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. 2023 Jun 24;13(13):2089.
doi: 10.3390/ani13132089.

Identification of SNPs Associated with Goose Meat Quality Traits Using a Genome-Wide Association Study Approach

Guangliang Gao  1   2 , Keshan Zhang  1   2 , Ping Huang  1 , Xianzhi Zhao  1   2 , Qin Li  1   2 , Youhui Xie  1   2 , Chunhui Yin  1   2 , Jing Li  1   2 , Zhen Wang  1   2 , Hang Zhong  1   2 , Jiajia Xue  1   2 , Zhuping Chen  1   2 , Xianwen Wu  3 , Qigui Wang  1   2
Affiliations

Identification of SNPs Associated with Goose Meat Quality Traits Using a Genome-Wide Association Study Approach

Guangliang Gao et al. Animals (Basel). .

Abstract

(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.

Keywords: genome-wide association study; goose; marker-assisted selection; meat traits; single nucleotide polymorphism.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The SNP density in the goose genome within 1Mb window size.
Figure 2
Figure 2
The results of PCA conducted on the goose population based on the whole genome SNPs. Note: The points in the plot represent individual members of the population.
Figure 3
Figure 3
The Manhattan and Q-Q plots for different meat quality traits in male Sichuan white geese. Note: The plots are presented for the following traits: CFC (A,B); CLR (C,D); L* (meat lightness) (E,F); b* (meat yellowness) (G,H); SF (I,J). The threshold for significance is set at 1 × 10−7.
Figure 4
Figure 4
The functional analysis for the genes within 1 Mb within SNPs associated with goose meat quality traits.
See this image and copyright information in PMC

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