Animal Molecular Breeding, 2025, Vol.15, No.1, 19-28 http://animalscipublisher.com/index.php/amb 25 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.
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