Development of a 76k Alpaca (Vicugna pacos) Single Nucleotide Polymorphisms (SNPs) Microarray

Abstract

Small farm producers’ sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic improvement programs. Hence, the aim of this project was the generation of an alpaca single nucleotide polymorphism (SNP) microarray. A sample of 150 Huacaya alpacas from four farms, two each in Puno and Cerro de Pasco were used for SNP discovery by genotyping by sequencing (GBS). Reduced representation libraries, two per animal, were produced after DNA digestion with ApeK1 and double digestion with Pst1-Msp1. Ten alpaca genomes, sequenced at depths between 12× to 30×, and the VicPac3.1 reference genome were used for read alignments. Bioinformatics analysis discovered 76,508 SNPs included in the microarray. Candidate genes SNPs (302) for fiber quality and color are also included. The microarray SNPs cover 90.5% of the genome length with a density of about 39 ± 2.51 SNPs/Mb of DNA at an average interval of 26.45 ± 18.57 kbp. The performance was evaluated by genotyping 30 family trios and comparing them to their pedigrees, as well as comparing microarray to GBS genotypes. Concordance values of 0.93 and 0.94 for ApeK1 and Pst1-Msp1 generated SNPs were observed. Similarly, 290 fiber quality and color candidate gene SNPs were validated. Availability of this microarray will facilitate genome-wide association studies, marker-assisted selection and, in time, genomic selection.

ssGBLUP Method Improves the Accuracy of Breeding Value Prediction in Huacaya Alpaca

“…A recently developed DNA microarray consisting of 76,508 SNPs from 37 pairs of chromosomes, 36 autosomal chromosomes, and one sex chromosome [ 16 ], was used to genotype 431 alpacas. For quality control, all SNPs with a call rate ≤ 95% and minor allelic frequency (MAF) ≤ 0.05 were removed, leaving 60,624 SNP markers.…”

“…However, this has not been possible because there was no specific genomic beadchip for alpacas until recently. This genomic beadchip has just been built and with it, it has been possible to establish a map of 76,508 Single Nucleotide Polymorphism (SNP) markers [ 16 ]. Therefore, the objective of this work was to compare, for the first time, the prediction accuracy of three important fiber traits: fiber diameter (FD), standard deviation of fiber diameter (SD), and percentage of medullation (PM) using BLUP and ssGBLUP methods in Huacaya alpacas.…”

Genotyping‐by‐sequencing reveals a high number and quality of single nucleotide polymorphisms in guinea pigs (Cavia porcellus) from the Peruvian Andes

“…Owing to lack of previous GBS studies on guinea pigs, comparison was not possible. However, SNP discovery by GBS in other native farm animals, such as Erhualian pigs, Pekin ducks or Alpacas, presented lower numbers of SNPs: 217 517 (Wang et al, 2017), 55 920 (Zhu et al, 2016) and 513 467 SNPs (Calderon et al, 2021), respectively. These differences may reflect GBS methodology constraints regarding restriction enzyme selection, sequencing depth, DNA quality or the SNP calling tool for a given animal population (Brouard et al, 2017; Gorjanc et al, 2015; Gurgul et al, 2019).…”

“…Recently, a GBS-based microarray of 76 508 SNPs for alpaca was developed in Peru. The SNP set was used to validate 290 candidate gene SNPs for fiber quality and color (Calderon et al, 2021). Despite their potential advantages, the application of high-throughput SNP technologies has not been described in guinea pigs yet.…”

Genotyping-by-sequencing (GBS) as a tool for interspecies hybrid detection

“…Recent studies involving the SACs genome (Fan et al, 2020) have been aimed at determining their origin and ancestry, but to our knowledge, no genomic studies (e.g., GBS) have been performed to identify specific hybrid individuals of these species. To date, a bovine array has been tested to identify SNP markers in alpacas (More et al, 2019), and a 76k microarray was designed that is specifically dedicated to alpacas (Calderon et al, 2021). However, the authors did not test these tools for hybridisation detection.…”