Author details

Fabrice Teletchea

Address all correspondence to: fabrice.teletchea@univ-lorraine.fr

UR AFPA, Université de Lorraine, Vandoeuvre-Les-Nancy, France

#### References

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**Chapter 2**

**Provisional chapter**

**A Genomics Perspective on Pig Domestication**

**A Genomics Perspective on Pig Domestication**

DOI: 10.5772/intechopen.82646

Land animal domestication has typically led to remarkable phenotypic diversity, stemming from a broad genetic background. The process of land animal domestication turns out to be a complex, long-term event with extensive gene-flow between wild and captive populations. Using pig as model, this chapter provides an in-depth overview of domesticationrelated events leading towards the genetic diversity in extant pig breeds. Five events in the evolutionary history and domestication of pigs can be recognized that are important for the genetic variation in modern pig genomes: (1) Speciation of Sus species in Island South-East Asia (ISEA); (2) Divergence between European and Asian lineages; (3) Independent domestication leading to separate domesticated clades in Europe and Asia; (4) Hybridization between domesticated pigs from Asia and Europe; and (5) Breed formation. Remarkably, the extensive mixture of genetic material leading towards the current European commercial pigs has resulted in domestic breeds that are genetically more diverse than their wild ancestors. Nowadays, commercial breeding and genomics go hand in hand. Genomics has not only proven useful to provide understanding about the domestication history of pigs but also about the molecular mechanisms underlying traits of interest. Moreover, genomic

Domestication of land animals has typically led to a wide variety of domestic forms, with remarkable phenotypic diversity not seen in the wild. However, the underlying molecular variation resulting in a specific phenotype often stems from mutations predating domestication. Although domestication generally leads towards a reduction in effective population size, land animal domestication cannot be seen as a simple split of a subset of individuals from

selection is an important tool integral to modern commercial breeding.

**Keywords:** genomics, pig, hybridization, selection, domestication

**1. The process of livestock domestication**

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

© 2018 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use,

distribution, and reproduction in any medium, provided the original work is properly cited.

Additional information is available at the end of the chapter

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/intechopen.82646

Mirte Bosse

Mirte Bosse

**Abstract**

#### **A Genomics Perspective on Pig Domestication A Genomics Perspective on Pig Domestication**

DOI: 10.5772/intechopen.82646

#### Mirte Bosse Mirte Bosse

Additional information is available at the end of the chapter Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/intechopen.82646

#### **Abstract**

Land animal domestication has typically led to remarkable phenotypic diversity, stemming from a broad genetic background. The process of land animal domestication turns out to be a complex, long-term event with extensive gene-flow between wild and captive populations. Using pig as model, this chapter provides an in-depth overview of domesticationrelated events leading towards the genetic diversity in extant pig breeds. Five events in the evolutionary history and domestication of pigs can be recognized that are important for the genetic variation in modern pig genomes: (1) Speciation of Sus species in Island South-East Asia (ISEA); (2) Divergence between European and Asian lineages; (3) Independent domestication leading to separate domesticated clades in Europe and Asia; (4) Hybridization between domesticated pigs from Asia and Europe; and (5) Breed formation. Remarkably, the extensive mixture of genetic material leading towards the current European commercial pigs has resulted in domestic breeds that are genetically more diverse than their wild ancestors. Nowadays, commercial breeding and genomics go hand in hand. Genomics has not only proven useful to provide understanding about the domestication history of pigs but also about the molecular mechanisms underlying traits of interest. Moreover, genomic selection is an important tool integral to modern commercial breeding.

**Keywords:** genomics, pig, hybridization, selection, domestication

#### **1. The process of livestock domestication**

Domestication of land animals has typically led to a wide variety of domestic forms, with remarkable phenotypic diversity not seen in the wild. However, the underlying molecular variation resulting in a specific phenotype often stems from mutations predating domestication. Although domestication generally leads towards a reduction in effective population size, land animal domestication cannot be seen as a simple split of a subset of individuals from

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2018 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

their wild progenitors. The meaning of the word domestication is poorly defined and lacks consistency across different scientific disciplines [1]. From a population genetics perspective, domestication results in a deliberate separation of the captive, and then domesticated population from its parent population. Domestication is, therefore, initially indistinguishable from any other event that results in reduction of gene-flow between populations, and creating opportunity to respond to new selective pressures [2]. The simplest definition of domestication considers a domestic population as a subset of the wild population with cessation of gene-flow [3]. Therefore, one can expect that domestication results in a reduction of genetic variation in the domesticated population. The onset of domestication occurred in multiple geographically distinct areas during the late Pleistocene to early Holocene transition (12,000–8200 B.P, [4]). The process of land animal domestication, however, turns out to be a complex, long-term event initiated by cultural transitions related to food production [5, 6]. The definition of an animal to be considered domesticated varies, however, some common characteristics emerge from literature. Teletchea and Fontaine propose that a domesticated animal should be selectively bred in captivity and modified from its wild ancestors [7]. It is important to realize that those early considered domestic populations were genetically and phenotypically hardly distinguishable from wild types, and therefore geographical location was a better predictor of local characteristics than domestication status [3]. The general assumption that multiple centers of domestication exist has important implications for the source of genetic and phenotypic variation in domesticated species. In cattle, for example, two distinct cattle lineages that separated ~300,000 ya, contributed to two major lineages of extant cattle, that is, taurine cattle (originating from *Bos taurus*) and indicine cattle (originating from *Bos indicus*) [8]. It is not unlikely that multiple populations of wild land animals that are now extinct contributed to the genetic diversity that is observed in modern breeds [9]. The domestic animal populations accompanying human settlements did not necessarily remain at their original location of domestication. Rather, they moved along with early farmers spreading in Asia and from Eastern Anatolia throughout Europe [10]. During this process, the connection of domestic animals and farmers was relatively loose, enabling animals to hybridize with local wild populations [11]. Only centuries later, animals were actually kept in strict enclosures and intentionally bred for specific purposes, leading towards the best-known characteristic of domestic animals: docility [12]. This controlled environment drastically reduced the opportunity of domestic herds to interbreed with local wild populations, which enabled strong divergence between domestic and wild forms. We should realize the genetic basis of the modifications leading towards morphological differences in domestic animals compared to their wild ancestors is mostly provided by standing genetic variation, that is, mutations that were already present before the onset of domestication and selection. Therefore, indicating the genetic underpinnings of domestication remain challenging [13, 14]. Arguably, we can speak about a domestic population if not only the gene pool is distinct from the wild variety, but also (artificially) selected variants leading to desired phenotypes are at high(er) frequency in the domestic population [15–18]. In this chapter, an in-depth overview is provided for the complex process of domestication, admixture, and selection leading towards the genetic diversity in extant breeds, using pig as model.

**2. Genomic insight in pig domestication**

Domesticated species are good models to study genomic and phenotypic consequences of demography and selection [19]. The use of higher DNA marker densities has enabled researchers to reveal the complexity of livestock domestication, which was shown to be far more complex than a single sampling from the wild [20]. Genotyping and sequencing technologies have opened up many opportunities to reveal the complex history of domestication, admixture, and selection in livestock [4, 20]. Combining modern sequence technologies with extensive studies on fossil records and land animal usage now enables the reconstruction of domestication in details. Apart from a suitable history and documentation, the availability of detailed genetic information is crucial to be able to study genomic alterations due to domestication. Pig (*Sus scrofa*, Linnaeus, 1758) was the first livestock species for which a genome consortium was established with the intention to completely map the genome [21, 22]. The design of a 60k single nucleotide polymorphism (SNP) chip for pigs in 2009 greatly contributed to the applicability of genomics techniques in pig breeding, and simultaneously increased possibilities for population genomics studies [23]. The establishment of a consortium to sequence the pig genome in 2003 and publication of the pig reference genome in 2012 opened up an even greater window of opportunities to study various aspects of the genetics of pig, since the highest resolution possible became reality [21, 24]. Together with the evolutionary history of pig, these provide an unprecedented study system to demonstrate the impact of domestication from a genomics perspective. Pig genomes contain a complex composition of segments, reflecting the different backgrounds that contributed to the domestic animal it is today. Disentangling these genomic signatures provides enormous information about the complex

A Genomics Perspective on Pig Domestication http://dx.doi.org/10.5772/intechopen.82646 23

background and history of the worlds' most consumed meat type [25].

Here I will discuss genomic variation within and between different populations of pigs, providing deeper understanding of how domestication has influenced genetic diversity of pigs. Five major events in the evolutionary history and domestication of pigs can be recognized that are of importance for the distribution of genetic variation in modern pig genomes (**Figure 1**).

Knowledge about the source of the domesticated form, the origin of the species, is essential to understand genetic variation within modern breeds. The Suidae family is particularly interesting for molecular genetic studies as it is one of the few mammalian lineages that has closely related species living today. Multiple *Sus* species originated roughly ~4 million years ago on Island Southeast Asia (ISEA). The island structure in this region probably promoted speciation, since the bearded pig *Sus barbatus*, the warty pigs *S. celebensis* and *S. verrucosus* but also wild *S. scrofa* occur on separate islands. The phylogenetic structure within the genus *Sus*

**3. Conceptual history of the pig (***Sus scrofa***)**

**3.1. Speciation of** *Sus* **in island South-East Asia**
