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (<i>Lupinus mutabilis</i>), with High Quality SNPs |
| title_full | Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (<i>Lupinus mutabilis</i>), with High Quality SNPs |
| title_fullStr | Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (<i>Lupinus mutabilis</i>), with High Quality SNPs |
| title_full_unstemmed | Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (<i>Lupinus mutabilis</i>), with High Quality SNPs |
| title_short | Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (<i>Lupinus mutabilis</i>), with High Quality SNPs |
| title_sort | assessment of the genetic diversity and population structure of the peruvian andean legume tarwi i lupinus mutabilis i with high quality snps |
| topic | Fabaceae bioinformatics molecular markers neglected crop genomics |
| url | https://www.mdpi.com/1424-2818/15/3/437 |
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