A multiallelic indel in the promoter region of the Cyclin-dependent kinase inhibitor 3 gene is significantly associated with body weight and carcass traits in chickens

Many studies have reported that cyclin-dependent kinase inhibitor 3 (CDKN3) is involved in the cell cycle. However, the function of CDKN3 has not been well elucidated in organisms. In this study, a multiallelic indel caused by a 19-bp fragment and a 2 x 19 bp fragment was shown for the first time to be inserted into the promoter of the CDKN3 gene in 1994 chickens from 9 different breeds. In addition, 6 genotypes ((CC5)-C-5, (CC4)-C-4, (CC3)-C-3, (CC5)-C-4, (CC4)-C-3, and (CC5)-C-3), were observed ((CC3)-C-3, (CC4)-C-4, (CC5)-C-5 have 3 x 19 bp, 4 x 19 bp, and 5 x 19 bp, respectively). Among these genotypes, the (CC4)-C-4 genotype was the most dominant genotype in 9 breeds. The results of chi(2) analysis of CDKN3 gene in different breeds showed that there were significant differences in the distribution of genotypes among different cultivars (P < 0.01). In addition, association study with F2 chicken resource population which produced by Anka and Gushi chickens showed that the (CC4)-C-3 genotypes had the greatest semi-evisceration weight (SEW, 1163.94 +/- 46.84), evisceration weight (EW, 964.15 +/- 41.16), head weight (HW, 45.55 +/- 1.43), claw weight (CW, 63.42 +/- 2.86), wing weight (WW, 129.15 +/- 5.48), liver weight (LW, 29.96 +/- 1.27), carcass weight (cW, 1286.96 +/- 49.53), weight at 10 (1190.68 +/- 45.68) and 12 (1430.65 +/- 54.45) wk, followed by (CC3)-C-3, (CC4)-C-4, (CC5)-C-5, (CC5)-C-4 whereas (CC5)-C-3 genotypes having the lowest SEW (989.21 +/- 47.71), EW (841.38 +/- 40.55), HW (41.03 +/- 1.46), CW (54.36 +/- 2.81), WW (116.31 +/- 5.39), LW (27.31 +/- 1.25), cW (1093.29 +/- 49.99), weight at 10 (1036.10 +/- 44.99) and 12 (1246.28 +/- 53.59) wk. Expression levels of CDKN3 in breast muscle of chickens with (CC4)-C-4 (0.72 +/- 0.02), (CC3)-C-3 (0.95 +/- 0.41), and (CC5)-C-4 (0.74 +/- 0.13) genotypes were significantly lower than those with (CC5)-C-5 (1.80 +/- 0.01) and (CC5)-C-3 (2.14 +/- 0.17) genotypes (P < 0.05). In conclusion, we investigated the effect of a multiallelic indel in the CDKN3 gene on the economic traits of chickens, and this indel was significantly associated with growth and carcass traits in chickens. Collectively, our findings provide useful information about the repeat sequence indel in the promoter region of the CDKN3 gene as a potential molecular marker for chicken breeding.