Two variants of AUTS2 gene are associated with high lean meat percentage in Pekin ducks

Duck meat is starting to receive more attention due to its unique meaty characteristics. Pekin duck is an important breed resource of meat duck, which has been used in meat production and product research. However, the study about whole genome resequencing analysis of ducks for meat production has not been reported and the underlying mechanisms of meat production remain undefined. Here, lines with high lean meat percentage (S, n = 30) and low lean meat percentage (Z, n = 30) were used to analyze. The values of body weight, breast meat weight and leg meat weight in S line (body weight: 3,071 ± 26.83 g), breast meat: 391.3 ± 6.670 g; leg meat: 121.1 ± 2.184 g) were significantly higher than those in Z line (body weight: 2,584 ± 38.53 g, breast meat: 263.9 ± 6.984 g; leg meat: 110.1 ± 3.645 g). The values of body size in Z line (26.47 ± 0.1571 cm) were significantly higher than that in S line (25.38 ± 0.2475 cm). A total of 14,220,037 SNPs were obtained from 19 individuals by whole-genome resequencing, and the separate analyses of FST (range from 0.30 to 0.52) and log₂θπ ratio (range from 5.8 to 8.1) revealed 50 and 124 candidate genes in the top 0.1% regions respectively, which involved in 209 and 298 candidate regions. The integration of two approaches resulted in 7 overlapping genes. Notably, AUTS2 gene is related to activator of developmental regulator. As expected, we found that in the chr29:2.29–2.30 Mb region of AUTS2, the FST value is 0.32, and the S line (π = 7.3 × 10 ⁻⁵) shows a very low level of π value compared with Z line (π = 8.8 × 10 ⁻³). Genotyping and GWAS analysis showed that 2 candidate SNPs (chr29:2,296,787 and chr29:2,296,832) were associated with high meat percentage, which were verified by Sanger sequencing. Taken together, lean meat percentage was much higher in S line individuals by comparing with Z line. The integration of FST and θπ resulted in only 7 overlapping genes that in the top 0.1% candidate regions of them. The chr29:2,296,787 and chr29:2,296,832 in the AUTS2 gene could be important molecular markers for high lean meat adaptation selection in S line.