Chromosomal Localization of Candidate Genes for Fiber Growth and Color in Alpaca (Vicugna pacos)

Abstract

The alpaca ( Vicugna pacos ) is an economically important and cultural signature species in Peru. Thus, molecular genomic information about the genes underlying the traits of interest, such as fiber properties and color, is critical for improved breeding and management schemes. Current knowledge about the alpaca genome, particularly the chromosomal location of such genes of interest is limited and lags far behind other livestock species. The main objective of this work was to localize alpaca candidate genes for fiber growth and color using fluorescence in situ hybridization (FISH). We report the mapping of candidate genes for fiber growth COL1A1 , CTNNB1 , DAB2IP , KRT15 , KRTAP13-1 , and TNFSF12 to chromosomes 16, 17, 4, 16, 1, and 16, respectively. Likewise, we report the mapping of candidate genes for fiber color ALX3 , NCOA6 , SOX9 , ZIC1 , and ZIC5 to chromosomes 9, 19, 16, 1, and 14, respectively. In addition, since KRT15 clusters with five other keratin genes ( KRT31 , KRT13 , KRT9 , KRT14 , and KRT16 ) in scaffold 450 (Vic.Pac 2.0.2), the entire gene cluster was assigned to chromosome 16. Similarly, mapping NCOA6 to chromosome 19, anchored scaffold 34 with 8 genes, viz., RALY , EIF2S2 , XPOTP1 , ASIP , AHCY , ITCH , PIGU , and GGT7 to chromosome 19. These results are concordant with known conserved synteny blocks between camelids and humans, cattle and pigs.

10×Genomics Single-cell Sequencing Reveals Differential Cell Types in Skin Tissues of Liaoning Cashmere Goats and Key Genes Related Potentially to the Fineness of Cashmere Fiber

“…COL1A1 (Collagen type I α 1 is a major component of collagen type I. The study has showed that COL1A1 can regulate the growth of Alpaca villi 39 . Collagen 1 alpha 1 (COL1A1) is suggested to participate in the progression of brotic diseases and wound healing.…”

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

“…However, the first approximation of the use of markers was reported by Mamani et al [ 26 ], where it was possible to cover 40% of the alpaca genome. Subsequently, the identification and location of some genes related to the genetic control of the diameter and color of the coat were described by Mendoza et al [ 27 ].…”

Genomics and animal production

“…Three strategies have been carried out, first using an HD bovine beadchip (Mamani et al 2017;More et al 2019), second using comparative genome analysis among genes related to fiber growth of sheep, goat and alpacas (Fernandez et al 2019), and third using sequences of DNA reduced libraries from 150 alpacas and 6 sequenced genomes at 30X depth (Unpublished data). In addition, some genes and SNPs have been localized, by fluorescent in situ hybridization (FISH) on alpaca chromosomes (Mendoza et al 2019). Since the size of the alpaca genome is about 2.1 x 10 9 bp, we seek to select about 50,000 SNPs, each one separated by 40,000 bp, and covering about 90% of its genome.…”