International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 20 process, resulting in different crown phenotypes. It is worth noting that mutations in crown type genes often affect not only appearance but also reproductive performance. For example, rose crown mutations reduce sperm quality in roosters, while pea crown alleles are associated with ovarian function in hens. This may explain why these crown types are mainly fixed in ornamental or fighting cock breeds, while high-yielding laying hens are mostly single-combed. The annual egg production of domestic chickens has increased significantly from more than 10 eggs in wild jungle fowl to more than 300 eggs in laying hens, and there are complex changes in the physiological regulatory network behind this. The secretion rhythm of prolactin (PRL) and gonadotropins (such as FSH and LH) has been artificially modified, allowing domestic chickens to lay eggs almost all year round without brooding. Population genetics studies have found that in high-producing egg-producing breeds, there is an insertion mutation in the promoter region of the PRLR (prolactin receptor) gene, which weakens the prolactin signal and inhibits brooding behavior. At the same time, the THSR gene of high-producing laying hens has been introduced, and its mutation also helps to break seasonal reproduction. At the same time, ovarian factor genes such as GDF9 and BMP15 related to follicle development carry specific haplotypes in high-producing chickens, increasing the probability of multiple ovulation. Recent epigenetic studies have also found that the DNA methylation patterns of high-producing laying hens on reproductive axis genes are systematically different from those of low-producing chickens, suggesting that egg-laying selection also works at the epigenetic level (Figure 1) (Pan, 2024; Shi et al., 2024). It can be seen that the improvement of egg-laying performance involves multi-gene and multi-level regulatory changes, including both DNA sequence variation and expression regulation and epigenetic modification changes. Comparative genomes can only capture changes at the sequence level. To fully analyze the genetic mechanism of egg-laying, it is necessary to combine transcriptome, methylome and other data. 5.3 Adaptive evolution of behavioral and neurological genes Domestic chickens show significantly different behavioral characteristics compared to wild jungle fowl, including a more docile temperament, weaker flying ability and changes in social-level behavior. These behavioral differences are also the result of domestication selection. Humans prefer to retain docile and easy-to-manage individuals, thereby changing the neural regulation system of domestic chickens. Comparing the genomes and brain transcriptomes of domestic chickens and jungle fowl, it can be found that genes related to neural development and neurotransmitters have undergone adaptive evolution or expression regulation changes. Zhou et al. (2023) compared Luxi fighting chickens (highly aggressive) with ordinary laying hens and identified a group of candidate genes related to nervous system function at the whole genome level. Combined with RNA sequencing of brain tissue, it was found that the expression of these genes was significantly different between fighting chickens and laying hens. Among them, genes involved in neural development pathways (such as the CAMK2 pathway) are highly expressed in fighting chickens, which may give them stronger attack and response capabilities; while genes related to calmness and social behavior, such as AVPR1A (arginine vasopressin receptor), are more highly expressed in laying hens, making their temperament more docile. This change in gene expression pattern may be driven by genetic variation, such as mutations in regulatory regions or differences in epigenetic modifications. This study revealed that the domestication of behavioral traits has a complex genetic basis, but key regulatory factors can still be excavated through comparative genomics. A classic behavioral domestication gene is SERPINE3, which was previously proposed as a "domestication gene" in fox domestication experiments. In the chicken genome, genes that affect neurotransmitter metabolism, such as SERPINE3 and MAOA (monoamine oxidase A), also show signs of selection: the variation composition near these genes in chicken breeds is significantly different from that in wild chickens (promoting changes in the levels of serotonin, dopamine, etc.), which may explain why chickens are less susceptible to fright and less aggressive. Other studies focused on circadian rhythms and stress response pathways, and found that several synchronously evolved amino acid substitutions accumulated in the ADCYAP1 (PACAP gene) sequence of chickens, which are speculated to be related to reduced vigilance and prolonged foraging time (Cai et al., 2022). Domestication-related variations have also been detected in the genes of the auditory and visual pathways of chickens. For example, regulatory mutations in the TH gene reduce the dependence of chicken chicks on the call of the hen, so that they can be artificially raised in batches.
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