1 Introduction

The goose was one of the earliest domestic fowls domesticated by humans. The domestication history of geese in China can be traced back to over 7 000 years ago, and the global domestication history also exceeds 6 000 years. It is an important representative animal in the research of bird domestication and agricultural origin (Lu et al., 2015; Eda et al., 2022; Huang et al., 2025). Geese have high economic value and can provide meat, eggs and feathers. They also have some unique physiological characteristics such as fast growth, strong disease resistance and strong lipid storage capacity of the liver (Lu et al., 2015). Geese are very important in agriculture. However, compared with other domestic fowls such as chickens and ducks, the genetic basis and domestication process of geese have not been systematically studied (Lu et al., 2015; Chen et al., 2023).

Genomic technology has developed rapidly in recent years, making it easier to conduct a comprehensive study of the domestication mechanism of geese (Li et al., 2024). Chen et al. (2023) and Zhang et al. (2023) discovered through whole-genome resequencing and comparative genomics studies that geese have undergone the selection of multiple key genes during the domestication process. These genes are related to many important traits such as the nervous system, immune function, metabolism, vision, bone structure and blood oxygen transport. Heikkinen et al. (2020) and Chen et al. (2023) demonstrated that frequent hybridization and gene flow between wild geese and domestic geese also had an impact on the domestication process. These factors have made the population structure of geese more complex and also caused domestic goose groups in different regions of Central Europe to exhibit obvious genetic mixed characteristics.

This study introduces the origin and population structure of domestic geese, identifies some key genetic variations and related pathways selected during the domestication process, and explains the important role of gene flow and hybridization in the formation of the genetic characteristics of modern domestic geese. This study aims to deepen people's understanding of the domestication process of geese and provide scientific references for future breeding and conservation work.

2 Origins and Historical Trajectories of Goose Domestication

2.1 Geographic centers and dual domestication events

The domestication of geese mainly occurred in the two regions of East Asia and Europe. In East Asia, archaeological and genetic studies conducted by Eda et al. (2022) indicated that people in the lower reaches of the Yangtze River in China began domesticating swan goose (Anser cygnoides) approximately 7 000 years ago. This is one of the earliest known records of domestic poultry domestication. Kozák (2019) discovered that in Europe, the domestication of the greylag goose (Anser anser) began approximately around 4 000 BC. Genomic studies also support this view, indicating that domestic geese have a dual origin, that is, Chinese geese originated from swan goose, while European geese originated from greylag goose (Jing et al., 2022). Chinese geese show obvious geographical differentiation in terms of genes, while the origin of European geese is more complex, including genetic mixing with Chinese geese (Chen et al., 2023; Zhang et al., 2023).

2.2 Morphological and behavioral changes post-domestication

During the domestication process of geese, many obvious morphological and behavioral changes occurred, such as weight gain, loss of migratory ability, change in feather color, early sexual maturity, and a significant increase in egg production (Kozák, 2019; Jing et al., 2022). Kozák (2019) reported that domestic geese such as Toulouse geese and African geese weighed more than 300% higher than their wild ancestors, and the egg production of some domestic geese increased by 600% to 1 200%. Some studies have also found that the unique forehead tumor structure of Chinese geese is related to certain specific genetic variations. The breeding process of domestic geese focuses on genes in aspects such as the nervous system, immunity, metabolism, vision, bone structure and blood oxygen transport, which reflects their continuous adaptation to the captive environment (Jing et al., 2022; Chen et al., 2023).

2.3 Historical hybridization and gene flow

Heikkinen et al. (2020) found through genome-wide analysis that there has always been bidirectional gene flow between wild geese and domestic geese. Among the current European domestic geese, 3.2% to 58% of the genes come from wild greylag geese, and more than 10% of the ancestral origins are from Chinese domestic geese, indicating that multiple hybridization occurred at different stages (Figure 1). The research on mitochondrial and nuclear DNA by Heikkinen et al. (2015) and Honka et al. (2018) also found that although the overall genetic basis of domestic geese is relatively narrow, in some regions, there has been or is still gene exchange with wild species in the past. Ottenburghs et al. (2017) demonstrated that the evolutionary process of true geese was influenced by ancient interspecific gene infiltration, which led to a “patchwork genetic structure” in their genomes.

3 Phenotypic Traits Associated with Domestication

3.1 Plumage color and feather pattern variability

Wild geese generally have grey feathers, but domestic geese have many different color types such as white, white and brown, and white and grey. White feathers have become the main type in many areas (Azalou et al., 2024). Wen et al. (2021) found through genetic research that the KIT gene is a key factor for the differences between white and gray feathers in Chinese domestic geese, especially a 18-base deletion mutation, which has a significant relationship with the characteristics of white feathers. Genes like TYRP1 are also believed to be related to feather color, especially in specific breeds such as Huoyan geese (Wen et al., 2023). Whether for aesthetic needs or practical uses, artificial selection has played a significant role in the appearance traits such as feather color during the domestication process.

3.2 Growth, body conformation, and reproduction

The weight of domestic geese has significantly increased compared to their wild ancestors. Some breeds are even more than three times heavier than wild species (Kozák, 2019). The morphological studies of Abdel-Kafy et al. (2021) and Azalou et al. (2024) indicated that there were significant differences among different domestic geese in terms of body length, tarsal bone length, wingspan, chest circumference, etc., and male geese were generally larger than female geese. Domestic geese show earlier sexual maturity and higher egg production in terms of reproduction. The egg production of some breeds is more than ten times that of wild geese (Kozák, 2019). The genomic studies of Zheng et al. (2022), Chen et al. (2023), and Zhang et al. (2023) also identified genes such as TGFBR3L, CMYA5, and LHCGR that are related to traits such as growth rate, reproductive capacity, and reproductive performance.

3.3 Behavior and tameness

When domesticating, people tend to choose those individuals who are gentle in temperament, easy to manage and can adapt to human life (Kozák, 2019). Chen et al. (2023) found that these behavioral changes are related to the selection signals of genes associated with the nervous system, indicating that such personality changes have a clear genetic basis. Some domestic goose breeds have also undergone a behavioral shift from monogamy to polygyny, as well as a weakening of brooding behavior. These changes may be related to the expression regulation of genes such as CSMD1 and NUDT9 (Chen et al., 2023; Liu et al., 2023).

4 Genomic Resources for Goose Domestication Studies

4.1 Assembly and annotation of reference genomes

In recent years, researchers have constructed high-quality chromosomal level reference genomes of multiple goose breeds, including Lion-head geese, Tianfu geese and Hungarian White geese, with the aid of localization techniques such as PacBio, Bionano and Hi-C. The establishment of these genomes is helpful for identifying and annotating a lot of important genetic information, such as tens of thousands of protein-coding genes, some gene families that have been magnified or reduced, as well as the number of repetitive sequences and chromosome structure, etc. The genomic coverage of Lion-head reached 97.27%, and more than 21 000 protein-coding genes were identified by consensus. 19 550 genes and 286 miRNAs were found in the genome of the Hungarian white goose, laying a solid foundation for subsequent functional studies and evolutionary analyses (Li et al., 2020; Zhao et al., 2023; Zhou et al., 2024b).

4.2 Whole-genome resequencing and SNP panels

Whole-genome resequencing technology is mainly used in the research of various geese to analyze genetic diversity, population structure and selection signals related to domestication. Researchers resequenced hundreds of individuals of multiple breeds such as white geese and gray geese and identified tens of thousands of SNPS, some of which were related to economic traits such as growth, reproduction, immunity and feather color of geese (Zheng et al., 2022; Zhang et al., 2023; Chen et al., 2024). Scientists have identified SNP loci significantly associated with important traits such as body weight through genome-wide association studies (GWAS). Selective clearance analysis discovered some candidate genes related to breed characteristics.

4.3 Comparative genomics with other domesticated birds

By comparing the genomes of geese with those of other domestic fowls, such as ducks and landfowl, researchers have discovered evolutionary differences between species, gene family expansion and some unique adaptive features. The analysis by Lu et al. (2015) and Zhao et al. (2023) revealed that geese and ducks began to differentiate approximately 28 million years ago, and geese showed significant amplification in some gene families related to metabolism, immunity, and life in water (Figure 2).

The genetic composition of geese in terms of disease resistance, fat metabolism and certain domestication characteristics is also different from that of other birds. Lu et al.'s research in 2015 suggested that the deletion of the lep gene in geese might be related to their special energy storage capacity and migratory behavior.

5 Genetic Basis of Domestication Traits

5.1 Candidate genes for domestication-related traits

The EXT1 gene is related to the specific forehead tumor structure of Chinese domestic geese. The CSMD1 and LHCGR genes are respectively related to the brooding behaviors of Chinese geese and European geese. TGFBR3L, CMYA5, FOXD1, ARHGEF28 and SUCLG2, etc. are closely related to the growth rate, reproductive capacity and reproductive performance of geese. KIT and EDNRB2 are two key genes in terms of feather color. KIT has an 18-base deletion mutation and EDNRB2 has a 14-base insertion mutation. Both of these mutations are closely related to the characteristics of white feathers (Wen et al., 2021; Jing et al., 2022). GATA3 is related to meat quality, Sloc2a1 is related to reproduction, and PTPRM and TYRP1 are respectively related to eyelid structure and feather color (Chen et al., 2023; Zhang et al., 2023; Chen et al., 2024).

5.2 Regulatory elements and gene expression changes

During the domestication process of geese, the ways of gene regulation and the patterns of gene expression have all changed in the nervous system, immune system and metabolic pathways. The selection signals that emerged in these pathways indicate that geese gradually adapted to the captive environment during domestication. Genes related to vision, bone development and blood oxygen transport have also shown a trend of being selected. These regulatory changes may be the key reasons for the emergence of various phenotypic characteristics and differences in adaptability in geese after domestication, such as in aspects like climate adaptation, stress response and reproductive capacity (Jing et al., 2022; Chen et al., 2023; Wen et al., 2023).

5.3 Polygenic adaptation and domestication syndrome

The domestication of geese shows the characteristics of polygenic adaptation. Many genes, along with the pathways they are in, influence a series of traits, which are known as "domestication syndrome". Scientists have identified a large number of SNPS and haplotypes related to reproductive capacity, growth rate and meat quality through genome-wide association studies (GWAS), indicating that selection pressure acts on many different genetic loci. The frequencies of some key alleles increased rapidly during domestication, indicating that they underwent intense artificial selection. genetic hitchhiking also accelerated the evolution of these traits. The gene flow and hybridization between wild geese and domestic geese have been ongoing. This exchange has formed a complex genetic structure, which is helpful for maintaining and spreading some domesticated traits (Wen et al., 2021; Gao et al., 2022; Chen et al., 2024).

6 Population Genomics and Selection Signatures

6.1 Genetic diversity and bottleneck events

Genomic analysis shows that the genetic diversity of native goose breeds in China is higher than that of European domestic geese, supporting the "dual origin" hypothesis that domestic geese originated from Anser cygnoides and Anser anser. This genetic diversity is of great significance for the conservation and improvement of goose breeds, as it is helpful for preserving the genetic differences within the breeds. The genetic basis of European domestic geese is relatively narrow, and many individuals have very similar haplotypes, indicating that during their domestication process, they may have experienced a genetic bottleneck or the founder effect. Ancient DNA studies have found that the genetic differences among early domestic goose populations were more obvious, while in modern domestic geese, due to long-term directed breeding and genetic drift, the genetic diversity has gradually decreased (Heikkinen et al., 2015; Honka et al., 2018; Jing et al., 2022).

6.2 Detection of selection sweeps and differentiated regions

Analysis of selection signals in Central European domestic geese revealed that genomic regions related to functions such as the nervous system, immunity, metabolism, vision, bone development, and blood oxygen transport have been strongly artificially selected. In Chinese geese, the 14-base insertion mutations of the EDNRB2 gene are closely related to the characteristics of white feathers. The two SNPS within the EXT1 gene are related to the unique frontal tumor structure of Chinese geese. CSMD1 and LHCGR are respectively related to the brooding behavior of Central European domestic geese. The candidate genes TGFBR3L, CMYA5, FOXD1, ARHGEF28 and SUCLG2 are closely related to the growth rate, reproductive ability and reproductive performance of geese (Jing et al., 2022; Chen et al., 2023; Zhang et al., 2023).

6.3 Population structure and admixture

Most Chinese goose breeds can be traced back to a common ancestor, but some breeds like the Yili goose show signs of genetic hybridization with other Chinese geese. The origin of European domestic geese is more complex. Genetic components from Chinese swan goose (Anser cygnoides) have also been found in some European breeds, indicating that gene flow occurred in history. The two-way gene exchange and frequent hybridization between wild geese and domestic geese are also ongoing. These factors together have shaped the complex genetic pattern of modern geese. The study confirmed through cluster analysis and demographic models that there was continuous gene exchange in the modern domestic goose population and presented a "Mosaic ancestral structure" (Ottenburghs et al., 2017; Chen et al., 2023; Zhang et al., 2023).

7 Mitochondrial and Nuclear Genome Perspectives

7.1 Maternal lineage tracing using mtDNA

Heikkinen et al. (2015) and Qi et al. (2024) analyzed the mitochondrial control regions and cytochrome b (CYTB) genes of wild geese and domestic geese and found that the mtDNA diversity of European domestic geese was relatively low, with most individuals having only a few haplotypes that were very close to each other, indicating that their maternal genetic sources were relatively single. Qi et al. (2024) also found that Chinese domestic geese exhibit higher haplotype diversity and a more complex population structure. Some breeds also have frequent gene exchanges, suggesting that Chinese geese may have multiple maternal origins. These findings support the view that Chinese geese originated from swan goose (Anser cygnoides), while European geese originated from greylag goose (Anser anser) (Ren et al., 2016).

7.2 Discordance between mtDNA and nuclear genomes

Chen et al. (2023) demonstrated that although mtDNA can provide clear maternal genetic information, nuclear genome studies have shown that there is significant gene exchange and genetic mixing between domestic geese in China and Europe, as well as between domestic geese and wild geese. Ren et al. (2016) and Zhang et al. (2023) both hold that Yili geese cluster with European geese on the mtDNA phylogenetic tree, which may indicate that there was once genetic infiltration between them or that they shared an ancient haplotype. Further analysis of the nuclear genome also found that during the domestication process of geese, selection was mainly concentrated on genes related to growth, reproduction, immunity and morphological traits, and these characteristics were also continuously affected by genetic mixing events.

7.3 Integrative phylogenomic approaches

Ren et al. (2016) and Li et al. (2020) demonstrated that the phylogenetic analysis method combining high-quality nuclear genomes and complete mitochondrial genomes has enhanced the understanding of the domestication and evolution process of geese. Li et al. (2020) demonstrated that researchers can conduct a more in-depth analysis of gene content, structural changes, and the organization of chromatin through chromosomal genomic assembly, thereby more comprehensively revealing how genetic adaptation and selection changes occur in domestic geese during the long-term domestication process. The identification and annotation of mitochondrial DNA fragments (NUMTs) existing in the nuclear genome also provide more information for the analysis of evolutionary relationships. Ren et al. (2016) believed that these fragments were helpful for a better understanding of the complex evolutionary connections between some ancient haplotypes and Central European domestic geese.

8 Case Study: Genetic Dissection of the Chinese Wanxi White Goose

8.1 Breed history and domestication context

The Wanxi White Goose is a very important local goose breed in China. It is often used as the father in hybrid breeding, and it has a strong adaptability to the local ecological environment. Its domestication history is very obvious in its genes. This genetic differentiation is mainly caused by artificial selection rather than geographical isolation. Phylogenetic analysis shows that the Wanxi White Goose has formed an independent evolutionary branch among all domestic geese, indicating that it has a unique breeding history and reflecting its special position in the evolution of goose species diversity in China.

8.2 Genomic findings

Genetic studies conducted using RAPD and microsatellite markers have found that the genetic diversity of Wanxi White Goose is very high. Its heterozygosity and polymorphism information content (PIC) both exceed 0.5, indicating that it has strong adaptability and a rich genetic basis (Li et al., 2005; Chen et al., 2012; Dong et al., 2015). Cheng et al. (2008) found in the study of candidate genes that the Pit-1 gene has multiple polymorphic loci, and some of these alleles are related to the weight gain of young geese, indicating that this gene has application potential in breeding growth traits. Zhou et al. (2024a) also identified thousands of proteins related to reproductive regulation through proteomics research. Key genes such as CDC42, RAC2, and SOX9 are involved in regulating developmental and metabolic pathways and are of great significance for enhancing reproductive performance. The study by Chen et al. (2012) also found that the polymorphism of the Wnt6 gene can affect the development of feather sacs and may serve as a molecular marker for downy feather traits.

8.3 Implications for conservation and selective breeding

The genetic diversity of the Wanxi White Goose is relatively high, making it of great value in the protection and sustainable utilization of genetic resources. Early studies found that the genetic structure of the Western Anhui White goose was significantly different from that of other domestic geese, emphasizing the importance of protecting this breed (Li et al., 2005). By using the discovered candidate genes such as Pit-1 related to growth and Wnt6 related to feathers for marker-assisted selection (MAS), the breeding efficiency of economic traits can be improved without losing genetic diversity (Cheng et al., 2008; Chen et al., 2012).

9 Challenges and Future Directions

9.1 Limitations in current genomic data

The research conducted by Jing et al. (2022), Chen et al. (2023) and Zhang et al. (2023) indicates that most current studies only focus on a few species or specific populations, and there is a problem of uneven geographical representation.This makes it necessary to have a comprehensive understanding of the domestication origin and evolutionary process of geese. Especially in those local breeds with complex hybrid backgrounds or less research, it becomes difficult. Heikkinen et al. (2015) and Honka et al. (2018) argued that some studies only used mitochondrial DNA or partial genomic data, which limited the ability to analyze the population structure of geese and select signals. The research by Jing et al. (2022) indicates that there is currently a lack of high-quality reference genomes covering all major goose lineages, which has a significant impact on comparative analysis among different breeds and the identification of functional variation sites.

9.2 Functional validation of domestication genes

Many candidate genes and gene regions related to domestication traits have now been identified, but there are still challenges in truly verifying their functions (Jing et al., 2022; Chen et al., 2023; Zhang et al., 2023). Most of the results are based on statistical analysis or inferences of selected signals, lacking experimental evidence to prove whether a specific mutation really causes these trait changes. EXT1, CSMD1 and LHCGR have been found to be possibly related to tumor structure or brooding behavior, but their specific functions in geese remain unclear. To confirm the roles of these genes, further studies through gene editing, expression analysis or transgenic experiments are still needed (Chen et al., 2023; Zhang et al., 2023). The interaction between genes and the environment, as well as the phenomenon that one gene affects multiple traits (pleiotropy), also make these functional verifications more complex.

9.3 Toward a holistic understanding of avian domestication

Many studies on the domestication of geese mainly focus on a certain species or lineage, and the understanding of the entire process of bird domestication is still relatively limited. There is extensive genetic flow between wild geese and domestic geese, and there is also hybridization among different domestic goose breeds. This indicates that it is necessary to adopt an interdisciplinary and comprehensive approach to combine genomic, archaeological data and ecological data in order to better reconstruct the domestication process of geese (Heikkinen et al., 2020). Ottenburghs et al. (2017) hold that through comparative studies among different species, the common and unique genetic mechanisms in the domestication process can be identified, and the impacts of hybridization and gene infiltration on genetic diversity and trait evolution can be clarified. Future research should focus on establishing standardized genomic resource libraries and functional genomic technology platforms, and strengthen multidisciplinary cooperation, so as to truly promote the overall understanding of the domestication process of geese and even the entire bird species.

Acknowledgments

The authors appreciate the modification suggestions from two anonymous peer reviewers on the manuscript of this study.

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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