Examinando por Materia "Molecular markers"

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Assessment of the genetic diversity and population structure of the peruvian andean legume, tarwi (Lupinus mutabilis), with high quality SNPs
(MDPI, 2023-03-16) Huaringa Joaquin, Amelia Wite; Saldaña Serrano, Carla Lizet; Saravia Navarro, David; García Bendezú, Sady; Rodriguez Grados, Pedro Manuel; Salazar Coronel, Wilian; Camarena Mayta, Felix; Injante Silva, Pedro Hugo; Arbizu Berrocal, Carlos Irvin
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.
Assessment of the genetic structure and diversity of arracacha (Arracacia xanthorrhiza) using genotyping-by-sequencing
(International Society for Horticultural Science, 2024-04-13) Arbizu Berrocal, Carlos Irvin; Saldaña Serrano, Carla Lizet; Lazo, E.; Suca Damiano, Esther Stefany; Santa Cruz Padilla, Angel Esteban; Chávez Cabrera, Alexander; Cabrera Hoyos, Héctor Antonio; Guerrero Abad, Juan Carlos; Maicelo Quintana, Jorge Luis
Arracacha, also known as “Peruvian carrot”, is a native crop from the Andean region, and is considered an unexplored root. To date, studies on this crop were mainly focused at the morphological and agronomic level. However, its genetics remains unclear. Today it is feasible to study the genetic composition of this Andean root by next-generation sequencing techniques such as genotyping-by-sequencing (GBS). We here for the first time employed 183 accessions of arracacha from six Andean localities of Peru and identified 8976 SNP markers. STRUCTURE analysis revealed this Andean crop is clustered into four populations, and with few accessions intermingled. A dendrogram was generated using the UPGMA clustering algorithm, and, similar to the principal coordinate analysis (PCoA), it showed four groups. Genetic diversity estimation was conducted considering the four populations identified, revealing very high expected heterozygosity (0.432). AMOVA revealed the greatest variation within populations (89.66%) and indicated that variability between populations is 10.34%. Population divergence (Fst) ranged from 0.02 (cluster 1 vs. cluster 3) to 0.036 (cluster 1 vs. cluster 4). Negative Fis values were also detected for all populations of arracacha, indicating it depends on cross-pollination. We hope this work stimulates the development of additional molecular tools for this orphan crop in order to establish a modern breeding program and conservation strategies of this important Andean crop.
Genetic Diversity and Population Structure of Capirona (Calycophyllum spruceanum Benth.) from the Peruvian Amazon Revealed by RAPD Markers
(MDPI, 2021-08-22) Saldaña Serrano, Carla Lizet; Cancan, Johan D.; Cruz Hilacondo, Wilbert Eddy; Correa, Mirian; Ramos León, Haydeé Miriam; Cuellar Bautista, José Eloy; Arbizu Berrocal, Carlos Irvin
Capirona (Calycophyllum spruceanum Benth.) is a tree species of commercial importance widely distributed in South American forests that is traditionally used for its medicinal properties and wood quality. Studies on this tree species have been focused mainly on wood properties, propagation, and growth. However, genetic studies on capirona have been very limited to date. Currently, it is possible to explore genetic diversity and population structure in a fast and reliable manner by using molecular markers. We here used 10 random amplified polymorphic DNA (RAPD) markers to analyze the genetic diversity and population structure of 59 samples of capirona that were sampled from four provinces located in the eastern region of the Peruvian amazon. A total of 186 bands were manually scored, generating a 59 × 186 presence/absence matrix. A dendrogram was generated using the UPGMA clustering algorithm, and, similar to the principal coordinate analysis (PCoA), it showed four groups that correspond to the geographic origin of the capirona samples (LBS, Irazola, Masisea, Iñapari). Similarly, a discriminant analysis of principal components (DAPC) and STRUCTURE analysis confirmed that capirona is grouped into four clusters. However, we also noticed that a few samples were intermingled. Genetic diversity estimation was conducted considering the four groups (populations) identified by STRUCTURE software. AMOVA revealed the greatest variation within populations (71.56%) and indicated that variability among populations is 28.44%. Population divergence (Fst) between clusters 1 and 4 revealed the highest genetic difference (0.269), and the lowest Fst was observed between clusters 3 and 4 (0.123). RAPD markers were successful and effective. However, more studies are needed, employing other molecular tools. To the best of our knowledge, this is the first investigation employing molecular markers in capirona in Peru considering its natural distribution, and as such it is hoped that this helps to pave the way towards its genetic improvement and the urgent sustainable management of forests in Peru.
Genetic diversity and population structure of the Peruvian Andean legume, tarwi (Lupinus mutabilis), with high quality SNPs
(MDPI, 2023-01-19) 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
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.
Genetic structure and diversity of a peruvian collection of a high-quality wood tree species, Ulcumano (Retrophyllum rospigliosii, Podocarpaceae
(Universidad de Concepción, 2022-12-27) Saldaña Serrano, Carla Lizet; Cancán Loli, Johan Deyvid; Salazar Hinostroza, Evelin Judith; Chumbimune Vivanco, Sheyla Yanett; Jhoncon Kooyip, Jorge Hugo; Arbizu Berrocal, Carlos Irvin
Ulcumano, which is native to South America, is an important conifer in Peru. Molecular studies are scarce, limiting modern breeding and appropriate conservation activities. Currently, molecular markers are widely employed to explore genetic structure and diversity parameters of plant species in a fast and precise manner. The objective of this study was to analyze the genetic diversity and population structure of ulcumano in Peru by using DNA-based molecular markers. Nine Randomly Amplified Polymorphic DNA (RAPD) markers were used, while 95 individuals of ulcumano were sampled from three departments of Peru. A total of 265 DNA fragments were manually scored, but 247 of them were kept after removing the non-polymorphic markers. Genetic distances were calculated using R software based on Provesti´s coefficient. A dendrogram was obtained using the UPGMA clustering algorithm, showing no clear clustering. The principal coordinate analysis agreed with two population structure analyses, demonstrating that ulcumano is contained within two clusters, (i) Junín + Pasco, and (ii) Cajamarca, while very few individuals are intermixed. Genetic diversity parameters were estimated considering the two groups (populations) identified by STRUCTURE software. Nei’s genetic diversity estimate varied between 0.22 and 0.28, while Shannon index ranged from 3.43 to 4.16. Population divergence (Fst) between the two clusters revealed low genetic differentiation (0.064). AMOVA analysis revealed that 87.31 and 12.69% of the total genetic variation were found within populations and between individuals, respectively. To the best of our knowledge, this is the first molecular study in ulcumano in Peru, and provides valuable information for the genetic improvement and sustainable management of this conifer in the country.
In-depth genetic diversity and population structure of endangered Peruvian Amazon rosewood germplasm using Genotyping by Sequencing (GBS) technology
(MDPI, 2021-02-08) Azhar Nadeem, Muhammad; Vasquez Guizado, Stalin Juan; Qasim Shahid, Muhammad; Amjad Nawaz, Muhammad; Habyarimana, Ephrem; Ercişli, Sezai; Ali, Fawad; Karaköy, Tolga; Aasim, Muhammad; Hatipoğlu, Rüştü; Castro Gómez, Juan Carlos; Marapara Del Aguila, Jorge Luis; Adrianzén Julca, Pedro Marcelino; Torres Canales, Esperanza; Hwan Yang, Seung; Chung, Gyuhwa; Shehzad Baloch, Faheem
Research studies on conservative genetics of endangered plants are very important to establish the management plans for the conservation of biodiversity. Rosewood is an evergreen tree of the Amazon region and its essential oil has great acceptance in the medical and cosmetic industry. The present study aimed to explore the genetic diversity and population structure of 90 rosewood accessions collected from eight localities of Peruvian Amazon territory through DArTseq markers. A total of 7485 informative markers resulted from genotyping by sequencing (GBS) analysis were used for the molecular characterization of rosewood germplasm. Mean values of various calculated diversity parameters like observed number of alleles (1.962), the effective number of alleles (1.669), unbiased expected heterozygosity (0.411), and percent polymorphism (93.51%) over the entire germplasm showed the existence of a good level of genetic variations. Our results showed that the Mairiricay population was more diverse compared to the rest of the populations. Tamshiyacu-2 and Mairiricay-15 accessions were found genetically distinct accessions. The analysis of molecular variance (AMOVA) reflected maximum variations (75%) are due to differences within populations. The implemented clustering algorithms, i.e.; STRUCTURE, neighbor-joining analysis and principal coordinate analysis (PCoA) separated the studied germplasm on the basis of their geographical locations. Diversity indices for STRUCTURE-based populations showed that subpopulation A is more diverse population than the rest of the populations, for such reason, individuals belonging to this subpopulation should be used for reintroduction or reinforcement plans of rosewood conservation. We envisage that molecular characterization of Peruvian rosewood germplasm with DArTseq markers will provide a platform for the conservation, management and restoration of endangered rosewood in upcoming years.