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Simple Summary: To screen and identify single nucleotide polymorphisms (SNPs) associated with geese meat quality traits, we performed genome-wide association study (GWAS) in a population of male Sichuan white geese (a Chinese local breed) at 70 days old to screen the SNPs in the goose genome. Additionally, genotypes of the selected SNPs associated with goose meat were detected using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOP MS) method. The results revealed 43 SNPs that showed potentially significant associations with these traits. Additionally, we detected 28 annotated genes as potential candidate genes for the five meat quality traits. The enrichment analysis of genes within a 1Mb vicinity of SNPs showed potentially significant enrichment in the protein digestion and absorption pathway, as well as the Glycolipid metabolism pathway. The findings of this study offer novel genetic markers and candidate genes that can be used for marker-assisted selection of geese, laying the groundwork for understanding the genetic basis of goose meat quality traits and establishing a foundation for comprehending their genetic basis. (1) Background: Goose meat is highly valued for its economic significance and vast market potential due to its desirable qualities, including a rich nutritional profile, tender texture, relatively low-fat content, and high levels of beneficial unsaturated fatty acids. However, there is an urgent need to improve goose breeding by identifying molecular markers associated with meat quality. (2) Methods: We evaluated meat quality traits, such as meat color, shear force (SF), cooking loss rate (CLR), and crude fat content (CFC), in a population of 215 male Sichuan white geese at 70 days of age. A GWAS was performed to identify potential molecular markers associated with goose meat quality. Furthermore, the selected SNPs linked to meat quality traits were genotyped using the MALDI-TOP MS method. (3) Results: A dataset of 2601.19 Gb of WGS data was obtained from 215 individuals, with an average sequencing depth of 10.89×. The GWAS revealed the identification of 43 potentially significant SNP markers associated with meat quality traits in the Sichuan white goose population. Additionally, 28 genes were identified as important candidate genes for meat quality. The gene enrichment analysis indicated a substantial enrichment of genes within a 1Mb vicinity of SNPs in both the protein digestion and absorption pathway and the Glycerolipid metabolism pathway. (4) Conclusion: This study provides valuable insights into the genetic and molecular mechanisms underlying goose meat quality traits, offering crucial references for molecular breeding in this field. [ABSTRACT FROM AUTHOR]

Background: Modern breeding in the poultry industry mainly aims to produce high-performance poultry lines and breeds in two main directions of productivity, meat and eggs. To understand more about the productive potential of lowly selected Chinese native chicken populations, we selected 14 representative SNP markers strongly associated with growth traits or carcass traits and 14 SNP markers strongly associated with egg laying traits through previous reports. By using the MassArray technology, we detected the genotype frequency distributions of these 28 SNP markers in seven populations including four lowly selected as well as one moderately selected Sichuan native chicken populations, one commercial broiler line and one commercial layer line. Results: Based on the genotype frequency distributions of these 28 SNP markers in 5 native chicken populations and 2 commercial lines, the results suggested that these Chinese indigenous chicken populations have a relatively close relationship with the commercial broiler line but a marked distinction from the commercial layer line. Two native chicken breeds, Shimian Caoke Chicken and Daheng Broilers, share similar genetic structure with the broiler line. Conclusions: Our observations may help us to better select and breed superior domestic chickens and provide new clues for further study of breeding programs in local chicken populations. [ABSTRACT FROM AUTHOR]