Examinando por Materia "SNP"

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Genome-wide association study of fiber diameter in alpacas
(MDPI, 2023-10-25) More, Manuel; Veli Rivera, Eudosio Amancio; Cruz, Alan; Gutiérrez, Juan Pablo; Gutiérrez, Gustavo; Ponce de León, F. Abel
The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical Andean regions in Peru (Pasco and Puno), and three alpaca farms within each region. The samples were genotyped using an Affymetrix Custom Alpaca genotyping array containing 76,508 SNPs. After the quality controls, 960 samples and 51,742 SNPs were retained. Three association study methodologies were performed. The GWAS based on a linear model allowed us to identify 11 and 35 SNPs (−log10(p-values) > 4) using information on all alpacas and alpacas with extreme values of fiber diameter, respectively. The haplotype and marker analysis method allowed us to identify nine haplotypes with standardized haplotype heritability higher than six standard deviations. The selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) allowed us to identify 180 SNPs with XP-EHH values greater than |3|. Four candidate regions with adjacent SNPs identified via two association methods of analysis are located on VPA6, VPA9, VPA29 and one chromosomally unassigned scaffold. This study represents the first analysis of alpaca whole genome association with fiber diameter, using a recently assembled alpaca SNP microarray.
Genotyping-by-sequencing reveals a high number and quality of single nucleotide polymorphisms in guinea pigs (Cavia porcellus) from the Peruvian Andes
(John Wiley & Sons Inc., 2023-10-05) Borja Lozano, María Victoria; Vigil Santillán, Bianca Estefani; More Montoya, Manuel J.; Morón Barraza, Jonathan A.; García Serquén, Aura Liz; Gutiérrez Reynoso, Gustavo; Yalta Macedo, Claudia Esther
Guinea pigs are a major source of animal protein for Peruvian Andean families. Despite the economic and cultural relevance of guinea pigs, their genomic characterization has been scarcely addressed. Genotyping-by-sequencing (GBS) has emerged as an affordable alternative to genotyping of livestock and native animals. Here, we report the use of GBS for single nucleotide polymorphism (SNP) discovery of traditionally raised guinea pigs from six regions of the Peruvian Andes and one group of breeding animals. The paired-end (2 × 150 bp) sequencing of 40 guinea pig DNA samples generated a mean of 6.4 million high-quality sequencing reads per sample. We obtained an average sequencing depth of 10× with an 88.5% mapping rate to the Cavia porcellus reference genome. A total of 279 965 SNPs (102 SNPs/Mbp) were identified after variant calling and quality filtering. Based on this SNP set, we assessed the genetic diversity and distance within our selected guinea pig populations. An overall average minor allele frequency of 0.13, an observed heterozygosity of 0.31, an expected heterozygosity of 0.35, and an F-value of 0.1 were obtained, while the SNP-based neighbor-joining tree suggests a closer genetic relationship between individuals from geographically close locations. We showed that GBS is a cost-effective tool for SNP discovery and genetic characterization of Peruvian guinea pig populations. Therefore, it may be considered as a suitable and affordable tool for genomic characterization of poorly studied native animal species.
SNP profiling of Elaeis oleifera (H.B.K) cortes germplasm in Ucayali, Peru using genotyping-by-sequencing (GBS)
(Springer Nature, 2025-07-17) Camacho Villalobos, Alina Alexandra; Mestanza, Orson; Cabrera Pintado, Rosa María; Sanchez Sunción, Glendy; Bendezu, Jorge
Objectives Elaeis oleifera, commonly known as the American oil palm, plays a crucial role in the agricultural economies of Central and South America due to its unique oil characteristics and resistance to certain diseases. Despite its importance, limited available genetic information has hindered the effective utilization of this species in breeding programs aimed at improving oil yield and disease resistance. This study employed Genotyping-bySequencing (GBS) to profile polymorphisms within Elaeis oleifera populations, the unique germplasm bank for Peru, located in Ucayali, Peru, aiming to characterize the gene pool. Data description The GBS analysis successfully identified 22,703 informative single-nucleotide polymorphisms (SNPs) across the twelve-year-old plant genomes (n=42). Observed heterozygosity (Ho=0.3086) and expected heterozygosity index (He=0.3385) were quantified. The fixation index (Fst=0.0048) indicated low genetic differentiation within the germplasm. However, the presence of two genetic clusters (C_1 and C_2) distributed homogenously within the studied population has been detected; the origin of these clusters could be mainly associated with the initial management of the germplasm nucleus within Peru. The extensive SNP dataset provides a comprehensive genetic map that is invaluable for the conservation and enhancement of Elaeis oleifera in our region.