Identificación bioinformática de Polimorfismos de Nucleótido Simple (PNSs) en genes candidatos para las características de la fibra en alpacas (Vicugna pacos)

Suárez, Alvaro Gonzalo Fernández; Reynoso, Gustavo Augusto Gutiérrez; León, F. A. Ponce de

doi:10.15381/rpb.v26i1.15911

Cited by 4 publications

(5 citation statements)

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“…As the goal of this study was cytogenetic mapping of candidate genes related to fiber growth and color synthesis, we bioinformatically inspected all VicPac2.0.2 scaffolds containing the 11 mapped markers (Table 2) for additional genes of interest. In scaffold 450 (331,325 bp, NW_005883152.1), which was newly assigned to chr16q12-q13 by FISH mapping KRT15 (Figure 1G), there is a tandemly arranged cluster of five more keratin genes around KRT15 , viz., 5′- KRT31 - KRT15 - KRT13 - KRT9 - KRT14 - KRT16 – 3 ′ (Fernández et al, 2019). Thus, our results allow the assignment of five more keratin genes to chr16q12-q13 (Table 3).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2019

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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.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2019

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“…Additionally, a set of exonic and intronic SNPs located in candidate genes for fiber quality and color include 302 SNPs (Accession code: ERZ1694264) as follows: KRT s (205), KRTAP s (56), MC1R (1), ASIP (2), KIT (18), TYRP1 (1). Similarly, SNPs reported in the literature for KRT s (16) [ 15 ], MC1R (1) [ 13 ], and TYRP1 (2) [ 14 ], are included.…”

Section: Resultsmentioning

confidence: 99%

“…A list of these SNPs and their corresponding MAFs are presented in Table S8 . With the exception of the 16 SNPs reported in the literature for these candidate genes [ 12 , 14 , 15 ], all other SNPs are novel and have now been positively identified by genotyping.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, single nucleotide polymorphisms (SNPs) have been identified in alpacas using a high-density bovine SNP microarray, allowing the identification of 6756 conserved SNPs between bovine and alpaca [ 10 ]. A small number (63) of SNPs and nucleotide mutations found in candidate genes for fiber quality and color have also been reported [ 11 , 12 , 13 , 14 , 15 , 16 ]. SNP microarrays have been developed for several domestic species.…”

Section: Introductionmentioning

confidence: 99%

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Development of a 76k Alpaca (Vicugna pacos) Single Nucleotide Polymorphisms (SNPs) Microarray

Calderon

Reynoso

et al. 2021

Genes

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Small farm producers’ sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic improvement programs. Hence, the aim of this project was the generation of an alpaca single nucleotide polymorphism (SNP) microarray. A sample of 150 Huacaya alpacas from four farms, two each in Puno and Cerro de Pasco were used for SNP discovery by genotyping by sequencing (GBS). Reduced representation libraries, two per animal, were produced after DNA digestion with ApeK1 and double digestion with Pst1-Msp1. Ten alpaca genomes, sequenced at depths between 12× to 30×, and the VicPac3.1 reference genome were used for read alignments. Bioinformatics analysis discovered 76,508 SNPs included in the microarray. Candidate genes SNPs (302) for fiber quality and color are also included. The microarray SNPs cover 90.5% of the genome length with a density of about 39 ± 2.51 SNPs/Mb of DNA at an average interval of 26.45 ± 18.57 kbp. The performance was evaluated by genotyping 30 family trios and comparing them to their pedigrees, as well as comparing microarray to GBS genotypes. Concordance values of 0.93 and 0.94 for ApeK1 and Pst1-Msp1 generated SNPs were observed. Similarly, 290 fiber quality and color candidate gene SNPs were validated. Availability of this microarray will facilitate genome-wide association studies, marker-assisted selection and, in time, genomic selection.

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“…Using a high-density bovine single nucleotide polymorphism (SNP) microarray to genotype alpacas, More et al [8] uncovered 6756 conserved SNPs between bovines and alpacas. Other studies have reported SNPs and other variants identified at candidate genes for fiber quality and color traits [9][10][11][12][13][14]. A recent study reported the development of an alpaca 76K SNP microarray [15], which is now available.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study of Fiber Diameter in Alpacas

More,

Veli,

Cruz

et al. 2023

Animals

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The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical Andean regions in Peru (Pasco and Puno), and three alpaca farms within each region. The samples were genotyped using an Affymetrix Custom Alpaca genotyping array containing 76,508 SNPs. After the quality controls, 960 samples and 51,742 SNPs were retained. Three association study methodologies were performed. The GWAS based on a linear model allowed us to identify 11 and 35 SNPs (−log10(p-values) > 4) using information on all alpacas and alpacas with extreme values of fiber diameter, respectively. The haplotype and marker analysis method allowed us to identify nine haplotypes with standardized haplotype heritability higher than six standard deviations. The selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) allowed us to identify 180 SNPs with XP-EHH values greater than |3|. Four candidate regions with adjacent SNPs identified via two association methods of analysis are located on VPA6, VPA9, VPA29 and one chromosomally unassigned scaffold. This study represents the first analysis of alpaca whole genome association with fiber diameter, using a recently assembled alpaca SNP microarray.

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Identificación bioinformática de Polimorfismos de Nucleótido Simple (PNSs) en genes candidatos para las características de la fibra en alpacas (Vicugna pacos)

Cited by 4 publications

References 11 publications

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

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

Development of a 76k Alpaca (Vicugna pacos) Single Nucleotide Polymorphisms (SNPs) Microarray

Genome-Wide Association Study of Fiber Diameter in Alpacas

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