Naiyi Xu

To elucidate the genetic basis underlying chicken adaptation to diverse environmental selection pressures, this study performed a genome-wide analysis of copy number variations (CNVs) using publicly available whole-genome resequencing data from global chicken populations. Population differentiation (FST) and nucleotide diversity (π ratio) were integrated to identify signatures of selection associated with thermal adaptation, domestication, and high-altitude adaptation, followed by the identification of candidate genes and enriched biological pathways. In total, 6862, 9348, and 9384 high-confidence copy number variations (CNVs) were identified in the heat adaptation group, domestication group, and high-altitude adaptation group, respectively. Candidate genes associated with heat adaptation include AQP9, SLC4A8, CAT, SMPD2, and CLOCK, which are mainly enriched in biological processes related to water and ion homeostasis, antioxidant defense, and circadian rhythm regulation. Candidate genes related to domestication, such as IL18R1, HTR2C, GRIN2A, PRKAG2, and FABP1, are mainly involved in neuroactive ligand-receptor interaction, energy metabolism, immune regulation, and melanogenesis. In contrast, candidate genes identified in high-altitude populations include EDNRB, ITPR1, OGDH, PPARA, and ADCY6, which are significantly enriched in vascular smooth muscle contraction, the tricarboxylic acid (TCA) cycle, the PPAR signaling pathway, and pathways related to hypoxic metabolic adaptation. The above findings indicate that distinct environmental selection pressures and artificial selection pressures have shaped population-specific CNV patterns in the chicken genome and promoted the formation of phenotypic adaptation through regulating water–salt balance, neural function, energy metabolism, vascular homeostasis, and hypoxic response pathways.

The local goat breeds of Chongqing represent the typical goat populations of Southwestern China and play a significant role in global goat research. However, studies on these goats remain limited. Chongqing goats exhibit diverse coat colors, a crucial economic trait essential for individual and breed identification. In this study, we performed genome-wide association analysis (GWAS) of Chongqing goats to identify candidate genes associated with coat color. The results of the GWAS revealed that the ASIP, AHCY, and ITCH genes on chromosome 13 are significantly associated with coat color variation in Chongqing goats. Furthermore, haplotype analysis, gene function annotation, and pathway analysis enrichment further confirmed that a significant region on chromosome 13 is associated with coat color in local Chongqing goats, and that ASIP and AHCY are related to black coat color, whereas ITCH is potentially associated with white coat expression. Additionally, we also identified TPK1 as being associated with coat color in goats, which has hardly been reported. The newly identified genes expand our understanding of the complex genetic architecture underlying pigmentation traits in livestock. Our study identifies the genes related to coat color in local goats, which enriches the genetic resource pool of goats and contributes to a deeper understanding of the genetic mechanisms underlying coat color in these breeds.

The advancement of sequencing technology and molecular breeding methods has provided technical support and assurance for accurate breeding. Genomic Selection (GS) utilizes genomic information to improve livestock breeding, and it is more accurate and more efficient than traditional selection methods. GS has been widely applied in domestic animal breeding, especially in cattle. However, there are still limited studies on the application and research of GS in sheep and goats. This paper outlines the principles, analysis methods, and influential factors of GS and elaborates on the research progress, challenges, and prospects of applying GS in sheep and goat breeding. Through the review of these aspects, this paper is expected to provide valuable references for the implementation of GS in the field of sheep and goat breeding.

The advancement of sequencing technology and molecular breeding methods have provided technical support and assurance for accurate breeding. Genomic Selection (GS) utilizes genomic information to improve livestock breeding and, it is more accurate and more efficient than traditional selection methods. GS has been widely applied in domestic animals breeding, especially in cattle. However, there is still limited study on the application and research of GS in sheep and goat. In this paper, we outlined the principle, analysis methods, the influential factors of GS, and elaborated on the research progress, challenges, and prospects of applying GS in sheep and goat breeding. Through the review of these aspects this paper is expected to provide valuable references for the implementation of GS in the field of sheep and goat breeding.