Abstract
Alpaca is a camelid species of broad economic, biological and biomedical interest, and an essential part of the cultural and historical heritage of Peru. Recently, efforts have been made to improve knowledge of the alpaca genome, and its genetics and cytogenetics, to develop molecular tools for selection and breeding. Here, we report cytogenetic mapping of 35 new markers to 19 alpaca autosomes and the X chromosome. Twenty-eight markers represent alpaca SNPs, of which 17 are located inside or near protein-coding genes, two are in ncRNA genes and nine are intergenic. The remaining seven markers correspond to candidate genes for fiber characteristics (BMP4, COL1A2, GLI1, SFRP4), coat color (TYR) and development (CHD7, PAX7). The results take the tally of cytogenetically mapped markers in alpaca to 281, covering all 36 autosomes and the sex chromosomes. The new map assignments overall agree with human–camelid conserved synteny data, except for mapping BMP4 to VPA3, suggesting a hitherto unknown homology with HSA14. The findings validate, refine and correct the current alpaca assembly VicPac3.1 by anchoring unassigned sequence scaffolds, and ordering and orienting assigned scaffolds. The study contributes to the improvement in the alpaca reference genome and advances camelid molecular cytogenetics.
Highlights
The alpaca (Vicugna pacos, VPA) is a South American camelid adapted to the Andean highlands and domesticated by native people about 6000–7000 years ago [1,2,3]
Among the single nucleotide polymorphisms (SNPs) selected for mapping, annotation was improved for five markers: intergenic UNA_272, UNA_369 and UNA_396 corresponded to putative noncoding RNA
Among the 28 SNP markers selected for cytogenetic mapping, 17 were located inside or near protein coding genes, two were in noncoding RNA (ncRNA) genes and nine were intergenic (Table 1)
Summary
The alpaca (Vicugna pacos, VPA) is a South American camelid adapted to the Andean highlands and domesticated by native people about 6000–7000 years ago [1,2,3]. Over 85% of the world alpaca population lives in Peru, where the species is a symbol of cultural heritage and of high economic importance [4,5,6]. Alpaca fiber, which is valued for its softness and resistance, is an important export item for Peru, and has made alpacas a popular livestock species worldwide [7]. Alpacas are of particular biological, biomedical and evolutionary interest due to their adaptations to extreme environments [10,11], unique and unusual features of their adaptive immune system [12,13,14,15]. The evolutionary history, genetic relationships and population structure of the alpaca and other South
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