International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 17 diversity (Cai et al., 2022; Zhang and Lin, 2024). The degree of this change can be quantified by comparing indicators such as nucleotide diversity (π value), heterozygosity, and linkage disequilibrium. Studies have shown that the average nucleotide diversity of domestic chickens is about 60%~70% of that of wild red jungle fowl, with slight differences between different breeds. The genetic diversity of some highly intensively selected commercial breeds (such as white Leghorn chickens and white Rock chickens) is even lower, manifested as longer linkage disequilibrium regions and large runs of homozygosity. In contrast, some free-range local breed chickens have retained more diversity and are close to the level of wild jungle fowl due to less rigorous selection (Huang et al., 2020). Another genetic consequence of the chicken domestication bottleneck is the accumulation of some recessive alleles associated with inbreeding depression and the loss of functional variation. Comparative genomic studies have found that some genes in domestic chickens have become "pseudogenized", that is, loss-of-function mutations have become fixed. This may be due to the bottleneck and random drift that make some deletion alleles that do not affect fitness popular in small populations. For example, some studies have observed that several olfactory receptor genes in domestic chickens have loss-of-function mutations, while they are functional in wild jungle fowl (probably because domestic chickens have reduced reliance on olfaction). Similarly, the W chromosome of domestic chickens has accumulated a large number of harmful mutations and repeated sequences due to long-term small populations and inbreeding. These facts show that the domestication bottleneck not only reduces allele diversity, but also changes the mutation load and selection balance of the genome, which may reduce the genetic adaptability of domestic chickens to environmental changes. However, there are also multiple opportunities to introduce new genetic components during the domestication process, which partially alleviates the decline in diversity. During the process of dissemination, domestic chickens often hybridize with jungle fowl or native chickens in different regions, thereby acquiring foreign genes. This is genetically manifested as the embedding of fragments of some other jungle fowl species or exotic breeds in the chicken genome. For example, studies have found that the chromosomes of chickens in South Asia and Southeast Asia contain fragments from the gray jungle fowl (G. sonneratii), which may have been brought in through artificial introduction or trade. This gene flow increases the overall genetic diversity of chickens and counteracts the bottleneck effect (Guo et al., 2022). Population structure analysis also shows that there are signals of gene exchange between chicken strains from different geographical origins, especially between breeds in neighboring regions. These hybridization events increase the level of local genetic variation and sometimes introduce beneficial exogenous alleles into the chicken gene pool. For example, there is evidence that some disease resistance gene alleles of wild gray jungle fowl in Southeast Asia have entered local chickens through hybridization, increasing the latter's resistance to parasites. The domestication of chickens accompanied by population bottlenecks has led to a decline in overall genetic diversity, but regional gene flow and multiple domestication centers have partially compensated for this loss, so that the global chicken population still retains a considerable amount of genetic variation. A study on the fine structure of the global domestic chicken population revealed that domestic chickens can now be divided into several genetic groups, each with a unique allele frequency pattern and related to its transmission and breeding history. This reminds us that when using domestic chicken genetic resources, we should fully protect the genetic diversity of different strains. Some traditional native chickens may carry rare beneficial mutations and have important conservation value (Huang et al., 2018). Molecular breeding techniques (such as whole genome selection) can help us monitor and maintain the genetic diversity of the population while improving production performance, and avoid excessive inbreeding leading to reduced adaptability. 4.3 Copy number variations and chromosomal rearrangements under selection Genome structural variation (SV), including copy number variation (CNV), large deletions, insertions, inversions and translocations, plays an important role in the selection of domestic chicken traits. Some significant economic traits are not caused by single point mutations, but are related to larger structural variations. For example, the "rose crown" trait in domestic chickens comes from an inversion rearrangement of about 7 Mb on chromosome 7.
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