Examinando por Materia "Single nucleotide polymorphism"

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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.
Genetic diversity and population structure of a Peruvian cattle herd using SNP data
(Frontiers Media S.A., 2023-03-10) Corredor Arizapana, Flor Anita; Figueroa Venegas, Deyanira Antonella; Estrada Cañari, Richard; Salazar Coronel, Wilian; Quilcate Pairazamán, Carlos Enrique; Vásquez Pérez, Héctor Vladimir; Gonzales Malca, Jhony Alberto; Maicelo Quintana, Jorge Luis; Medina Morales, Percy Edilberto; Arbizu Berrocal, Carlos Irvin
New-generation sequencing technologies, among them SNP chips for massive genotyping, are useful for the effective management of genetic resources. To date, molecular studies in Peruvian cattle are still scarce. For the first time, the genetic diversity and population structure of a reproductive nucleus cattle herd of four commercial breeds from a Peruvian institution were determined. This nucleus comprises Brahman (N = 9), Braunvieh (N = 9), Gyr (N = 5), and Simmental (N = 15) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N = 9), were incorporated. Female individuals were genotyped with the GGPBovine100K and ma les with the BovineHD. Quality control, and the proportion of polymorphic SNPs, minor allele frequency, expected heterozygosity, observed heterozygosity, and inbreeding coefficient were estimated for the five breeds. Admixture, principal component analysis (PCA), and discriminant analysis of principal components (DAPC) were performed. Also, a dendrogram was constructed using the Neighbor-Joining clustering algorithm. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 51.42% in Gyr to 97.58% in AFB. Also, AFB showed the highest expected heterozygosity estimate (0.41 ± 0.01), while Brahman the lowest (0.33 ± 0.01). Besides, Braunvieh possessed the highest observed heterozygosity (0.43 ± 0.01), while Brahman the lowest (0.37 ± 0.02), indicating that Brahman was less diverse. According to the molecular variance analysis, 75.71% of the variance occurs within individuals, whereas 24.29% occurs among populations. The pairwise genetic differentiation estimates (FST) between breeds showed values that ranged from 0.08 (Braunvieh vs. AFB) to 0.37 (Brahman vs. Braunvieh). Similarly, pairwise Reynold’s distance ranged from 0.09 (Braunvieh vs. AFB) to 0.46 (Brahman vs. Braunvieh). The dendrogram, similar to the PCA, identified two groups, showing a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh, Simmental, and AFB). Simmental and Braunvieh grouped closely with the AFB cattle. Similar results were obtained for the population structure analysis with K = 2. The results from this study would contribute to the appropriate management, avoiding loss of genetic variability in these breeds and for future improvements in this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.
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 of traditional cacao reveals four new genetic lineages in indigenous Amazonian sites in Peru
(Public Library of Science (PLOS), 2026-07-06) Motilal, Lambert A.; Calderon, Martha S.; Bustamante, Danilo E.; Gopaulchan, David; Tineo Flores, Daniel; Márquez Romero, Fanny R,; Lastra Paucar, Sphyros Roomel; Díaz Valderrama, Jorge R.; Guerrero Abad, Juan Carlos; Oliva, Manuel; Umaharan, Pathmanathan
Cacao genetic resources in Peru are largely uncharacterized. Knowledge of their genetic structure is needed for their conservation and use. Indigenous on-farm cacao trees (n = 390) from the Departments of Amazonas (n = 130), Ayacucho (n = 76), Cajamarca (n = 1), Cusco (n = 110), Madre de Dios (n = 10), Piura (n = 59), San Martín (n = 3) and Ucayali (n = 1) in Peru were fingerprinted with 192 single nucleotide polymorphic markers. Identity, group differentiation, phylogenetic, multivariate and ancestry analyses were conducted. Four new populations were identified guided by phylogenetic, accepted ancestral backgrounds of reference samples and least admixture among samples. The cacao from these eight Departments were variably mixed containing both pure members of new populations and admixed samples with these new populations and Amelonado, Contamana, Criollo, Curaray, Guiana, Iquitos, Marañon, Nacional, Nanay and Púrus. The findings of this study suggest that while the cacao germplasm is genetically related across different departments, each region harbors its own distinct genetic composition. The Clade IV (Chuncho 2) population was associated with the Contamana cluster and Clade I (Chuncho 1) was associated with Purus cluster. Clades II (Awajun) and III (Porcelana) were associated with the Nacional cluster. The ancestry of the economically desired CCN 51 cultivar was revealed to be better assigned as 15% Amelonado, 13% Criollo, 25% Iquitos and 45% Awajun. The results of this study will improve the understanding of the genetic landscape in Peru, enhance genebank collections in Peru and enable the differentiation of the fine flavour industry in Peru. The new groups of cacao identified in this study will help understand the genetic structuring of cacao and represent a valuable new resource to search for valuable traits for breeding and commercialization programmes in the fine flavour cacao industry in Peru.