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.

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.