Genetic diversity and population structure of the Peruvian Andean legume, tarwi (Lupinus mutabilis), with high quality SNPs
Lupinus mutabilis 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 p...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | info:eu-repo/semantics/workingPaper |
| Language: | Inglés |
| Published: |
MDPI
2024
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/20.500.12955/2451 https://doi.org/10.20944/preprints202301.0345.v1 |
| _version_ | 1855028495882649600 |
|---|---|
| author | Huaringa Joaquin, Amelia Saldaña Serrano, Carla Lizet Saravia Navarro, David García Bendezú, Sady Rodriguez Grados, Pedro Salazar Coronel, Wilian Camarena, Felix Injante Silva, Pedro Hugo Arbizu Berrocal, Carlos Irvin |
| author_browse | Arbizu Berrocal, Carlos Irvin Camarena, Felix García Bendezú, Sady Huaringa Joaquin, Amelia Injante Silva, Pedro Hugo Rodriguez Grados, Pedro Salazar Coronel, Wilian Saldaña Serrano, Carla Lizet Saravia Navarro, David |
| author_facet | Huaringa Joaquin, Amelia Saldaña Serrano, Carla Lizet Saravia Navarro, David García Bendezú, Sady Rodriguez Grados, Pedro Salazar Coronel, Wilian Camarena, Felix Injante Silva, Pedro Hugo Arbizu Berrocal, Carlos Irvin |
| author_sort | Huaringa Joaquin, Amelia |
| collection | Repositorio INIA |
| description | Lupinus mutabilis 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 (Fst) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative Fis for both populations, demonstrating that, like other Lupinus 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. |
| format | info:eu-repo/semantics/workingPaper |
| id | INIA2451 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | INIA24512024-02-28T21:38:13Z Genetic diversity and population structure of the Peruvian Andean legume, tarwi (Lupinus mutabilis), with high quality SNPs Huaringa Joaquin, Amelia Saldaña Serrano, Carla Lizet Saravia Navarro, David García Bendezú, Sady Rodriguez Grados, Pedro Salazar Coronel, Wilian Camarena, Felix Injante Silva, Pedro Hugo Arbizu Berrocal, Carlos Irvin Fabaceae Bioinformatics Molecular markers Neglected crop Genomics https://purl.org/pe-repo/ocde/ford#4.04.01 Fabaceae Bioinformatics Genetic markers Genomics Genetic diversity (as resource) Lupinus mutabilis Single nucleotide polymorphism Lupinus mutabilis 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 (Fst) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative Fis for both populations, demonstrating that, like other Lupinus 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. 2024-02-28T21:38:12Z 2024-02-28T21:38:12Z 2023-01-19 info:eu-repo/semantics/workingPaper 2310-287X https://hdl.handle.net/20.500.12955/2451 https://doi.org/10.20944/preprints202301.0345.v1 eng Preprints Preprints info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ application/pdf application/pdf MDPI CH Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | Fabaceae Bioinformatics Molecular markers Neglected crop Genomics https://purl.org/pe-repo/ocde/ford#4.04.01 Fabaceae Bioinformatics Genetic markers Genomics Genetic diversity (as resource) Lupinus mutabilis Single nucleotide polymorphism Huaringa Joaquin, Amelia Saldaña Serrano, Carla Lizet Saravia Navarro, David García Bendezú, Sady Rodriguez Grados, Pedro Salazar Coronel, Wilian Camarena, Felix Injante Silva, Pedro Hugo Arbizu Berrocal, Carlos Irvin Genetic diversity and population structure of the Peruvian Andean legume, tarwi (Lupinus mutabilis), with high quality SNPs |
| title | Genetic diversity and population structure of the Peruvian Andean legume, tarwi (Lupinus mutabilis), with high quality SNPs |
| title_full | Genetic diversity and population structure of the Peruvian Andean legume, tarwi (Lupinus mutabilis), with high quality SNPs |
| title_fullStr | Genetic diversity and population structure of the Peruvian Andean legume, tarwi (Lupinus mutabilis), with high quality SNPs |
| title_full_unstemmed | Genetic diversity and population structure of the Peruvian Andean legume, tarwi (Lupinus mutabilis), with high quality SNPs |
| title_short | Genetic diversity and population structure of the Peruvian Andean legume, tarwi (Lupinus mutabilis), with high quality SNPs |
| title_sort | genetic diversity and population structure of the peruvian andean legume tarwi lupinus mutabilis with high quality snps |
| topic | Fabaceae Bioinformatics Molecular markers Neglected crop Genomics https://purl.org/pe-repo/ocde/ford#4.04.01 Fabaceae Bioinformatics Genetic markers Genomics Genetic diversity (as resource) Lupinus mutabilis Single nucleotide polymorphism |
| url | https://hdl.handle.net/20.500.12955/2451 https://doi.org/10.20944/preprints202301.0345.v1 |
| work_keys_str_mv | AT huaringajoaquinamelia geneticdiversityandpopulationstructureoftheperuvianandeanlegumetarwilupinusmutabiliswithhighqualitysnps AT saldanaserranocarlalizet geneticdiversityandpopulationstructureoftheperuvianandeanlegumetarwilupinusmutabiliswithhighqualitysnps AT saravianavarrodavid geneticdiversityandpopulationstructureoftheperuvianandeanlegumetarwilupinusmutabiliswithhighqualitysnps AT garciabendezusady geneticdiversityandpopulationstructureoftheperuvianandeanlegumetarwilupinusmutabiliswithhighqualitysnps AT rodriguezgradospedro geneticdiversityandpopulationstructureoftheperuvianandeanlegumetarwilupinusmutabiliswithhighqualitysnps AT salazarcoronelwilian geneticdiversityandpopulationstructureoftheperuvianandeanlegumetarwilupinusmutabiliswithhighqualitysnps AT camarenafelix geneticdiversityandpopulationstructureoftheperuvianandeanlegumetarwilupinusmutabiliswithhighqualitysnps AT injantesilvapedrohugo geneticdiversityandpopulationstructureoftheperuvianandeanlegumetarwilupinusmutabiliswithhighqualitysnps AT arbizuberrocalcarlosirvin geneticdiversityandpopulationstructureoftheperuvianandeanlegumetarwilupinusmutabiliswithhighqualitysnps |