International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 24 6.3 Identification of disease resistance and environmental adaptation genes Local breeds are often formed under special environments or production conditions, and therefore have some stress resistance traits that commercial breeds do not have. For example, plateau Tibetan chickens are resistant to hypoxia, dryland fighting chickens are resistant to roughage, southern free-range chickens are resistant to humidity and heat, and some breeds are resistant to local diseases. These valuable adaptabilities are usually caused by genetic variations accumulated under long-term natural selection. By comparing the genomes of local chickens and ordinary breeds or red junglefowl, researchers can identify candidate genes related to these resistances and adaptabilities, providing references for genetic improvement and seed conservation. Tibetan chickens are local chicken breeds living in the Qinghai-Tibet Plateau and can grow and reproduce normally in a low-oxygen environment. Zhong et al. (2022) conducted genomic analysis of chickens at different altitudes and found that there were positive selection signals in multiple genomic regions in Tibetan chickens. One of the significant candidate genes is HBAD, which encodes an abnormal hemoglobin delta subunit. HBAD has unique mutations in Tibetan chickens, which is speculated to improve the ability of hemoglobin to bind oxygen. Genes involved in blood coagulation and cardiovascular efficiency, such as HRG (histone release protein) and ANK2 (ankyrin 2), are also selected in Tibetan chickens. The mutations in these genes together give Tibetan chickens stronger oxygen transport and cardiopulmonary function to adapt to the high-altitude hypoxic environment. In contrast, lowland chickens rarely have these mutations. Therefore, introducing these alleles of Tibetan chickens into other chicken populations may improve the plateau adaptability of offspring. Some local chickens have evolved strong disease resistance in the long-term coexistence with specific pathogens. For example, Pujiang chickens in the swamps of Sichuan have high resistance to chicken malaria parasites. Genome comparison found that the MHC-B complex genome type of Pujiang chicken is different from that of general chickens, with more alleles and higher heterozygosity (Fulton, 2020). This indicates that its immune system has a wider antigen presentation capacity, thus resisting diverse pathogens. For example, some free-range chickens in northern China are more tolerant to Marek's disease (a tumor caused by herpes virus). GWAS was conducted on sensitive and tolerant varieties, and CNV and haplotype differences in immune-related genes such as IRF2 and SMARCA4 were found to be associated with disease-resistant phenotypes. Further functional experiments confirmed that additional copies of the IRF2 gene help improve the antiviral ability of T cells. This discovery comes from the genetic comparison of local varieties and is instructive for breeding Marek's disease-resistant strains. Similarly, free-range chickens in the Jiangsu and Zhejiang areas are said to be more resistant to intestinal parasites, and multiple immune regulatory genes including candidate genes including CHIA (chitinase, anti-worm infection) have been detected to have undergone selection enrichment. In the future, molecular markers can be designed for these genes to carry out disease-resistant breeding. Many local chickens can survive under nutrient deficiency or adverse climatic conditions. For example, mountain black-bone chickens can still grow on coarse grains and weeds, and their AMY2B (amylase gene) copy number is higher than that of ordinary chickens, and their starch digestion ability is stronger (similar to dogs being domesticated to produce high amylase). Hainan Wenchang chickens are not prone to heatstroke in hot and humid climates, which may be attributed to the high expression level of heat shock protein genes such as HSP70, and gene promoter mutations make them sensitive to heat stimulation. Control experiments show that the induced expression of HSP70 in Wenchang chickens is higher than that of ordinary white chickens under high temperature conditions (data has not yet been published), which may be related to SNPs in the promoter region of its gene. For example, in the cold winter in Northeast China, some stupid chicken breeds have thick down feathers and are cold-resistant. Their UGP2 gene (regulating brown fat heat generation) has a unique haplotype that helps them maintain body temperature. These adaptive traits are often the result of complex physiological mechanisms, which cannot be fully explained by one or a few genes, but genome comparisons can narrow the scope and find related gene networks. For example, through the combined analysis of multi-omics in chicken breeds in the cold regions of Northeast China, it was found that genes in the PPARA/PPARG (peroxisome proliferator-activated receptor) pathway all have synergistic selection signals, pointing to the role of fat metabolism in cold resistance.
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