Keywords:

SNP panel

Animal genetic resources

Native pigs

Single-nucleotide polymorphism panels in the racial authentication of Hairless pigs in Mexico

Paneles de polimorsmos de un solo nucleótido en la autenticación racial del cerdo Pelón en México

Painéis de polimorsmo de nucleotídeo único na autenticação racial de porco Pelado no México

Clemente Lemus-Flores

Carlos Omar De la Cruz Moreno

Juan José Fernando Borrayo González

María Guadalupe Orozco Benítez

Miguel Angel Ayala-Valdovinos

Rev. Fac. Agron. (LUZ). 2025, 42(3): e254231

ISSN 2477-9407

DOI: https://doi.org/10.47280/RevFacAgron(LUZ).v42.n3.II

Animal production

Associate editor: Dra. Rosa Razz

University of Zulia, Faculty of Agronomy

Bolivarian Republic of Venezuela

Universidad Autónoma de Nayarit, CBAP, Ciudad de la

Cultura Amado Nervo C.P. 63000, Tepic, Nayarit, México.

Departamento de Producción Animal, División de Ciencias

Veterinarias, Centro Universitario de Ciencias Biológicas

y Agropecuarias, Universidad de Guadalajara, Camino

Ramón Padilla Sánchez 2100, C. P. 45200, Zapopan, Jalisco,

México.

Received: 01-04-2025

Accepted: 02-06-2025

Published: 30-06-2025

Abstract

Massive genotyping panels of single-nucleotide polymorphisms

(SNPs) were evaluated to create an authentication and racial

identication strategy for the Hairless pig. Three populations of

Hairless pigs from the states of Nayarit (n=10), Oaxaca (n=10) and

Yucatán (n=143), Mexico, were genotyped with the porcine-GGP-

50K chip, and genotypes for the Duroc (n=66), Hampshire (n=33),

Landrace (n=95), Large White (n=47), Pietrain (n=42) and Iberico

hairless (n=15) breeds were added. Three strategies involving

previously reported SNP panels and a fourth strategy involving

the combination of all SNP panels was evaluated. Using canonical

discriminant analysis (CDA), the canonical correlations and

percentages of racial discrimination were obtained, and with the rst

two canonical variables, distance trees between populations were

constructed. Racial separation was achieved with all four strategies;

the greater the number of SNPs used, the better the identication

of the Hairless pig. The combined panel with 96 SNPs achieved

100 % racial assignment and had the greatest canonical correlation

in the CDA, revealing a racial grouping of the three Hairless pig

populations close to the Iberian population. With SNP panels, it is

possible to achieve the racial authentication of the Hairless pig and

discriminate it from other pig breeds.

This scientic publication in digital format is a continuation of the Printed Review: Legal Deposit pp 196802ZU42, ISSN 0378-7818.

Rev. Fac. Agron. (LUZ). 2025, 42(3): e254231 July-September. ISSN 2477-9409.

2-6 |

Resumen

Con el objetivo de contar con una estrategia de autenticación e

identicación racial del cerdo Hairless, fueron valorados paneles de

polimorsmos de nucleótido único (SNP) de genotipicación masiva.

Tres poblaciones de cerdo Pelón de los estados de Nayarit (10),

Oaxaca (10) y Yucatán (143) México, fueron genotipicados con el

chip porcine-GGP-50K, asimismo, se adicionaron genotipos para las

razas Duroc (66), Hampshire (33), Landrace (95), Large White (47),

Pietrain (42) e Ibérico lampiño (15). Se valoraron tres estrategias

de paneles reportados y una cuarta estrategia con la combinación

de todos los paneles de SNP. Con el análisis de discriminación

canónica (ADC) se obtuvieron los valores de correlación canónica

de discriminación, porcentaje de discriminación racial y con las dos

primeras funciones canónicas se realizaron los árboles de distancias

entre poblaciones. Las cuatro estrategias logran la separación racial,

a mayor número de SNP empleados mejora la identicación del cerdo

Pelón. El panel combinado con 96 SNP tuvo una asignación racial al

100 %, con mayor correlación canónica en el ADC, observándose un

agrupamiento racial de las tres poblaciones de cerdo Pelón, cercano

a Ibérico. Con los paneles de SNP se puede lograr la autenticación

racial del cerdo Pelón y discriminarse de otras razas porcinas.

Palabras clave: panel SNP, cerdos nativos, recursos genéticos animales.

Resumo

Painéis massivos de genotipagem de polimorsmos de

nucleotídeo único (SNPs) foram avaliados para criar uma estratégia

de autenticação e identicação racial para porco Pelado. Três

populações de porco Pelado dos estados de Nayarit (n=10), Oaxaca

(n=10) e Yucatán (n=143), México, foram genotipadas com o

chip porcine-GGP-50K, e genótipos para as raças Duroc (n=66),

Hampshire (n=33), Landrace (n=95), Large White (n=47), Pietrain

(n=42) e Iberico hairless (n=15) foram adicionados. Três estratégias

envolvendo painéis de SNP relatados anteriormente e uma quarta

estratégia envolvendo a combinação de todos os painéis de SNP

foram avaliadas. Usando análise discriminante canônica (CDA), as

correlações canônicas e porcentagens de discriminação racial foram

obtidas e, com as duas primeiras variáveis canônicas, árvores de

distância entre populações foram construídas. A separação racial foi

alcançada com todas as quatro estratégias; quanto maior o número

de SNPs utilizados, melhor a identicação do porco Pelado. O painel

combinado com 96 SNPs alcançou 100 % de atribuição racial e teve

a maior correlação canônica no CDA, revelando um agrupamento

racial das três populações de porco Pelado próximo à população

ibérica. Com os painéis de SNP, é possível alcançar a autenticação

racial do porco Pelado e discriminá-lo de outras raças de suínos.

Palabras-chave: painel SNP, recursos genéticos animais, suínos

nativos.

Introduction

The use of single-nucleotide polymorphisms (SNPs) in the

genotyping of pig breeds enables the performance of population

studies and the identication of genes associated with production.

Another important use of SNP genotyping is racial discrimination

and the authentication of individuals in each breed (Muñoz et al.,

2020). SNP panels identied with 60K chips from Illumina (www.

illumina.com) and 50K chips from Neogen (www.neogen.com) have

been used in racial discrimination (Wilkinson et al., 2012; Schiavo et

al., 2020; Moretti et al., 2022; Pasupa et al., 2020). Various statistical

methodologies have been used to obtain these discriminant SNP

panels, such as average Euclidean distance (AED), xation index

(FST), principal component analysis (PCA), partial least squares

regression (PLSR), canonical discriminant analysis (CDA) and

dierences in allelic frequencies (Miao et al., 2023). A reference states

that the Hairless pig arrived in Mexico through the Caribbean Islands

on the second voyage of Christopher Columbus in the year 1493;

since that date, the Hairless pig has been distributed from the Yucatan

Peninsula to the shores of the Gulf of Mexico in the center, southwest

and west regions of Mexico, and its genetic closeness with the Iberian

pig has been recognized (Lemus-Flores et al., 2023). In Mexico, the

Hairless pig is important in rural nutrition; however, interest in its

production for use in gourmet tourism and the nutraceutical market

has increased. According to the Food and Agriculture Organization

(FAO, 2022), the Hairless pig is in danger of extinction; however, the

FAO does not provide data on its characterization, so it is necessary to

characterize and authenticate this breed to provide value, dierentiate

products and conrm its identity in conservation and rescue programs

(Lemus-Flores et al., 2023). The objective of this study was to use a

SNP panel strategy for racial discrimination of the Hairless pig to aid

in the dierentiation of animals that reproduce in local populations.

Materials and methods

Reference for animals and data collection

Three populations of Hairless pigs from the states of Nayarit

(n=10), Oaxaca (n=10) and Yucatán (n=143), Mexico, were used to

validate the SNP panels, and the populations were genotyped with

the GGP Porcine 50K chip (GeneSeek Genomic Proler Porcine)

(Lemus-Flores et al., 2023). DNA extraction, purication and PCR

process were performed by the Neogen company (www.neogen.

com). The low number of Hairless pig animals in Nayarit and Oaxaca

was due to the fact that they are small populations and a relationship

sample was selected. Genotypes of the Duroc (n=66), Hampshire

(n=33), Landrace (n=95), Large White (n=47), Pietrain (42) and

Iberian hairless (n=15) breeds were added to the Illumina 60K chip

database from previous studies (Yang et al., 2017). Individuals that

were assigned to their racial group by all the discrimination strategies

used were added to their breed in the database.

Racial verication strategy

Three separate SNP panels and a fourth strategy combining the

SNPs from all three panels (Moretti et al., 2022; Schiavo et al., 2020;

Wilkinson et al., 2012) were used in this study. The three separate

panels included 12 SNPs (Moretti et al., 2022), 38 SNPs (Schiavo

et al., 2020), and 49 SNPs (Wilkinson et al., 2012), and the fourth

panel included the 96 SNPs from these three panels. Common SNPs

between chips with the power of discrimination and racial allocation

were identied.

Discrimination analysis

According to the methodology of Moretti et al. (2022), for each

panel, the genotypes were assigned a value of 0 when the minor allele

frequency (MAF) indicated that the genotype was homozygous for

the major allele, 1 when the genotype was heterozygous, and 2 when

the genotype was homozygous for the minor allele. Using SPSS v9,

canonical discriminant analysis (CDA) was performed to create a

predictive model of group membership in each panel. Using these

four SNP panels and the combined databases including all races, the

This scientic publication in digital format is a continuation of the Printed Review: Legal Deposit pp 196802ZU42, ISSN 0378-7818.

Lemus-Flores et al. Rev. Fac. Agron. (LUZ). 2025, 42(3): e254231

3-6 |

linear discriminant canonical variables that provide the best possible

discrimination between the groups were identied, and the prediction

equation adjusted for the racial identication and discrimination of

Hairless pigs was obtained. Considering the canonical correlations

of discrimination, percentage of racial discrimination, and distance

trees between populations for the four panels, the best strategy to

discriminate Hairless pigs from other breeds was determined.

Results and discussion

Panels

The SNP panels formed according to the SNPs identied by the

two chips are presented in table 1. There are three SNPs in the 12-

SNP panel that are repeated in the 49-SNP panel.

Assessment of racial discrimination

According to the canonical correlations of the rst two variables

in the CDA, the panels with the most SNPs, those with 49 and 96

SNPs, are the panels with the greatest racial discrimination among the

four panels studied, as observed in table 2.

Based on the racial grouping according to canonical variables

1 and 2, the 96-SNP panel exhibited the best separation among the

groups (gure 1).

Table 1. SNPs in each panel (Sus domesticus).

Panel No. SNP

12 ALGA0027544

ALGA0047912 ASGA0004735 DBMA0000205 H3GA0016973 INRA0002279

INRA0029816 INRA0052808 M1GA0006536 MARC0027620

MARC0038980 MARC0042228

38 ALGA0026433 ALGA0033636 ALGA0038216 ALGA0047010 ALGA0047511 ALGA0055609

ALGA0060332 ALGA0061762 ALGA0062298 ALGA0088377 ALGA0092770 ALGA0093763

ALGA0096892 ALGA0105829 ALGA0111963 ALGA0119129 ALGA0119566 ASGA0028870

ASGA0054824 ASGA0066512 ASGA0103220 DRGA0008467 DRGA0011340 DRGA0016582

H3GA0024339 H3GA0032382 H3GA0043731 H3GA0046254 H3GA0048198 H3GA0056051

INRA0039368 INRA0039430 M1GA0007506 M1GA0021082 MARC0004055 MARC0019146

MARC0038400 MARC0081387

49 ALGA0001762 ALGA0003076 ALGA0003145 ALGA0010391 ALGA0010777 ALGA0026051

ALGA0036101 ALGA0042134 ALGA0042589

ALGA0047912 ALGA0048114 ALGA0071850

ALGA0074932 ALGA0085893 ALGA0103648 ALGA0106261 ALGA0108841 ASGA0014878

ASGA0019578 ASGA0024792 ASGA0025238 ASGA0038785 ASGA0053943 ASGA0069860

ASGA0073467 ASGA0073470 CASI0009493 DBMA0000259 DIAS0000043 DRGA0007655

H3GA0013097 H3GA0021745 H3GA0045081 H3GA0053839 H3GA0056129

INRA0002279

INRA0014142 INRA0022517 INRA0029891 INRA0029897 INRA0036473 INRA0040988

MARC0029724 MARC0030810

MARC0038980 MARC0056888 MARC0061507 MARC0075425

MARC0093043

SNP: single-nucleotide polymorphism.

Table 2. Percentage of variance and canonical correlations in each SNP panel.

SNP 12 38 49 96

Variable % V CC % V CC % V CC % V CC

1 50.0 .941 38.4 .931 56.9 .981 47.5 .988

2 28.1 .901 19.8 .877 16.8 .939 18.1 .969

3 14.6 .831 16.7 .859 10.4 .906 13.9 .960

4 4.9 .654 11.0 .806 8.2 .885 8.5 .937

5 1.9 .473 8.2 .761 5.3 .837 8.1 .934

6 .6 .293 5.9 .705 2.4 .719 3.9 .878

% V: percentage of variance. CC: canonical correlation. SNP: single-nucleotide polymorphism.

Racial grouping

In the CDA for racial grouping, the only panel that did not

correctly group 100 % of Hairless pigs was the 38-SNP panel; three

Hairless pigs were predicted as Landrace pigs, and one was predicted

as a Pietrain pig (Table 3).

The separation of the racial groups indicated that the Hairless

pigs are close to the Iberian, Hampshire and Duroc pigs, as shown

in gure 2.

In the separation of the Hairless pig populations with the 96 SNP

panel, the populations of Nayarit, Oaxaca and Yucatán were grouped

together (figure 3).

SNP panels identied with high-density chips have

been used in several species, and a high degree of racial assignment

was achieved with fewer than 100 SNPs in bovines (Wilkinson et al.,

2011). Another strategy for racial identication uses SNPs associated

with candidate genes with productive characteristics that are highly

expressed in certain races, such as the studies published by Óvilo et

al. (2022) and Palma-Granados et al. (2023) in Iberian pigs and Zhang

et al. (2014) in commercial pigs. Wang et al. (2022) constructed a

reference panel of haplotypes to impute genotypes to dierent pig

breeds with increased eciency.

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Rev. Fac. Agron. (LUZ). 2025, 42(3): e254231 July-September. ISSN 2477-9409.

4-6 |

Table 3. Predicted membership group according to each SNP panel.

Hairless Duroc Hampshire Landrace Large White Pietrain Iberian

SNP/n 163 66 33 95 47 42 15

12 100 100 100 100 100 100 100

38 97.5 100 100 100 100 100 100

49 100 100 100 100 100 100 100

96 100 100 100 100 100 100 100

SNP: single-nucleotide polymorphism.

A B

Figure 1. Plots of canonical variables 1 and 2. A, B, C and D, panels with 12, 38, 49 and 96 SNPs, respectively.

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Lemus-Flores et al. Rev. Fac. Agron. (LUZ). 2025, 42(3): e254231

5-6 |

Figure 2. Dendrogram of the square distances between racial

groups with the 96-SNP panel.

allocation when using FST and CDA in commercial breeds, Nero

Siciliano, Casertana and Cinta Senese. The results suggest that racial

assignment condence depends on the discrimination methodology

(Schiavo et al., 2020). When analyzing genotypes with SNP chips and

combining the statistical methods delta, FST and ln, Zhao et al. (2023)

achieved 99 % racial assignment. In another study, Dadousis et al.

(2022) obtained a racial assignment above 97 % using discriminant

PCA. These studies allow us to conclude that chips are an optimal

strategy for racial identication, regardless of the statistical method

used.

Using the panel of 96 SNPs obtained from 14 British races

originally proposed by Wilkinson et al. (2012) with the Bayesian

partial assignment methodology, a complete racial classication was

obtained, except in Hampshire, Landrace, Large White and Pietrain,

which had 99 % accuracy. Using the Wilkinson et al. (2012) panel

reduced to 49 SNPs via CDA, a racial assignment of 100 % for the

Hairless pig was achieved. These authors grouped the genetically close

Landrace, Large White and Pietrain pigs. Combining the three panels

into a fourth panel with 96 SNPs, the racial assignment improved to

100 %, with a higher canonical correlation of the rst two variables

in the CDA. The Hairless pig populations of the three localities are

close, and it is possible to discriminate and achieve adequate racial

authentication among them using this strategy. The Hairless pig

populations were grouped close to the Iberian pig populations, as

has been reported in other studies (Lemus-Flores et al., 2023). The

SNP bases identied in the four panels tested may be used in future

analyses. Muñoz et al. (2020) used a 64-SNP panel to authenticate

Iberian pigs, separating them from Duroc pigs, and proposed the use

of this strategy for the regulation of Iberian meat products. Miao et

al. (2023) evaluated the methodological proposals of discrimination

and concluded that racial identication is feasible and that reliability

increases with an increasing number of SNPs. Pasupa et al. (2020)

reported that the number of SNPs used for racial identication can be

reduced, but the best strategy for reliable classication is to combine

methodologies. In accordance with that theory, the 96-SNP panel,

combining the three previously reported panels, resulted in better

racial separation in the Hairless pig in this study.

Conclusions

Using SNP panels identied by 50K or 60K chips, racial

authentication of the Hairless pig can be achieved, as it can be

discriminated from other breeds. The four strategies evaluated

achieved racial separation; the greater the number of SNPs used,

the better the identication of the Hairless pig. The 96-SNP panel

achieved 100 % racial assignment and a higher canonical correlation

of the rst two variables in the CDA.

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