Utilizing Indigenous Animal Genetic Resources—Based on Research Into Indigenous Cattle Breeds in the Basque Country in Northern Spain and Indigenous Pig Breeds in Vietnam

ABSTRACT

Biodiversity, climate change, and food security are closely related and increasing worldwide concerns. Therefore, sustainable productivity and changes to the livestock industry are required for the maintenance or amelioration of the global environment and the future of humanity. This review describes the potential of animal genetic resources and their expected roles in livestock improvement. Herein, I report the findings of my previous collaborative research project on the domestication of cattle and pigs, and genetic analysis of native cattle in the Basque Country, Spain, to improve the meat quality of native livestock genetic resources. In addition, I review another research on the diversity of native pigs in Vietnam and the establishment of a gene bank. The conservation of native livestock genetic resources is important for sustainable food production in each region, the inheritance of food culture, and to be available for future needs because native livestock adapted to their habitat's environment can coexist with locally cultivated crops. This encourages livestock researchers to consider sustainable production through the future use of native livestock genetic resources and to seek feasible solutions.

1. Introduction

The domestication of animals and plants is one of the most prominent events in human history, as it symbolized a gradual but significant change in early human societies from nomadic hunter‐gatherers to sedentary farmers (Diamond 2002). As humans lived alongside livestock, our ancestors benefited from the diverse products that livestock produced, as well as their ability to plow fields and transport goods, allowing for the global expansion of their settlements. Domestic animals bred for human use are classified into forms that share genetic characteristics defined as “populations” or “breeds.”

This review discusses the potential utility of livestock genetic resources for sustainable production by introducing the native Spanish cattle breeds, with their superior genetic characteristics and meat quality, as well as the genetic diversity of Vietnamese native pig breeds. In addition to recent efforts to create new industries based on my previous research on the utilization of native livestock populations.

This review begins with a brief introduction to the recent recognition of the domestication of cattle and pigs, the two largest meat‐producing livestock species worldwide, and the current status of native livestock. Additionally, I briefly introduce the current status of animal genetic resources according to reports from the United Nations. The goal of this review is to extrapolate past events by analyzing the current situation and estimate future conditions for a better future.

2. Cattle Domestication

The two modern lineages of domestic cattle, Bos taurus and B. indicus , are believed to have evolved from the common ancestor B. primigenius approximately 250,000 years ago (Pitt et al. 2019). The domestication of the taurine cattle ( B. taurus ) is estimated to have occurred around 10,000 years ago in the Fertile Crescent in the Near East, based on B. primigenius (Ajmone‐Marsan et al. 2010; Bollongino et al. 2012; Bruford et al. 2003; Götherström et al. 2005). However, the Indicine ( B. indicus ) was domesticated as a separate lineage approximately 1500 years following the domestication of the taurine in the Neolithic cultures of the Indus Valley, as Bos primigenous nomadicus (Loftus et al. 1994; Pitt et al. 2019). European Taurus‐domesticated cattle subsequently spread throughout Europe with the migration of agricultural people, giving rise to the belief that they were established through sporadic hybridization between domesticated cattle and native European aurochs (Ajmone‐Marsan et al. 2010). Two hundred fifty years ago, domestic cattle had lower productivity than modern standards. At the time, cattle were primarily used for subsistence agriculture and were maintained through extensive management; this is still the case in Africa and South Asia (Felius et al. 2014).

Modern European domestic cattle, B. taurus , are phylogenetically differentiated into three main populations: northwest (British and Irish [BRI] and Netherland [NLD]), Iberian Peninsula (Iberian [IBR]), and Balkan and Italian (Balkan and Italian [BAI]) (Upadhyay et al. 2017). According to Upadhyay et al. (2017), the cattle lineage observed in BAI was established by human exchange between North‐Central Europe and India due to the large‐scale migration of Indo‐European Yamnaya steppe livestock breeders, as supported by ancient human genome studies (Haak et al. 2015; Jones et al. 2015). This may have led to the introduction of Indian zebu and Ukrainian steppe cattle, resulting in the introgression of indicine genes into taurine cattle in the same region (Reich et al. 2009). Likely due to the geographically isolated nature of the Iberian Peninsula, the level of gene flow within the IBR is assumed to be high; however, the genetic similarity between populations is high, indicating that genetic diversity between breeds is low. Herd books for IBR breeds were introduced relatively late (after the 1920s). Prior to this, the exchange of breeding materials was only carried out within neighboring regions, which may have resulted in the formation of relatively similar homogeneous gene pools (Cañas‐Álvarez et al. 2015). In addition, NLD varieties are considered productive against primitive BRI. The analysis results of the maximum likelihood estimation of individual ancestries based on genetic polymorphisms, namely, ADMIXTURE, reflect the influence of Dutch sire exports to England since the 16th century (Felius et al. 2014; Upadhyay et al. 2017). Owing to its geographical isolation since 1763, Jersey shows genetic uniqueness (Felius et al. 2014; Upadhyay et al. 2017). In relation to long‐term isolation, the NLD and BRI varieties have many small runs of homozygosity (ROH), indicating a pattern of isolation based on the size of the source population. In particular, the Galloway and Holstein Friesian varieties may have been successful in maintaining their population size, isolating them from other genetically related populations because of successful breeding management (Figure 1).

FIGURE 1.

ADMIXTURE analysis showing model‐based population assignments for the values of K = 2 (upper) and K = 3 (lower). Almost all BAI, AU, and HE samples display a possible zebu genetic component at K = 2 and K = 3. The number below each bar represents the number of samples for the respective population. Abbreviations: ALP, Alpine; BAI, Balkan and Italy; BRI, British and Irish; HE, Heck; IBR, Iberian; JE, Jersey; MP, Maremmana × Pajuna; NE, Nelore; NLD, Dutch. Breed abbreviations: AL, Alentejana; AN, Angler; AR, Arouquesa; bc, Berrenda en Colorado; BK, Boskarin; BN, Berrenda en Negro; BS, Brown Swiss; BU, Busha; CA, Cardena; CC, Cachea; CH, Chianina; CL, Caldela; DB, Dutch Belted; DF, Dutch Friesian; EL, English Longhorn; FL, Fleckvieh; GA: Galloway; GW: Groningen Whiteheaded; HE: Heck; HF: Holstein Friesian; HL: Highland; JE: Jersey; KC: Kerry Cattle; LI: Lidia; LM: Limia; MA: Maremmana; MA: Maltese; ME: Maronesa; MI: Mirandesa; MRY: Meuse Rhine Issel; NE: Nelore; PA: Pajuna; PO: Podolica; RO: Romanian Grey; SA: Sayaguesa; TU: Tudanca; WP: White Park. The figure and captions are based on Upadhyay et al. (2017).

In summary, two theories of origin are believed to have established the domestication of the main modern domestic cattle: taurine ( B. taurus ) and indicine cattle ( B. indicus ), with B. primigenius being a common ancestor. Pitt et al. (2019) further analyzed population structure, domestication, and demographic dynamics using large‐scale single‐nucleotide polymorphism (SNP) data, including both taurine and indicine cattle from 180 populations distributed geographically worldwide, and examined the possibility of a third cattle domestication in the Western Desert of Egypt. Using several mathematical statistical models that considered ascertainment bias, a technical issue in SNP array analysis, high lineage differentiation between African and European taurine cattle and high admixture of African indicine cattle with Asian indicine and African taurine cattle was observed. Consistent with multiple model analyses, results revealed only two instances of cattle domestication, eliminating the theory of the third domestication in Egypt; instead, subsequent hybridization from local aurochs in the region explained the additional genetic variation (Pitt et al. 2019). In the future, if the migration relationship between African indicine and European taurine cattle becomes clear, conducting ancient genome analysis will become possible, revealing the complex phenomena underlying the human‐mediated microevolution of domestic cattle.

3. Pig Domestication

Wild boars, the ancestors of domestic pigs (both Sus scrofa ), are widely distributed in Eurasia and were valuable hunting targets for hunter‐gatherers in the early Neolithic period. The domestication of wild boars to pigs and that of other wild mammalian species radically shifted the hunter–predator relationship between humans and wild boars (Larson et al. 2005). The pig was first domesticated approximately 9000 years ago in the Near East, according to extensive zooarchaeological records (Epstein and Bichard 1984). Recent molecular and archaeological evidence suggests that a second independent domestication event occurred in the Far East (Giuffra et al. 2000; Jing and Flad 2002). Wild ancestors of domestic animals in Eurasia are either extinct (e.g., aurochs [Troy et al. 2001] and wild horses [Jansen et al. 2002]) or have lost or retained only slightly vestigial phylogeographic structures (e.g., wolves [Savolainen et al. 2002]). However, the widespread distribution of wild boar populations in the “Old World” provides a unique opportunity for analyzing the origins of modern domesticated pig lineages.

Previous studies have identified three subpopulations of modern S. scrofa mtDNA sequences (Giuffra et al. 2000; Kijas and Andersson 2001), an Asian clade, and two European groups (of which, one consisted only of Italian boars). Although both Asian and European groups contain domesticated pig breeds, molecular clock estimates suggest that the divergence between the two groups is significantly longer than previously assumed, indicating that evidence for pig domestication may date further back; that is, domestication occurred independently of the divergent wild boar lineages in each region (Giuffra et al. 2000; Kijas and Andersson 2001).

The basal lineage of S. scrofa was found on the islands of Southeast Asia. From where, an initial spread into the Indian subcontinent was followed by a subsequent radial spread into East Asia and, finally, a gradual spread throughout Eurasia and Western Europe. The characteristic East–West divergence of wild boars is consistent with the results of morphological analyses, as the morphology of Southeastern Asian wild boars ( S. scrofa vittatus ) is particularly distinctive. Only 2% of wild boar samples showed discrepancies in the concordant phylogeny–geography relationship, which may have emerged as a result of past events, human‐mediated introductions, and/or dispersal (Figure 2).

FIGURE 2.

Bayesian (MCMC) consensus tree of 122 sus mtDNA control region haplotypes rooted by a common warthog ( Phacochoerus aethiopicus ). In total, 14 clusters (represented by a specific color and corresponding region on the Eurasian map) are contained within four major clades on the tree (1–4). Tips associated with the island of Sulawesi represent the native wild boar Sus celebensis . All other tips represent wild S. scrofa unless indicated by the following two‐letter codes: sb, S. barbatus ; sv, S. verrucosus . D1–D6 represent suggested centers of domestication. D1–D3 indicate areas where native wild boar have haplotypes identical to those of domestic pigs from the same region. Figure and caption are based on Larson et al. (2005).

In Europe, domestic pigs originating from the Near East are estimated to have reached the Paris Basin by at least the early 4th millennium bc and were introduced into Europe during the Neolithic period. According to Larson et al. (2005), mtDNA haplotypes' analysis of ancient genomes and modern pig databases indicates that European wild boars were also domesticated around that time, probably due to the direct influence of the introduction of domestic pigs. Two routes of domestic pig dispersal from the Near East have been estimated: northwest along the north bank of the Danube River and west along the north coast of the Mediterranean Sea. Once domesticated, the European pig quickly spread throughout Europe, replacing pigs from the Near East (Bramanti et al. 2009). Some European pig populations migrated to the Near East between 700 bc and 1500 ad (Ottoni et al. 2013), but it is unclear whether this was due to human migration or trade.

Regarding the origin of Asian domestic pigs, first, independent pig domestication in China (at least 8000 years ago in the north and south) is supported by genetic and archaeological evidence (Jing and Flad 2002; Flad et al. 2007; Luo and Zhang 2008). Furthermore, five indigenous wild boar populations that may have independently domesticated pigs are discussed: one in India, three in the Southeast Asian Peninsula, and one along the coast of Taiwan. However, the lack of archaeological evidence compelled its labeling as “cryptic domestication,” until advances in ancient genome analysis were made. Research was conducted based on information obtained from geographical and morphological animal samples and archaeological evidence; in some cases, sufficient evidence has not been obtained. Thus, the multiple‐origin hypothesis of pig domestication has long been debated. However, recent advances in ancient genome analyses have provided new insights (Larson et al. 2010).

4. Current Status of Animal Genetic Resources

Next, I provide an overview of the current state of livestock genetic resources based on the latest articles published by the Food and Agriculture Organization (FAO) of the United Nations (2023).

The majority of both Cattle and Pig breeds are identified on the Eurasian continent. Typical differences between cattle and pigs are observed in Africa, where greater varieties of cattle (18.4%) are found than those of pigs (9.7%); in the Near and Middle East regions, only one local pig is recorded for 31 varieties of cattle (Table 1).

TABLE 1.

Numbers of reported local breeds of mammalian species.

Species	Cattle	Pig	Total a
Africa	193	55	601
Asia	262	232	1334
Europe and the Caucasus	379	194	2154
Latin America and the Caribbean	138	58	443
Near and Middle East	31	1	186
North America	14	10	99
Southwest Pacific	32	16	137
World b	1049	566	4954

^a Total includes Ass, Bactrian camel, Buffalo, Dromedary, Goat, Guinea pig, Horse, Rabbit, Sheep, Yak, and others (Alpaca, American Bison, deer, dog, dromedary × Bactrian camel, guanaco, llama, and Vicunia).

^b Overall, 4954 mammalian species are recorded as local domestic breeds. Among these, cattle and pig breeds occupy 21.2% (1049 breeds) and 11.4% (566), respectively.

The guidelines published by the FAO and International Society of Animal Genetics describe the key concepts and standard research methods that should be used when investigating the diversity of current livestock genetic resources (Ajmone‐Marsan et al. 2023).

The guidelines outline several key points for maintaining and utilizing the genetic diversity of animal genetic resources, as follows:

Loss of biodiversity: Erosion of animal genetic resource (AnGR) diversity has become a major concern (Bruford et al. 2015; FAO 2007a; Hodges 2006). The negative consequences of genetic erosion and inbreeding depression may manifest as loss of viability, fertility, and disease resistance, as well as the frequent occurrence of recessive diseases (FAO 2007b; Howard et al. 2017; Taberlet et al. 2008). Approximately 7% of livestock breeds have become extinct, and > 25% are considered at risk of extinction (FAO 2021). Moreover, for > 50% of breeds, most of which are reared in developing countries, the situation is currently unknown.

Ecological adaptation: Owing to recent climate changes, the use of indigenous livestock genetic resources adapted to the local environment has attracted attention. Furthermore, ecosystem regeneration through the reintroduction of species that have become feral (or semiferal) due to abandonment is being considered.

A key concern in considering measures to address these issues is the lack of relevant knowledge and information. Therefore, it is important to conduct research, using such guidelines, on bereaved families based.

5. Genetic Characterization and Utilization of Livestock Genetic Resources

5.1. Genetic Studies on Local Cattle Breeds in the Basque Country in Northern Spain

Several indigenous cattle breeds are located in Basque Country, including Pirenaica, Terrena, and Salers; however, Pirenaica is the most important indigenous cattle breed, as it is certified as a “100% autochthonous breed,” according to federal law, by the Spanish Ministry of Agriculture (Official Bulletin of the Spanish State 2008). In addition, this breed is certified by the Protected Geographic Indication quality label, which is a standard defined by the European Union and, thus, satisfies health and welfare standards (European Commission 2003). Thus, DNA markers that enable individual identification and variety discrimination are used to ensure food quality and safety as well as prevent brand leakage (Baldo et al. 2010; López‐Oceja et al. 2017).

Microsatellite, in other words, short‐tandem repeat (STR) markers, is generally employed to identify cattle breeds. An 11‐STR panel (StockMarks, Applied Biosystems, currently Thermo Fisher Scientific, Waltham, MA, USA), followed by 12‐STR core and 18‐STR panels (Bovine Genotype Panels 1.2 and 2.2, Thermo Fisher Scientific, Waltham, MA, USA) with six additional markers, was launched if Panel 1.2 was insufficient. From the perspective of production site efficiency, identifying varieties using fewer markers is what is best. However, the resolution and separation ability of commercially available identification products are insufficient for European varieties (Van de Goor et al. 2011). Therefore, Gamarra et al. (2020) aimed to (1) evaluate the genetic diversity of Pirenaica, (2) verify the effectiveness of the FAO30STR, and (3) develop an STR panel and verify traceability. In addition to Pirenaica, the target breeds included Terrena, Blonde d'Aquitaine, Limousers, Salers, and Holstein, which are bred in the Basque Country.

To achieve a combined power of exclusion (CPE) > 0.9999 (99.99%), which is required for parent–offspring identification, 21, 13, and 11 STR markers were necessary for parent–offspring identification for CPE1, when one parent is known, CPE2 when both parents are known, and CPE‐SI when paternal half‐siblings are known, respectively. That study's findings caused the development of a marker set suitable for PGI certification of local Pirenaica, providing a tool to address issues such as food safety and loss of varieties. While STR markers are effective for this method, they also have cost advantages (EUR 10–20/head at publication). However, considering the recent reduction in the cost of genome‐wide SNPs and whole‐genome sequencing, it is possible that more accurate, simpler, and cheaper methods will be developed in the future.

In terms of beef meat quality, consumers are becoming increasingly concerned about the quality of fat in their food. As saturated and trans fatty acids have adverse health effects (World Health Organization 2003), monounsaturated fatty acids and polyunsaturated fatty acids (PUFA) have health benefits (Burlingame et al. 2009). Taniguchi et al. (2004) isolated the stearoyl‐CoA desaturase (SCD) gene in Japanese Black cattle breeds and revealed the relationship between gene polymorphism and fatty acid composition. Subsequently, polymorphisms and their association with fat‐related traits have been explored in various cattle breeds, including beef and dairy breeds (Ibeagha‐Awemu et al. 2008). We examined the quality of its fat, as the native Basque cattle is a highly valued beef cattle breed and to assess its value. In addition to Pirenaica, which is used exclusively for meat, we used the Salers (a dual‐purpose dairy and meat breed developed in central France valued for its high environmental adaptability in Basque Country, North America, Africa, and etc.) and Holstein–Frisian breeds (a dairy breed popular worldwide; castrated males are fattened for meat production) to examine how breed and sex affect the expression levels of fatty acid synthesis genes and composition in subcutaneous fat. To eliminate the influence of genetic background, individuals of the same breed were selected by checking pedigree, excluding parent–child relationships and maternal half‐siblings—keeping paternal half‐siblings at a low level. Regarding fatty acid composition, the content of monounsaturated fatty acids in the subcutaneous fat of female Pirenaica was significantly higher than that in males and other breeds (Salers males and Holstein–Frisian females).

The content of 10t, 12c‐CLA, which suppresses Δ9 enzyme (SCD1) activity, was higher in female Pirenaica than in other breeds. In contrast, the n‐6 PUFA content was higher in male Salers than in other breeds. Concerning fat synthesis genes, a correlation between the major transcription factor, sterol regulatory element‐binding protein 1 (SREBP1), and Δ9 enzyme gene SCD1 was observed in all breeds. In particular, the highest correlation coefficient in female Pirenaica was R ² = 0.491, whereas the lowest was 0.239 in male Pirenaica, indicating that the fat synthesis gene expression levels differ depending on sex (sex‐dependent manner), even within breeds. GH in sexually differentiated mammals increases the expression of the SREBP1 and SCD1 genes in females (Ameen et al. 2004). Similarly, when we examined the correlation between the expression levels of SREBP1 and SCD5, a significant correlation was found in Holstein–Frisian and Pirenaica males (R ² = 0.213, 0.114, respectively), although the correlation coefficients remained low. The correlation between the gene expression levels of SCD1 and SCD5 was significant only in Holstein–Frisians, with a positive correlation of R ² = 0.266. In contrast, male Salers and male and female Pirenaica showed a tendency toward a negative correlation, although this was not significant. The difference in the expression patterns of SCD isoforms, especially SCD5, is probably due to their susceptibility to environmental influences. The Holstein–Frisian breed used in that study was significantly different from the other breeds as it was bred for meat instead of dairy. Regarding the relationship between fatty acid composition and fat synthesis gene expression, Salers males showed a positive correlation between many desaturation indices (DIs) and SCD1 expression; Pirenaica males showed a positive correlation between DI and SCD1 expression. Similar to SCD1, the correlation between DI and SREBP1 was positive in Salers males and Pirenaica males and females. In contrast, DI and SCD5 were negatively correlated. This may have been influenced by the fact that Salers and Pirenaica are young meat breeds (13 months old on average), whereas Holstein–Frisians are older dairy breeds (70 months old). Producers hope that by clarifying the relationship between fatty acid composition and expression of fat synthesis genes, particularly the strong correlation observed in Salers, they may be able to improve meat quality uniformity.

In relation to the aforementioned previous publication (Gamarra et al. 2020), we explored polymorphisms in the SREBP1 gene, a main transcription factor for fat synthesis in native Basque cattle breeds, and the effects of SREBP1 polymorphisms on the expression levels of fat synthesis genes and fatty acid composition in subcutaneous fat (Gamarra et al. 2018, 2021). A detection of SREBP1 gene polymorphisms revealed an 84 bp‐indel in intron 5, which was identical to that found in Japanese Black cattle (Hoashi et al. 2007). Deletion was defined as S‐type, a minor allele, and insertion was defined as L‐type, a major allele. The frequencies of the S‐type allele were 0.385 in Salers males, 0.214 in Pirenaica females, and 0.135 in Pirenaica males. No S‐type was found in Holstein–Frisians. Regarding the transcription factor SREBP, each isoform is specific to its corresponding metabolites, such as SREBP1 for fatty acid metabolism and SREBP2 for cholesterol metabolism (Horton et al. 2002). This may be generated by gene duplication when the need for independent metabolic mechanisms for fatty acids and cholesterol arises (Osborne and Espenshade 2009). S‐del homozygosity has only been found in Japanese Black cattle (Hoashi et al. 2007), and a report showed the frequencies of S‐type at 0.28 and L‐type at 0.72 in the Hanwoo breed (Bhuiyan et al. 2009). Additionally, the S allele was detected in the Fleckvieh breed; however, the frequency was low at 0.080 with no SS homozygosity (Barton et al. 2010). In Canadian commercial crossbreds, the frequency was 0.99 for L‐type and 0.01 for S‐type; however, no SS‐type was found. In this study, the S‐type was discovered in the Basque native cattle, Pirenaica, and Salers at the above allele frequency, with SS‐homo. Since European cattle breeds were introduced to improve Japanese Black cattle (Hirooka 2014), the S‐type may have originated from European beef cattle breeds. The S‐type frequency was reported to be as high as 0.368 in Japanese Black Cattle, a temporary foreign species (Kaneda et al. 2011).

When the homology of this indel polymorphism site with other mammals was examined, rodents were determined to have clearly diverged from the even‐toed livestock species of cattle, goats, sheep, and pigs, as well as horses, dogs, and humans (Figure 3). Intron 5, which contains an indel polymorphism, shows high homology among animal species that is comparable to the exon region. ssc‐miR‐33b was detected in intron 16 of the pig SREBP1 gene, and its inhibitory effect on fat synthesis genes was revealed (Taniguchi et al. 2014). The Bovine SREBP1 gene also contains bta‐miR‐33b in the same region (Strozzi et al. 2009). Further research is required to confirm if the intron 5 indel region is related to the functionality of similar epigenetic regulations.

FIGURE 3.

Representation of the nucleotide sequence similarities of the SREBP1 gene among mammalians. (a) maximum‐likelihood tree using the mRNA of SREBP1 in different mammals (the length of branches represents the expected number of substitutions per site) and percentage of bootstrap replicates (up to 100) supporting each node. (b) Area graphs (histograms) show the similarity and alignment of the bovine genomic sequence of SREBP1, intron 5, and 84 bp‐indel region along with homologous sequences of different mammals. Figure and caption are based Gamarra et al. (2021).

In case a simple association analysis of genotypes and fatty acid composition was performed for Salers, Pirenaica, and Holstein–Frisian (Table 2), the n‐3 fatty acid content was significantly higher in the SS/SL type than in the LL type in the Pirenaica males. However, the LL type had a higher 18:3n‐6 content than the SS/SL type. Thus, significant differences were observed for only a few fatty acids. The n‐6/n‐3 ratio is recognized as an indicator of health; thereby, foods high in n‐3 are advantageous. Although no clear correlation was found between the SREBP1 indel polymorphism and expression levels of SREBP1 and SCD genes in Basque native cattle breeds, significant differences in n‐3 PUFA levels were found due to indel polymorphism, which is useful for producing distinctive beef.

TABLE 2.

Regression equations between the genotype (SS/SL vs. LL) and fatty acid content (mg/g of fat) of subcutaneous adipose tissue of Pirenaica (bulls and heifers).

	Pirenaica bulls and heifers			Pirenaica bulls			Pirenaica heifers
Fatty acid	Slope	SEM	p	Slope	SEM	p	Slope	SEM	p
18:0	−15.8	6.740	0.22	−24.2	10.9	0.034	−6.81	6.41	NS
n‐6	−2.04	1.788	NS	−2.81	2.705	NS	−0.948	2.16	NS
18:2n‐6	−1.96	1.784	NS	−2.87	2.702	NS	−0.849	2.10	NS
18:3n‐6	0.023	0.016	NS	0.045	0.021	0.036	0.008	0.022	NS
n‐3	−0.371	0.156	0.020	−0.504	0.234	0.038	−0.202	0.206	NS
18:2n‐3	−0.377	0.149	0.15	−0.488	0.224	0.036	−0.235	0.189	NS

Abbreviation: SEM, standard error of the mean.

p indicates p‐values of the analysis of variance. Significant difference is defined as p < 0.05. Otherwise it is denoted as NS (not significant).

Table and caption are cited from Gamarra et al. (2021), unadjusted.

5.2. Genetic Studies on Vietnamese Native Pig Breeds

Then, we introduce a research example of the genetic analysis of native Vietnamese pig breeds. This was part of a Science and Technology Research Partnership for Sustainable Development (SATREPS) project entitled “Establishment of Cryo‐bank System for Vietnamese Native Pig Resources and Sustainable Production System to Conserve Bio‐diversity” and conducted with the support of the Japan International Cooperation Agency and Japan Science and Technology Agency (JST 2015), in collaboration with research institutes, universities, and private companies from both Japan and Vietnam (JST/SATREPS/Projects/Establishment of Cryo‐bank System for Vietnamese Native Pig Resources and Sustainable Production System to Conserve Bio‐diversity, https://www.jst.go.jp/global/english/kadai/h2604_vietnam.html).

The objective of SATREPS is to establish a gene bank for the conservation of genetic resources. To this end, we first planned a study to elucidate these genetic characteristics. When collecting pig samples for DNA extraction, we performed interviews with pig farmers and compiled information on the external and morphological characteristics of the Vietnamese native pigs (VNP), such as coat color, into a database.

Approximately 26 local pig breeds exist in Vietnam (Dang‐nguyen et al. 2016; Pham et al. 2014; Thuy et al. 2006), suggesting abundant local pig genetic resources as it is a worldwide pig domestication site (Larson et al. 2010; Ramos‐Onsins et al. 2014). Based on our previous genetic analysis of native pigs in Vietnam (Ishihara et al. 2018), the northern region is rich in native pig genetic resources. We collected DNA from 1136 pigs from 21 provinces across Vietnam (Figure 4). Then, we performed a large‐scale genetic analysis using International Society for Animal Genetics (ISAG)/FAO‐recommended microsatellite markers as previously described (Ajmone‐Marsan et al. 2023).

FIGURE 4.

Sampling locations of Vietnamese native pigs analyzed. Circles in black, red, blue, and green indicate provinces with native pig habitation in the northeast, northwest, north‐central coast, and central highland‐south regions, respectively, followed by administrative regions defined by the Vietnamese government. In contrast, the purple circle indicates the farm from which the Western pig breeds were collected. Figure and caption are cited from Ba et al. (2020) unadjusted.

The genetic VNP relationship based on the NJ phylogenetic tree shows the geographical relationship of each population's habitat (Figure 5). In Branch 1, black (Ban Yen Bai, Ban Bac Kan, Tap Na, Lung Pu, Hung, Moung Khuong), and red (Ban Dien Bien, Ban Lai Chau, Moung Te) are the northern mountainous regions, and blue is the central region closer to the northern region (Meo Xao Va). In Branch 2, blue is the central coastal region (Van Pa, Co A Luoi), and green is the central highland region (Co Quang Nam, Kieng Sat, Chu Proung, Soc, Co Binh Thuan). Branch 3 included Western breeds, and Vietnamese pigs were distributed throughout the northern, central, and southern regions. In addition, the population structure was assessed using principal component analysis, and the results indicated that O Lam was hybridized with Western breeds. While the northern mountainous and central coastal regions were not clearly differentiated, the pig populations in the northeastern Mong Cai and central highlands had specific population structures.

FIGURE 5.

Phylogenetic tree designed using the neighbor‐joining method based on Nei's distance for Vietnamese native pigs. Black, red, blue, and green characters indicate these pig breeds were derived from northeast, northwest, north‐central coast, and central highland‐south regions, respectively. In contrast, the purple characters indicate Western pig breeds. The figures and captions are cited from Ba et al. (2020) without adjustments.

Furthermore, the results of the ADMIXTURE analysis of genetic differentiation between the VNP and Western breeds supported the above‐mentioned relationships among populations (Figure 6). In this study, we investigated the genetic structure, diversity, and relatedness of the VNP populations from various perspectives (Ba et al. 2020). Vietnam is a long country that stretches from north to south with rich and various environments. Furthermore, the pig farms in each region are small scale. Generally, native pigs adapt to their environment of origin (Mignon‐Grasteaua et al. 2005). However, it can be inferred that the VNP, which has adapted to various environments, has rich genetic diversity.

FIGURE 6.

Genomic structure of Vietnamese native pigs. Putative ancestral populations and their relationships among Vietnamese native pigs were denoted with different colors according to the K. Figure and caption are cited from Ba et al. (2020), unadjusted.

The results of the present review clearly demonstrate this phenomenon. However, hybridization with Western species has progressed in some populations. Following this review's collection and survey, African swine fever spread to Vietnam in February 2019, and many genetic resources were lost. In addition to the results of the present study, material stored in gene banks through the development of breeding techniques (Somfai et al. 2019; Nguyen et al. 2020) will play an important role in reviving Vietnamese pig genetic resources.

A following study showed that despite Vietnamese pigs being rich in genetic diversity, however, some populations are at risk of extinction because of the introduction of foreign breeds and shrinking means. In this study, when collecting pig samples for genetic analysis, we interviewed farmers, collected external characteristics, and classified them to create a database (Ishihara et al. 2020b). The sample regions and populations included those in a previous study, and 1918 individuals from 32 populations, 61 districts, and 166 communes were used for this analysis. The external characteristics of the native pigs are listed in (Table 3). The VNPs were classified based on coat color, coat type, skin color, skin type, presence or absence of fangs, nose and ear morphology, and body shape.

TABLE 3.

Characteristics of Vietnamese native pigs and their classification.

Characteristic	Classification
Coat color	Black	White	Black + White	Brown	No data
Coat pattern	Plain	Spotted	6 spots	4 spots	No data
Hair_Charact	Straight	Curly	No data
Hair_Density	Average	Dense	Scattered	No data
Hair_Mane	TRUE	FALSE
Skin_Color	Black	White	Black + White	Brown	Spotted	No data
Skin_Charact	Smooth	Wrinkled	No data
Tusks	TRUE	FALSE
Face	Straight	Concave	No data
Snout_A	Long	Short	No data
Snout_B	Straight	Concave	No data
Shape_Ear	Horizontal	Upward curved	Downward	No data
Shape_Belly	Slim	Drooping	No data
Shape_Leg	Straight	Curved	No data
Shape_Walk	On toe	On foot	No data
Backline	Straight	Upward curved	Swayback	No data

Cited from Ishihara et al. (2020a) without adjustment.

Multiple correspondence analyses showed that many of the VNP populations overlapped in the negative direction for both PC1 and PC2 (Figure 7, bottom left of the figure), but Hung (HU), Huong (HUO), Ha Lang (HL), Mong Cai (MC), O Lam (AG), and Chu Prong (CP) (encircled by ellipses) were separate. The contributions of principal components 1 and 2 were 15.7% and 7.3%, respectively. Some populations, such as HU, HUO, HL, MC, AG, and CP, were separated from the other populations, but almost all populations were integrated with each other (Figure 7a). The category distribution is illustrated in Figure 7b. Skin_Spotted, Skin_White, Skin_Black–White, Face_Others, Coat_White, Coat_Brown, Leg_Bandy, and Leg_Curved were separated from the other factors (Figure 7b). The morphological characteristics depicted in Figure 7b comprise various external and morphological characteristics such as coat color, skin color, and bone structure in the plot (lower left) and are found in most of the native Vietnamese pig breeds. The Hu, HUO, HL, and MC breeds in northern Vietnam may be influenced by their relationship with Chinese pigs, consistent with our previous genetic analysis (Ishihara et al. 2018). Supporting a previous paper with similar genetic diversity results, the findings determined that diversity existed in external characteristics. Notably, characteristic data for each population were recorded in the form of a relational database for viewing purposes.

FIGURE 7.

Multiple correspondence analysis of the characteristics of Vietnamese native pig populations. Upper panel (a) shows the distributions of the various Vietnamese native pig breeds and ellipses (95% confidence levels) for the O Lam (AG), Chu Prong (CP), Mong Cai (MC), Hung (HU), Huong (HUO), and Ha Lang (HL) populations. Lower panel (b) shows the distribution of the various characteristic factors, with some individuals completely overlapping because they had identical characteristics. Figure and caption are cited from Ishihara et al. (2020b), unadjusted.

The small size and physiological characteristics of Vietnamese pigs were suggested to make them a suitable biomedical animal model (Lai et al. 2002). When considering the use of pigs as medical models, particularly for the generation of human replacement organs for transplantation, porcine endogenous retroviruses (PERVs) in the porcine genome are a concern (Magre et al. 2003). As European wild boars and Chinese miniature pigs contained fewer copies of PERVs than Western breeds (Liu et al. 2011; Mang et al. 2001), we decided to investigate the PERV copy number in Vietnamese native pigs (Ishihara et al. 2020a).

Real‐time PCR was used to measure the gene copy numbers in indigenous PERV pigs in Vietnam. After examining several lotus‐keeping genes, ACTB showed the most stable value; therefore, the ACTB gene was utilized as the baseline and measured the copy numbers of gag, pol, and env, which comprised PERV. PERV is classified into PERV A, B, and C, and as all of them have high sequence homology, the gag and pol genes were detected simultaneously using a primer probe common to PERV A, B, and C, and env was detected separately for AC and B. PERV copy number measurements showed that VNP had significantly lower copy numbers for all PERV genes compared to Western (Figure 8). Subsequently, when comparing VNP populations, several VNP varieties had low copy numbers, whereas some had high copy numbers. The gag, pol, and env genes were similar to each other, but the copy numbers varied for each gene type. It is presumed that the retroviral genes themselves are inactivated in the genomic regions; therefore, some sequences are fragmented, deleted, or mutated. Comparable to those of the western Landrace variety, Ha Lang, Muong Khuong, Van Pa, and Ba Xuyen had relatively high PERV copy numbers, reflecting the possibility that these varieties may have been introduced by foreign species in the past, as determined by previous genetic analyses and morphological characterizations and is consistent with our results.

FIGURE 8.

Comparison of the PERV copy numbers in each Vietnamese native and western pig breeds. The box‐and‐whisker plots of the PERV genes for each breed type are shown. The middle line in the box represents the median, upper and lower areas of the center box indicate the 25th (Q1) and 75th (Q3) percentiles, respectively, and upper and lower whisker indicate maximum and minimum value, respectively. The values either exceed Q3 + 1.5 IQR or fall below Q1 − 1.5 IQR, and IQR = Q3 − Q1 are considered outliers. The red circle illustrates the mean, and red line denotes standard deviation. The vertical axis depicts the copy number of PERV. The envAC + B value refers to the total envAC and envB copy number. The average value refers to an average of the copy number of gagABC, polABC, and envAC + B. Letters denote that significant difference (p < 0.05) was detected among breeds. Figure and caption are cited from Ishihara et al. (2020a), unadjusted.

The production of pigs with PERV removed by CRISPR‐Cas9 genome‐editing technology was reported (Niu et al. 2017). Genome‐editing technology has advanced sufficiently to allow for the knockout of dozens of copies scattered throughout the genome. Nevertheless, the creation of low‐copy pig strains through breeding may increase the probability of a successful pig models designed for organ transplantation through genome editing. While real‐time PCR was used to measure the copy number in the genome, the digital droplet method is currently popular. If this initiative continues, the measurement method should be updated. In conjunction with this study, we devised a method to identify loci found within the PERV genome but not in the reference genome (Ishihara et al. 2022) to verify the success of genome editing using genome sequencing data when producing PERV‐free pigs.

6. Conclusion

Biodiversity is closely related to global environmental change as economic activities place a considerable burden on the global environment (Jayachandran 2022). Therefore, it is necessary to monitor biodiversity as an indicator of a sustainable and healthy living environment for humans. Food insecurity remains a pressing issue for humanity, with statistics showing that approximately 733 million people were in a state of hunger in 2023 (WHO 2024). However, while some people suffer from this level of hunger, others suffer from lifestyle‐related diseases owing to overeating; thus, an imbalance exists. Recently, advances in animal breeding for high productivity have led to the rapid development of high‐performing livestock genetic lines, which have been disseminated around the world (Ajmone‐Marsan et al. 2023). To improve the efficiency of food production, the creation of high‐performing genetic lines is necessary. However, when everyone is looking in the same direction with “a big thumbs up!” listening to the footsteps of approaching danger may be a good idea. When considering maintaining the diversity of livestock populations worldwide and genetic resources, domestic pigs consist of wild boars, but domesticated cattle no longer consist of Aurochs; however, a bias toward the production of only a few genetically high‐performing strains may be a risk. Compared to highly bred commercial breeds, indigenous livestock are less productive, and therefore, less economically advantageous. Therefore, foreign species are being introduced into indigenous livestock production sites (e.g., the once endangered Basque indigenous cattle, Pirenaica, and Vietnam's native pigs today). This makes it difficult to maintain indigenous genetic lines.

In contrast, several good examples of maintaining indigenous livestock and realizing circular livestock production exist; of which, the Pirenaica breed of cattle native to the Basque Country in Spain has been revived and obtained a designation of origin. In addition, the production and global spread of the Spanish Iberian pig producing world‐famous “Jamon” brand, and the Hungarian Mangalica pig breed are national treasures. Although the situation differs slightly, China, the world's top pig‐producing country, has many indigenous pig breeds. An important implication of our case study is that some indigenous livestock genetic resources may have “hidden potential.” By applying constantly evolving molecular biology techniques, the usefulness and potential applications of native livestock will become even clearer. However, countries or regions blessed with indigenous genetic resources are not necessarily economically well off to be enthusiastic about genetic resource research. This is another imbalance.

Food insecurity is a common issue in all of humanity that should be addressed internationally, as race or country of origin should not be an issue. During attendance at the Fatty Pig International Conference and International Symposium on the Mediterranean Pig, I observed the participants' research efforts and was reminded that the role of native livestock research is to emphasize the importance of native livestock, apply it to production sites, and make recommendations for livestock promotion policies. The conservation of native livestock genetic resources is important for sustainable food production in each region, the inheritance of food culture, and to be preserved for future needs. This may be because native livestock are adapted to the natural environment of their habitats and formed an agricultural environment, coexisting with the locally cultivated crops.

To raise public awareness, it is necessary to grasp the actual situation through steady research and investigation and to disseminate information about the usefulness of genetic characteristics globally by submitting articles to international journals. This review should aid readers involved in animal science in recognizing the importance of research on native livestock genetic resources.

Conflicts of Interest

The authors declare no conflicts of interest.

Data Availability Statement

All the data presented in this review article were derived from the previous publications.