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Development of a 76k Alpaca (Vicugna pacos) Single Nucleotide Polymorphisms (SNPs) Microarray
Marcos Calderon1,2, Manuel J More1, Gustavo A Gutierrez1
1Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru.
Genes
|March 6, 2021
Summary
A new alpaca single nucleotide polymorphism (SNP) microarray was developed using genotyping by sequencing. This tool will advance genetic improvement programs for fiber characteristics, benefiting small farm producers.
Area of Science:
- Animal Genetics
- Genomic Technologies
- Agricultural Science
Background:
- Alpaca fiber production is crucial for smallholder farmer livelihoods.
- Genetic improvement of fiber traits can enhance economic benefits and quality of life.
- Molecular markers are key to overcoming limitations in alpaca genetic improvement programs.
Purpose of the Study:
- To generate a single nucleotide polymorphism (SNP) microarray for alpacas.
- To facilitate genetic improvement of fiber characteristics in Huacaya alpacas.
Main Methods:
- SNP discovery was performed using genotyping by sequencing (GBS) on 150 Huacaya alpacas.
- Reduced representation libraries were created after DNA digestion.
- Bioinformatics analysis aligned reads to reference genomes to identify SNPs.
Main Results:
- A microarray containing 76,508 SNPs was generated, covering 90.5% of the alpaca genome.
- Included are 302 SNPs for candidate genes related to fiber quality and color.
- Microarray performance showed high concordance (0.93-0.94) with GBS genotypes and validated SNPs.
Conclusions:
- The developed alpaca SNP microarray is a valuable tool for genetic research.
- It will enable genome-wide association studies and marker-assisted selection.
- This technology will accelerate genomic selection for improved alpaca fiber traits.
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