1 Introduction

Goats (Capra aegagrus hircus) are one of the earliest domesticated animals. They were domesticated in the Fertile Crescent about 10,000 years ago (Amills et al., 2017; Taheri et al., 2023). Goats are very important in agriculture. They are raised for milk, meat, wool, and skin (Guan et al., 2016).

Goats are adaptable to many different environments, so they are found in many parts of the world. They are of high economic value in both developed and developing countries (Giannico et al., 2020). Goats can also survive in places with few resources, making them particularly important for food security and nutrition in many regions (Bherey et al., 2023).

To make better use of goats, we need to understand their evolutionary process and genetic composition. First, it can help us understand how goats have evolved from their wild ancestors (Capra aegagrus) to what they are today (Takada et al., 1997; Dong et al., 2015). Second, this knowledge is also helpful for breeding, for example, if we want goats to produce more milk, have better meat, or be less susceptible to disease (Guan et al., 2016; Zhang et al., 2018). In addition, understanding their genes can also help protect genetic diversity, which is critical to the long-term development of goat populations (Amills et al., 2017).

Molecular studies have also found many genetic changes and selection pressures. These are affecting what domestic goats look like today, indicating that it is very important to continue studying this area (Pidancier et al., 2006; Giannico et al., 2020).

This article mainly wants to understand the evolutionary background, genetic changes, and genetic diversity of domestic goats. We pay special attention to the genetic differences between domestic goats and their wild ancestors, as well as genetic changes within domestic populations. At the same time, the article also introduces some recent advances in genomic technology and the use of these technologies in goat genetic breeding. We hope that this study can provide some theoretical support and practical help for goat breeding and conservation.

2 Taxonomy and Evolutionary Origins

2.1 Overview of the taxonomic classification of goats

The domestic goat (Capra hircus) belongs to the genus Capra. There are some wild goats that are closely related to it, such as the bull goat (Capra aegagrus), the northern goat (Capra ibex) and the markhor (Capra falconeri) in this genus (Pidancier et al., 2006; Pogorevc et al., 2023). The genus Capra is part of the family Bovidae, which also includes sheep, cattle and antelopes. Using molecular biological methods, researchers have found that there are great genetic differences within the genus Capra. The domestic goat and its ancestors, especially the bull goat, are very close genetically (Takada et al., 1997). Later, scientists have a clearer understanding of the classification of goats and a better understanding of their evolutionary relationships through the analysis of mitochondrial DNA and Y chromosomes (Pidancier et al., 2006).

2.2 Relationship between domestic goats and wild relatives

Many phylogenetic studies have pointed out that domestic goats (Capra hircus) and wild bezoar goats (Capra aegagrus) are most closely related (Takada et al., 1997; Pogorevc et al., 2023). When studying the SNP sites of the whole genome, it was found that there were obvious differences between the bezoar type and other wild goat types, while domestic goats and bezoar types were grouped together (Pogorevc et al., 2023). Other studies have used mitochondrial DNA for analysis and found that all haplogroups of domestic goats can also be found in bezoar, which further shows that they are very closely related (Naderi et al., 2008). In addition, the markhor (Capra falconeri) may also have made some contributions to the genes of domestic goats, although it is more distantly related to bezoar (Pidancier et al., 2006).

2.3 History of goat domestication: time and place

Scientists believe that goats were domesticated by humans about 10,000 years ago in the mountainous area of western Iran, namely the Zagros Mountains (Zeder and Hesse, 2000; Naderi et al., 2008). From archaeological and genetic studies, more than one place was involved in the domestication of goats. Places such as the central plateau of Iran and the southern Zagros Mountains had an important influence on the early domestication process (Naderi et al., 2008). At that time, people would specifically select some sub-adult male goats to capture, which also marked the beginning of the transition from hunting to herding (Zeder and Hesse, 2000). Later, goats followed humans all the way and soon spread throughout the Old World, such as the Iberian Peninsula and southern Africa (Amills et al., 2017). Genetic studies have also found that there is gene flow between domestic goats and some wild goats. That is to say, there was gene exchange between them at the beginning of domestication, and even after that (Pogorevc et al., 2023).

3 Genomic and Molecular Characterization

3.1 Advances in goat genome sequencing and its significance

Recently, scientists have done more sequencing work on the genome of domestic goats (Capra aegagrus hircus). This has given us a clearer understanding of the genetic composition of goats. A high-quality reference genome called ARS1 has been completed, which is a very important achievement and lays the foundation for subsequent genetic research (Muriuki et al., 2019). In this genome, researchers found more than 24 million single nucleotide variants (SNPs), 1.9 million insertion or deletion sites, and 2317 copy number variations (Zhang et al., 2018). This information helps us understand how goat genes changed during domestication and how some of their traits were selected. In addition, scientists have also produced a gene expression map of goats, which helps analyze the functions of different genes. By comparing with ruminants such as sheep, they also found some transcriptional differences (Muriuki et al., 2019). These genomic data allow us to better link goat genes with their external traits, which is very helpful for improving economic traits.

3.2 Genetic comparison with other ruminants

Genetic comparisons between goats and other ruminants, such as cattle, sheep, and deer, have also brought many new discoveries. These studies help us understand the selection pressures that different animals encounter in evolution and how they adapt to the environment. For example, the T cell receptor β (TRB) and γ (TRG) genes of goats have been amplified. This amplification is also found in sheep and cattle, indicating that it is a common feature of ruminants (Giannico et al., 2020). This amplification increases the variety of T cell receptors, thereby enhancing their immune capacity. In addition, goats and sheep also have differences in gene expression, especially in genes related to immunity (Muriuki et al., 2019). These differences show that each species has its own unique way of adaptation. This type of comparative study is very helpful for us to understand the disease resistance and environmental adaptability of animals.

3.3 Map of important genes and traits in goats

Researchers have also found a number of genes related to important traits in goats, such as milk production, disease resistance, and hair quality. Through genome-wide association analysis (GWAS), scientists found regions on chromosome 19 of Saanen goats that are related to somatic cell count (SCC) and mammary traits. These traits are closely related to resistance to mastitis and milk production. There are also some key genes, such as RARA, STAT3, STAT5A, and STAT5B, which are all related to the response to mammary gland infection (Martin et al., 2018). In addition, the two genes GDF5 and FGF5 control bone development and hair growth, respectively, and these two traits directly affect the meat quality and fiber yield of goats (Zhang et al., 2018). After finding these key genes, scientists can use them as molecular markers to select goats in a targeted manner during breeding. This is very useful for improving economic traits.

4 Genetic Diversity and Population Structure

4.1 Genetic variation within domestic goat populations across different regions

Domestic goats vary greatly in genes, and there are also obvious differences between populations in different regions. A study analyzed the mitochondrial DNA (mtDNA) of goats in the Central Asian Mountain Corridor (IAMC) and found that they have high genetic diversity. In addition to the common A lineage, the relatively rare C and D lineages were also found (Hermes et al., 2020). A similar situation is found in the Mahabadi goats in Iran. The genetic distance between them is large, indicating that there are also many genetic differences within the population. In addition, researchers used microsatellite markers to study Karachayev hybrid goats and found that they also have a rich number of alleles at each locus, which once again proves that genetic diversity is high (Fomenko and Petrov, 2021). These studies tell us that domestic goats in different places are very different in genes. This diversity makes it easier for them to adapt to the environment and also helps the population recover when encountering difficulties.

4.2 Genetic bottleneck and founder effect in goat domestication

There are two important genetic phenomena in the domestication of domestic goats: genetic bottleneck and founder effect. Simply put, the number of goats domesticated at first was small, which reduced the genetic diversity of the entire population later. For example, in the North Eurasian Steppe (NES) region, it was found that these goats mainly had A-lineage mitochondrial DNA. This may be because these goats came from an isolated ancestral group in Eastern Europe or the Caucasus (Hermes et al., 2020). However, there are exceptions. Studies have found that most of the diversity of casein genes in goats actually comes from genetic mutations very early (Guan et al., 2019). This shows that even after experiencing bottlenecks, goats still retain some important genes from wild ancestors. These genetic changes have a great impact on the health and adaptability of goats, so it is important to understand these historical processes.

4.3 Genetic diversity helps goats adapt to the environment

Genetic diversity is very important for goats, especially in adapting to different environments. Some genes, such as TRB and TRG, are amplified, which makes goats have more T cell receptors, thereby enhancing the adaptability of the immune system (Giannico et al., 2020). In addition, copy number variation (CNV) in goats is also related to environmental adaptation. Studies have found that highland and lowland goats have great differences in these genes, and these differences are related to vitamin and fat metabolism (Guo et al., 2020). In places like the Inner Amharashtra steppe and central Kazakhstan, goats also have abundant mitochondrial DNA. This shows that they have successfully adapted to alpine or arid environments by maintaining genetic diversity (Hermes et al., 2020).

5 Molecular Evolution of Domestic Goats

5.1 Evolutionary analysis of specific genes and genetic markers

By studying some specific genes and genetic markers, scientists have found that domestic goats (Capra aegagrus hircus) have undergone many changes during evolution. Using genome resequencing technology, they found many changes related to domestic traits, such as SNPs (single nucleotide polymorphisms), insertions/deletions, and copy number variations. For example, there are two genes - GDF5 and FGF5 - related to bone development and hair growth, respectively. These two genes are important for goat growth (Zhang et al., 2018). In addition, there are two T cell receptor genes, TRB and TRG, which are more replicated in goats, indicating that their evolutionary history is more complicated (Giannico et al., 2020). There is also a gene region called mitochondrial DNA (mtDNA), which has also been used to study the relationship between goat populations. Studies have found that this region has many changes, indicating that domestic goats are very different genetically.

5.2 The impact of selection pressure on genetic changes

A large part of the genetic changes in domestic goats are due to the effects of natural selection and artificial selection. Scientists have found some "selection markers" in both domestic goats and wild goats, which can tell us how they were domesticated step by step. For example, some genes are related to milk production, wool quality, and immune system function. These genes played a big role in the selection process (Taheri et al., 2023). In addition, some strongly selected areas are also related to body weight and environmental adaptability, which shows that human and natural selection have affected the genetic composition of goats together. Another example is that a gene called KITLG in Nubian wild goats has also entered the domestic goat populations in Africa and West Asia. This gene is related to climate adaptability (Nanaei et al., 2023).

5.3 Evolutionary evidence of adaptation to the environment

Domestic goats can adapt to a variety of environments, and there are actually many genes at work behind this. Genomic analysis has found that some goat populations can adapt to arid desert climates, such as goats living in Southwest Asia, whose genes have changes related to this environment (Nanaei et al., 2023). In the gene regions that affect body shape, meat quality, milk quality and immunity, scientists have also found structural variations (SVs), which are helpful for the domestication and environmental adaptation of goats (Cumer et al., 2021). Some specific genes, such as CNGA4 and Camk2b, have been found to be associated with enhanced immunity. Especially in goats living in high-altitude areas, these genes may make them more resistant to diseases and harsh environments. These studies tell us that domestic goats have been able to evolve successfully to the present because there is a complex set of genes that interact to help them adapt to different living environments.

6 Mitochondrial DNA and Phylogeography

6.1 Role of mitochondrial DNA in understanding goat evolutionary history

Mitochondrial DNA (mtDNA) has played a major role in studying the evolutionary history of domestic goats (Capra aegagrus hircus). In particular, its highly variable regions can tell us about the genetic diversity and evolutionary relationships of goats, and can also help analyze past population changes. Studies have found that mtDNA sequences can show genetic differences between domestic goats and their wild ancestors (such as goats Capra aegagrus). This also allows us to identify different haplogroups, which often come from different regions or different time periods (Hermes et al., 2020; Bherey et al., 2023). For example, the high variability of the D-loop in mitochondrial DNA can help us identify multiple lineages and more clearly see the genetic structure between goat populations in different regions (Bherey et al., 2023).

6.2 Phylogeographic studies reveal the distribution and migration of goats

Through the study of mitochondrial DNA, scientists have learned more about the distribution and migration patterns of domestic goats and their wild relatives. Taking the goat breeds in Egypt as an example, the study found that they mainly belong to haplogroup A, but there are three different lineages within them, which are related to Africa and the Middle East (Bherey et al., 2023). This shows that although they have a common background, there are still regional differences. The Mahabadi goats in Iran have also been studied, and the results show that their genetic variation is very rich and they are very close to wild bezoar goats. This shows that they have a common ancestor and retain rich genetic diversity. In the mountains of Central Asia, goats raised by some nomadic communities also show high mitochondrial DNA diversity. This may be because people continue to migrate and communicate with goats, thus maintaining the genetic diversity of these groups (Hermes et al., 2020). These studies show that the genetic structure of goats is not only affected by natural factors, but also by human activities, such as migration and communication.

6.3 Tracking the domestication of goats with mitochondrial DNA

Genetic markers in mitochondrial DNA can help us figure out how domestic goats were domesticated. Analysis shows that most domestic goats belong to haplogroup A. However, some belong to B, C or D, which shows that goat domestication was not completed in one go, but experienced multiple domestications and subsequent migrations (Tabata et al., 2018; Hermes et al., 2020). For example, in Indonesia, the proportion of B lineages in local goats is very high. This shows that their route into Southeast Asia may be different from that of goats in other places, showing that different regions have different domestication and dissemination methods (Mannen et al., 2020). In the Zagros Mountains, some ancient goat remains have been found, which contain many different mitochondrial haplotypes. This provides direct evidence of early domestication, indicating that humans were already managing goats at that time and were somewhat separated from wild goats (Daly et al., 2021). These findings show us that mitochondrial DNA can help us restore how goats were domesticated step by step by humans and reveal how they spread around the world.

7 Recent Advances in Genetic Tools and Technologies

7.1 CRISPR-Cas9 applications in goat genetic research

CRISPR-Cas9 is a tool that can precisely modify genes. This technology has been widely used in goat genetic research. Scientists use it to change certain genes in goats to get goats that produce more milk and are more disease-resistant. In experiments, people can first modify the genes of goats with CRISPR-Cas9, and then clone goats with the same genes through somatic cell nuclear transplantation (SCNT) (Skrzyszowska and Samiec, 2021). In this way, many goats with ideal traits can be quickly cloned. This method can not only speed up breeding, but also help us study the role of each gene more clearly, and can also be used to develop transgenic goats that are useful in medicine or agriculture.

7.2 Use of next generation sequencing (NGS) in genomic research

Next Generation Sequencing (NGS) technology can sequence the entire genome quickly and cheaply. This technology has made a lot of progress in goat genetic research. Scientists used NGS for genome-wide association analysis (GWAS) and found many genetic changes related to economic traits. For example, they found some single nucleotide variants (SNPs) and copy number variants (CNVs) related to milk production, meat quality, and disease resistance (Zhang et al., 2018; Guo et al., 2020). These genetic variants can be used as markers to help breeders select good genes more accurately and protect the genetic diversity of goat populations.

7.3 Functional genomics and the discovery of trait-related genes

Functional genomics mainly studies how genes work, that is, the relationship between genes and external traits of animals. In goats, researchers used RNA sequencing and other methods to establish gene expression maps in different tissues (Muriuki et al., 2019). These studies have found many genes related to milk production, meat quality, and fertility. Some genes are considered to be key points affecting these traits and have now been located (Wang et al., 2020; Pardo et al., 2022). Combining these genetic research results with traditional breeding methods not only improves the efficiency of seed selection, but also makes it easier for us to breed goats with excellent performance.

8 Conservation and Breeding Implications

8.1 Importance of understanding molecular evolution for goat conservation

To protect domestic goats (Capra aegagrus hircus), it is important to understand their molecular evolution process. By analyzing genetic data, scientists can better understand the genetic differences between different goat populations and their evolutionary history. This information helps maintain the genetic diversity of goats and enhance their resistance to the environment and diseases. For example, some "selection markers" found in domestic and wild goats can tell us which traits are most critical for survival and adaptation (Taheri et al., 2023). These research results can help us identify and protect genes that are important for the future survival of goats.

8.2 How molecular data helps breeding

Genetic data is also very useful in breeding. By finding genes related to traits (TAGs) and genes related to domestication processes (DAGs), breeders can more accurately select goats with good performance. For example, some studies have found genes related to milk, meat and cashmere production through genome resequencing. These genes can be used as breeding targets to select goats that perform better in these areas (Zhang et al., 2018). Another method called somatic cell nuclear transfer (SCNT) can also help a lot. It can replicate goat offspring with good genes to ensure that good traits can be passed down from generation to generation (Skrzyszowska and Samiec, 2021) (Figure 1). This method can not only increase production, but also help maintain the genetic diversity of the population.

8.3 How molecular evolution helps improve goat breeds

Molecular evolution research can help us improve goat breeds and make them more suitable for producing meat, milk and fiber. For example, the TRB and TRG genes of domestic goats have been amplified, which is a common feature of ruminants. This amplification allows goats to have more types of T cells, thereby improving immunity and overall health (Giannico et al., 2020). In addition, some genes that regulate growth are also important. For example, two genes, GDF5 and FGF5, the former is related to bone development, and the latter affects hair growth. These genes can be used to improve the quality of meat and wool (Zhang et al., 2018). Scientists have also established a gene expression map of domestic goats, which can show which genes are activated in which parts and when. This information can be used to optimize breeding plans and make breeding results more in line with the needs of agricultural production (Muriuki et al., 2019).

9 Challenges and Future Directions

9.1 Gaps in current research and areas that require further exploration

Although we are learning more and more about the goat genome, there are still many unresolved issues. One of the big problems is that we have not yet fully understood how the genes that affect important traits such as milk production, meat quality, and disease resistance work. At present, some trait-associated genes (TAGs) and domestication-associated genes (DAGs) have indeed been discovered, but the specific functions of many genes are still unclear (Zhang et al., 2018; Taheri et al., 2023). This makes it difficult for us to formulate breeding strategies. In addition, we still do not know enough about the genetic diversity and evolutionary relationships of different goat populations. And this information is actually very critical for breeding programs (Bherey et al., 2023). Another problem is that there is not enough data on gene expression in goats. Compared with other ruminants, the annotation of goat gene functions is still incomplete, which slows down the research progress (Muriuki et al., 2019; Fernández-Bastit et al., 2022).

9.2 Future technological development and possible changes

In the future, with the continuous advancement of technology, many research problems may be solved. High-throughput sequencing and more powerful bioinformatics tools will allow us to understand the goat genome more clearly and find new genes and regulatory regions more accurately (Zhang et al., 2018; Taheri et al., 2023). Gene editing technologies such as CRISPR/Cas9 are also improving. In the future, these methods may be used to modify certain genes in goats to make them healthier or have better traits (Skrzyszowska and Samiec, 2021). In addition, it is also important to establish a more complete gene expression map. It can help us understand how genes work in different tissues or at different growth stages, thus better explaining the relationship between genotype and traits (Muriuki et al., 2019; Fernández-Bastit et al., 2022).

9.3 Genetic tools for coping with diseases, climate change and achieving sustainable farming

Goat farming faces many challenges, such as diseases, climate change and the sustainability of farming. Genomic tools can be of great help in these areas. For example, by finding genes related to disease resistance, we can select goats that are more resistant to diseases and use them to improve the population (Taheri et al., 2023). For example, understanding which genes can help goats adapt to different environments can also help us develop strategies to cope with climate change (Giannico et al., 2020; Bherey et al., 2023). Finally, combining this genetic information with traditional breeding methods can also improve the efficiency and stability of farming. This is particularly important for developing regions as it not only helps to secure food but also helps to reduce poverty (Muriuki et al., 2019; Fernández-Bastit et al., 2022).

10 Concluding Remarks

This review introduces the evolutionary process and genetic background of domestic goats (Capra aegagrus hircus), helping us better understand their genetic history and changes. Domestic goats were domesticated from wild bezoar goats (Capra aegagrus). During this process, their genes underwent many changes, such as changes in coat color, behavior, stronger immunity and better production capacity. Studies have found that the mitochondrial DNA of domestic goats can be divided into several haplogroups, of which type A is the most common. At the same time, the genetic diversity of domestic goats is also high, partly because their ancestors are relatively rich, and partly because of the introduction of new genes by hybridization with other wild goats. Immune-related gene families such as TRB and TRG have also expanded significantly, indicating that the immune system has been under strong selection pressure during the evolution of goats.

These research results are of great help to breeding, genetic improvement and conservation. The more we understand how goats were domesticated, the easier it will be to improve their breeds. For example, we can select goats that produce more milk, have better meat quality and strong resistance. Finding genetic markers associated with these traits can also make breeding more targeted and efficient. In addition, understanding the phylogenetic relationships of domestic goats can help us determine which groups are genetically different and need special protection in order to maintain overall biodiversity. Combining phylogenetic knowledge with genetic technology is very important for the long-term management of goats. Now that whole genome sequencing and genotyping are becoming more and more advanced, these tools allow us to study the genetic background of goats in more depth and provide more accurate suggestions for breeding. In this way, we can increase production while maintaining genetic diversity.

In general, putting these evolutionary studies into practice will help the development of agriculture and protect the diversity of goat populations. This will make goats more adaptable and resilient in the face of various challenges in the future.

Acknowledgments

The authors are grateful to the reviewers for their meticulous revision suggestions, which allowed me to examine my research from new perspectives.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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