This study aimed to reveal the potential genetic basis for litter size, coat colour, black middorsal stripe and skin colour by combining genome-wide association analysis (GWAS) and selection signature analysis and ROH detection within the Youzhou dark (YZD) goat population (n = 206) using the Illumina GoatSNP54 BeadChip. In the GWAS, we identified one SNP (snp54094-scaffold824-899720) on chromosome 11 for litter size, two SNPs on chromosome 26 (snp11508-scaffold142-1990450, SORCS3) and chromosome 12 (snp55048-scaffold842-324525, LOC102187779) for coat colour and one SNP on chromosome 18 (snp56013-scaffold873-22716, TCF25) for the black middorsal stripe. In contrast, no SNPs were identified for skin colour. In selection signature analysis, 295 significant iHS genomic regions with a mean |iHS| score > 2.66, containing selection signatures encompassing 232 candidate genes were detected. In particular, 43 GO terms and one KEGG pathway were significantly enriched in the selected genes, which may contribute to the excellent environmental adaptability and characteristic trait formation during the domestication of YZD goats. In ROH detection, we identified 4446 ROH segments and 282 consensus ROH regions, among which nine common genes overlapped with those detected using the iHS method. Some known candidate genes for economic traits such as reproduction (TSHR, ANGPT4, CENPF, PIBF1, DACH1, DIS3, CHST1, COL4A1, PRKD1 and DNMT3B) and development and growth (TNPO2, IFT80, UCP2, UCP3, GHRHR, SIM1, CCM2L, CTNNA3 and CTNNA1) were revealed by iHS and ROH detection. Overall, this study is limited by the small population size, which affects the results of GWAS to a certain extent. Nevertheless, our findings could provide the first overview of the genetic mechanism underlying these important traits and provide novel insights into the future conservation and utilisation of Chinese goat germplasm resources.

Objective: This study aimed to investigate the significant single nucleotide polymorphisms (SNPs) and genes associated with nine reproduction and morphological traits in three breed populations of Chinese goats.Methods: The genome-wide association of nine reproduction and morphological traits (litter size, nipple number, wattle, skin color, coat color, black dorsal line, beard, beard length, and hind leg hair) were analyzed in three Chinese native goat breeds (n = 336) using an Illumina Goat SNP50 Beadchip.Results: A total of 17 genome-wide or chromosome-wide significant SNPs associated with one reproduction trait (litter size) and six morphological traits (wattle, coat color, black dorsal line, beard, beard length, and hind leg hair) were identified in three Chinese native goat breeds, and the candidate genes were annotated. The significant SNPs and corresponding putative candidate genes for each trait are as follows: two SNPs located on chromosomes 6 (CSN3) and 24 (TCF4) for litter size trait; two SNPs located on chromosome 9 (KATNA1) and 1 (UBASH3A) for wattle trait; three SNPs located on chromosome 26 (SORCS3), 24 (DYM), and 20 (PDE4D) for coat color trait; two SNPs located on chromosome 18 (TCF25) and 15 (CLMP) for black dorsal line trait; four SNPs located on chromosome 8, 2 (PAX3), 5 (PIK3C2G), and 28 (PLA2G12B and OIT3) for beard trait; one SNP located on chromosome 18 (KCNG4) for beard length trait; three SNPs located on chromosome 17 (GLRB and GRIA2), 28 (PGBD5), and 4 for hind leg hair trait. In contrast, there were no SNPs identified for nipple number and skin color.Conclusion: The significant SNPs or genes identified in this study provided novel insights into the genetic mechanism underlying important reproduction and morphological traits of three local goat breeds in Southern China as well as further potential applications for breeding goats.

Native goat breeds in China are highly valued for their distinctive flavor. This study integrated flavoromics, metabolomics, and transcriptomics to analyze the flavor compounds in the meat of Youzhou Dark (WY) and Local White (BY) goats. Ten 12-month-old castrated male WY and BY goats, five each, were selected for slaughter after undergoing the same feeding and management conditions. Longissimus dorsi muscle were collected from each group and subjected to flavoromics, metabolomics, and transcriptomics analyses. Flavoromics identified 228 volatile compounds, of which alcohols, ketones, and esters were the most prominent. Using multivariate statistical analysis and variable importance on projection (VIP) methods, 85 differential flavor compounds between WY and BY goats were identified. The key characteristic compounds, heptanal,1-octen-3-one,2,3-butanedione, 2-methyl-butanal, and 2-pentyl-furan, effectively distinguished between the volatile profiles of the two goat breeds. Untargeted metabolomics identified a total of 47 differential metabolites with significant differences between WY and BY goats. Differences in flavor compounds between the two goat breeds were linked to the expression of genes in metabolic pathways. The genes involved in tyrosine and phenylalanine metabolism were different in the two groups of goat meat. This variation may contribute to the differences in the sensory flavor profiles of WY and BY goats. Overall, these findings provide insight into the molecular mechanisms of flavor formation in native Chinese goats and offer a foundation for improving meat quality.

Objective: The study was conducted to identify the molecular mechanism of the phenotype formation of Youzhou black sheep by histological cytology and transcriptomics. Materials and Methods: In this study, HE and IHC staining were used to explore the patterns and cytological differences in skin pigment deposition between Youzhou Dark goats and Banjiao goats. In addition, the DEGs related to the black skin phenotype were identified via transcriptomic analyses. Finally, the expression pattern of the agouti signal protein (ASIP) gene in the skin from individuals with different skin color phenotypes was verified by FISH. Results: The results showed that compared with that on the skin surface of Banjiao goats, melanin deposition on the skin surface of Youzhou Dark goats was abnormally increased. The transcriptomic analyses showed that the expression of the ASIP genes decreased significantly in Youzhou Dark goats. FISH confirmed that the expression of the ASIP gene in Youzhou Dark goats was significantly lower than that in Banjiao goats. Conclusion: The present study showed that a decrease in ASIP gene expression and an increase in melanin production are important factors associated with skin pigmentation in Youzhou Dark goats.