Bibliographic citations
More, M., (2022). Identificación de polimorfismos de nucleótido simple y su asociación con el diámetro de fibra en alpacas Huacaya (Vicugna pacos) [Universidad Nacional Agraria La Molina]. https://hdl.handle.net/20.500.12996/5368
More, M., Identificación de polimorfismos de nucleótido simple y su asociación con el diámetro de fibra en alpacas Huacaya (Vicugna pacos) []. PE: Universidad Nacional Agraria La Molina; 2022. https://hdl.handle.net/20.500.12996/5368
@phdthesis{renati/1115241,
title = "Identificación de polimorfismos de nucleótido simple y su asociación con el diámetro de fibra en alpacas Huacaya (Vicugna pacos)",
author = "More Montoya, Manuel José",
publisher = "Universidad Nacional Agraria La Molina",
year = "2022"
}
The aim of the research was the identification of single nucleotide polymorphisms (SNPs) and their association with fiber diameter in Huacaya alpacas. In a first stage, DNA samples from 40 Huacaya alpacas were genotyped using a 777,962 SNPs microarray designed for cattle (BovineHD Genotyping Beadchip, Illumina). The data analysis included the use of combinations of the threshold parameters of no-call threshold (≥0.05, ≥0.15, and ≥0.25) and call frequency (≥0.9 and =1.0); Average GenCall (GC) score (≥0.70) and GenTrain score (≥0.25) were also considered. SNPs with minor allele frequency (MAF) ≥ 0.05 or ≥ 0.01 were retained. All positive SNP flanking sequences showing perfect alignments between the bovine and alpaca genomes for the first 21 or 26 nucleotides flanking the variant nucleotide at either side were selected. Only SNPs localized in one scaffold were assumed unique. Unique SNPs identified in both reference genomes were kept and mapped on the Vicugna_pacos-2.0.2 genome. The use of the no-call threshold ≥ 0.25, call frequency = 1 and average GC score ≥ 0.7 resulted in the lowest number of SNPs identified (6,756 SNPs), of which 400 were unique and polymorphic (MAF ≥ 0.01). Assignment to alpaca chromosomes was possible for 292 SNPs. Likewise, 209 SNPs were localized in 202 alpaca gene loci. In a second stage, DNA samples were collected from 881 female Huacaya alpacas from two geographical Andean regions, considering three herds of alpacas within each region. The samples were genotyped using a microarray of 76,508 SNPs, designed for alpacas (Affymetrix Custom Alpaca genotyping array). Two quality controls were developed using Axiom Analysis Suite v.4.0.3.3 and PLINK v1.90p. Four genome wide association study (GWAS) methods were performed: (i) GWAS based on a linear model, (ii) Haplotype and marker analysis, (iii) GWAS with eigenvector decomposition (EigenGWAS) and (iv) Selection signatures based on Cross Population Extended Haplotype Homozygosity (XP-EHH). After the first quality control, 861 samples and 69,685 SNPs were selected. After the second quality control, a total of 61,814 SNPs, localized on 1,838 scaffolds, were retained. According to each method: (i) 39 not significant SNPs with p-value less than 1 x 10-4, (ii) eleven haplotypes with standardized haplotype heritability higher than 6 standard deviations, (iii) 50 SNPs with corrected p-value less than 8.09 x 10-7, (iv) 217 SNPs with standardized XP-EHH values greater than |3|, were identified. A set of 337 SNPs distributed16 in 149 regions were identified, of which 53 regions are formed by two or more SNPs separated at a maximum distance of 500 kbp. Gene Ontology (GO) annotations of these genes included hair follicle morphogenesis (BCL2, SOSTDC1, WNT10A), hair follicle development (EDA, TNFRSF19, WNT10A) and skin development (ABCB6, EDA, WNT10A). Four candidate regions with adjacent SNPs identified by two methods were located on chromosomes VPA2, VPA5, VPA18 and VPA26. Significant SNPs localized on chromosomes VPA5, VPA18 and VPA27 were localized within o close to genes reported in goats for fiber traits, and could be considered candidate SNPs. This study represents the first alpaca genome wide association study for fiber diameter in Huacaya alpacas, using a SNP microarray designed for alpacas.
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