EVAapplication/xmlftp://ftp.ebi.ac.uk/pub/databases/eva/PRJEB42148/UNALM_alpaca_SNP_microarray_project_GBS.accessioned.vcf.gz.csiftp://ftp.ebi.ac.uk/pub/databases/eva/PRJEB42148/UNALM_alpaca_SNP_microarray_project_WGS.accessioned.vcf.gz.tbiftp://ftp.ebi.ac.uk/pub/databases/eva/PRJEB42148/UNALM_alpaca_SNP_microarray_project_GBS.accessioned.vcf.gz.tbiftp://ftp.ebi.ac.uk/pub/databases/eva/PRJEB42148/UNALM_alpaca_SNP_microarray_project_GBS.vcf.gzftp://ftp.ebi.ac.uk/pub/databases/eva/PRJEB42148/UNALM_alpaca_SNP_microarray_project_WGS.accessioned.vcf.gz.csiftp://ftp.ebi.ac.uk/pub/databases/eva/PRJEB42148/UNALM_alpaca_SNP_microarray_project_WGS.vcf.gz.tbiftp://ftp.ebi.ac.uk/pub/databases/eva/PRJEB42148/UNALM_alpaca_SNP_microarray_project_GBS.accessioned.vcf.gzftp://ftp.ebi.ac.uk/pub/databases/eva/PRJEB42148/UNALM_alpaca_SNP_microarray_project_WGS.vcf.gzftp://ftp.ebi.ac.uk/pub/databases/eva/PRJEB42148/UNALM_alpaca_SNP_microarray_project_WGS.accessioned.vcf.gzftp://ftp.ebi.ac.uk/pub/databases/eva/PRJEB42148/UNALM_alpaca_SNP_microarray_project_GBS.vcf.gz.tbiprimaryOK2000000Genotyping By Sequencing, Whole Genome SequencingGenomicsUniversidad Nacional Agraria La MolinaIllumina HiSeq 2500Vicugna Pacoshttps://www.ebi.ac.uk/eva/?eva-study=PRJEB42148EVAAnimalia, development, Tier, whole organism, single-organism developmental process, body, animalia, Metazoa, Koerper, postnatal development, postnatal growth, whole body, growth and development, metazoa, Animal, Nucleotide, growth, nucleotides, Breedings.SPI2, IPP2A2, cephalosporin acylase activity, Materials, single-organism developmental process, HSN1E, determination, AI573844, selection process, postnatal development, growth and development, CSMF, Xkl-1, CG30327, ASBP, 5730420M11Rik, CG11478, KL receptor activity, arteritis cranialis, Gsfsco1, Abc8, SCO5, SCO1, Serpin A3K, D8Ertd580e, AI256638, Gsfsow3, Gsfsco5, placement, SOW3, Serpin A3C, average, B, arteritis temporalis, DmelCG42257, SET, thymus nucleic acid, Occidental, Genomes, TAF-I, PPP1R118, hypoplasia, As, U.S., W, CA, ASP, DmelCG4299, b, IGAAD, set, NOR-1, e, DmelCG10574, sample, TRP-1, Bs, s, Double-Stranded DNA, deoxyribonucleic acids, isa, DNAn, Nucleotide, Sl, CXXC finger protein 9, phapii, SPI-2, CHN, AW413978, Klkbp, frequency, StF-IT-1, white, Tr-kit, Double-Stranded, cranial arteritis, A-lt-y-gt-, (Deoxyribonucleotide)n+m, Growth hormone-regulated proteinase inhibitor, PBT, 7beta-(4-carboxybutanamido)cephalosporanic acid acylase activity, Contrapsin-like protease inhibitor 1, European, brown, CG6393, kl1-A, Genetic Materials, relational spatial quality, KIT, desoxyribose nucleic acid, 5133401E04Rik, Genetic Material, nucleotides, Caucasians, SHEP2, tyrosine-protein kinase Kit, OCA3, ADCADN, Dmel_CG6393, pbt, Oca3, MSH-R, Atypical PKC isotype-specific-interacting protein, ASIP, HLA-DR-associated protein II, Algorithm., UNQ203/PRO229, DI-2, DNA (cytosine-5-)-methyltransferase 1, I-2Dm, Spin2, whole genome, CG4299, kit, GA, HiSeq 2500, surveillance, morbidity, Atypical PKC-specific-binding protein, Horton's arteritis, I-2PP1, Serpina3k, GCA, TAF-IBETA, Material, CPI-21, Ephrin-interacting protein, ds DNA, GCL, microarray, White, Cistron, SPI-2.3, TAF-Ibeta, PARD-3, DNA, glutaryl-7-ACA acylase activity, Spink3, TRP1, location, i2pp2a, CPi-21, krk1, Horton's temporal arteritis, CAS2, PAR3-alpha, DNS, (Deoxyribonucleotide)n, PAR3alpha, SCF receptor activity, Gene, SE2-5LT1, Deoxyribonucleic acids, PHAPII, SE2-5T2, Aim, AIM, Tob, Caucasian, Deoxyribonucleic Acid, reduced, scfr, Horton’s syndrome, Colors, tiny, Serine protease inhibitor 2, PHIP, SCFR, DNMT1, study, Fdc, Genetic, DNMT1_HUMAN, AI573420, occurrence, ipp2a2, prevalence, CATB, Double Stranded, 2pp2a, Deoxyribonucleic acid, SE2-5L16, CG10574, PAR-3, API6, Mshra, 2PP2A, taf-ibeta, 65K, CMM5, CG42257, Dmel_CG30327, dSET, dSet, snp, (Deoxyribonucleotide)m, Horton’s disease, AA960621, incidence, DNA MTase HsaI, DNA (cytosine-5)-methyltransferase 1, small, GHR-P63, proto-oncogene c-Kit, NOR1, cg11478, Nor1, CTCL tumor antigen se2-5, TTC20, Tyrp, DNAn+1, DNMT, igaad, TRP, Kallikrein-binding protein, MCMT, glutaryl-7-aminocephalosporanic acid acylase activity, (7R)-7-(4-carboxybutanamido)cephalosporanate amidohydrolase activity, Cistrons, group, development, read, TYRP, GP75, I-2PP2A, KIT ligand receptor activity, PARD3A, DNA methyltransferase HsaI, chemical analysis, Dm I-2, polymyalgia rheumatica, Spin2b, I2PP2A, sequence, Horton's giant cell arteritis, ds-DNA, cephalosporin C acylase activity, Library, outbreaks, Caucasoid, XKrk1, CXXC9, c-KIT, United States of America, CT-2, underdeveloped, MINOR, ensemble, postnatal growth, Kbp, KBP, Thyroid hormone-regulated protein, CD117, CXXC-type zinc finger protein 9, sample population, endemics, primary structure of sequence macromolecule, Pard3a, b-PROTEIN, dSET/TAF-Ibeta, 2610030F17Rik, c-kit, C-Kit, Whites, Ssm, Desoxyribonukleinsaeure, GL-7-ACA acylase activity, xkl-1, TEC, epidemics, assay, PAR3, Par3, AA407739, growth, Baz, Minor, CLEC2C, m.HsaI, Psti0falseIdentification of single nucleotide polymorphisms (SNPs) and development of a SNP microarray for the implementation of advanced technologies of animal breeding in alpacasThe aim of this study was the discovery of single nucleotide polymorphisms (SNPs) and the development of a SNP microarray in alpacas. DNA samples from 150 white Huacaya alpacas originating from two Peruvian Andean geographic regions were obtained to generate ApeKI and PstI/MspI reduced representation libraries for each sample. Libraries were sequenced on a HiSeq 2500 sequencer at an average read depth of ~6X per library. Bioinformatics analysis allowed to identify 4?283,956 variants across the VicPac3.1 alpaca reference genome (GCA_000164845.4). A list of 513,467 SNPs was generated considering the parameters phred-scaled quality score (>10), call rate (?0.15), minor allele frequency (? 0.01), Illumina Design Score (?0.60), and no other SNPs located within the 81 bp SNP sequence. Of these, 51,772 SNPs located at equidistant intervals of 40 Kbp were selected based on six selection waves and a location score. A second set of 28,429 PNSs was identified to increase the density of PNSs. In addition, 302 SNPs identified at candidate genes for fiber quality and color (KRTs, KRTAPs, MC1R, ASIP, KIT, TYRP1) were selected. A final set of 80,498 biallelic SNPs were retained and submitted to Neogen GeneSeek (Nebraska, United States). Of these, 76,508 unique alpaca SNPs were included in the microarray based on Affymetrix quality algorithms.2021-04-01PRJEB4214830538