International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 26 importance of coordinated trait changes. Domestication involves the simultaneous evolution of a series of traits, such as docile behavior often accompanied by changes in coat color (the famous “domestication syndrome”). Genomic analysis provides a possible explanation: some genes (or tightly linked gene clusters) have pleiotropic effects and affect multiple traits at the same time when selected. For example, the KIT gene affects both color spots and calmness, and similar reports have been made in the domestication of silver foxes. More evidence is needed in domestic chickens, but it has been observed that mutations in genes that control hormones often affect multiple aspects of reproduction and behavior (such as TSHR mutations that change seasonal rhythms and affect temperament). This suggests that when species adapt, the trade-offs and linkages at the genome level cannot be ignored, and many traits evolve together. Looking to the future, comparative genomic studies of Galliformes and domestic chickens will be further expanded in multiple directions. First, more extensive genome sampling is an inevitable trend. Although there are some high-quality genomes of representative species, they are still insufficient for the entire lineage of Galliformes. The international “Bird 1K Project” and others will sequence more Phasianids species, including some rare or limited distribution species. As the data increases, we will improve the Galliformes phylogenetic tree, especially clarify the positions of some controversial small lineages, and calibrate the divergence time more accurately. For domestic chickens, large-scale population resequencing will cover more local breeds and ecotypes, allowing us to construct a full genome variation map and pedigree network for domestic chickens. Chinese scholars have sequenced thousands of chicken genomes, and in the future, the genome information of all major chicken species in the world may be covered. These data will push the domestication model of domestic chickens from a rough single-center model to a refined multi-region network model. Secondly, functional genomic verification will become a research focus. After a large number of candidate selection genes are identified through comparative analysis, the next step is to verify their functions through molecular biology and genetic experiments. For example, gene editing is used to knock out/repair corresponding mutations in chicken embryos or cell lines, and the effects on phenotypes or cell functions are observed to confirm causal relationships. At present, the in vitro culture and gene editing technologies of chicken embryos have become increasingly mature (such as CRISPR/Cas9-mediated primordial germ cell editing), and it is expected that functional verification can be carried out on key genes for domestication of domestic chickens (TSHR, SOX5, etc.). In addition, single-cell sequencing, ATAC-seq and other technologies can also be applied to chicken tissues to explore how mutations in regulatory elements change gene expression, thereby leading to trait changes. This will advance our understanding of domestication selection to the level of regulatory networks. Thirdly, paleogenomics has the potential to answer some unresolved questions in the evolution of domestic chickens. Although modern genomes reveal the overall changes after domestication, only ancient DNA can record the intermediate processes intuitively. In recent years, mitochondrial and partial nuclear DNA of chicken bones from hundreds or even thousands of years ago (such as medieval chickens in Europe) have been successfully sequenced. In the future, DNA from remains of early Neolithic chickens in China may be obtained, and compared with modern chickens, it will be possible to directly observe how allele frequencies evolve over time. In particular, it can be verified when and where mutations such as TSHR appeared and spread, and whether domestic chickens experienced severe bottlenecks when they were first domesticated. This information will greatly enrich the details of the domestication model. Ancient DNA can also identify the genetic characteristics of some extinct ancient breeds, giving us a more complete picture of the historical evolution of genetic diversity in domestic chickens. Finally, in terms of breeding applications, comparative genomics results will guide precision molecular breeding. Once we have identified the key mutations that affect traits such as meat and egg production, disease resistance and environmental tolerance, we can use marker-assisted selection (MAS) and gene editing to aggregate favorable mutations into target varieties. For example, molecular markers can be used to quickly screen whether breeders carry high-egg alleles to improve the efficiency of traditional breeding. For targets where there are no ideal alleles yet, such as further improving plateau tolerance, gene editing can be used to directly introduce the Tibetan chicken's EPAS1 mutation into commercial breeds, thereby creating a “super chicken”. Of course, this involves regulatory issues for transgenic/gene-edited animals, but it is technically feasible. Comparative genomics can also help broaden the genetic basis of breeding. By comparing the genomes with local breeds, breeders can target which breeds to
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