Bioinformatic identification of Single Nucleotide Polymorphisms (SNPs) in keratin-associated protein genes in alpacas (Vicugna pacos)
DOI:
https://doi.org/10.15381/rpb.v31i1.24889Keywords:
Alpaca, single nucleotide polymorphism, KRTAPAbstract
This study aimed to identify single nucleotide polymorphisms (SNPs) in keratin-associated protein genes (KRTAPs), in alpacas (Vicugna pacos). The study was conducted on 34 KRTAPs genes that are annotated in the National Center for Biotechnology Information (NCBI) database. The reference genome VicPac3.1, nine genomes (NCBI) and reads from 300 alpaca reduce representation DNA libraries were used to compare KRTAPs sequences to identify SNPs, using BLASTN. The minor allele frequency (MAF) and the genotyping rate were calculated using KGD and PLINK software. The Illumina Score was calculated with the Illumina Design Studio software for each SNP. Markers with minor allele frequency ≥0.05, a genotyping rate > 45% per SNP based on read sequences and an Illumina Score ≥ 0.6 were selected. Sixty-seven SNPs identified in intron, exon and/or untranslated regions of the keratin-associated protein genes met these parameters. Of these, 35 SNPs were included in the 76K alpaca SNP microarray and 32 SNPs were confirmed in a population of 936 alpacas.
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