Table 4.
Contributions of five missense mutations and genomic regions to eggshell quality traits at different wk of age
| SNP | rs312347405 | rs14837998 | rs316793137 | rs14840004 | rs316607577 | Region 1 | |
|---|---|---|---|---|---|---|---|
| Chromosome | GGA1 | GGA1 | GGA1 | GGA1 | GGA1 | GGA1 | |
| Position (bp) | 64,287,542 | 65,472,759 | 67,081,703 | 67,315,919 | 67,961,420 | 57.3–71.4 Mb | |
| Gene symbol | PIK3C2G | RECQL | ABCC9 | CASC1 | ITPR2 | - | |
| EA/AAa | C/G | A/G | A/G | T/G | C/T | - | |
| MAF | 0.485 | 0.353 | 0.414 | 0.386 | 0.413 | - | |
| Amino acid change | Leu/ Val | Cys/ Arg | Asn/ Asp | Thr/ Pro | Ger/ Gly | - | |
| ESW32 | beta (SE)b | −0.253 (0.048) | 0.276 (0.051) | 0.269 (0.049) | −0.151 (0.051) | 0.246(0.052) | - |
| CPV (%) | 5.25 | 3.36 | 3.12 | 0.82 | 4.90 | 8.55 | |
| ESW40 | beta (SE) | −0.361 (0.050) | 0.320 (0.050) | 0.349 (0.049) | −0.264 (0.050) | 0.347(0.051) | - |
| CPV (%) | 7.21 | 4.79 | 5.67 | 3.08 | 4.78 | 12.5 | |
| ESW44 | beta (SE) | −0.285 (0.046) | 0.280 (0.052) | 0.302 (0.049) | −0.265 (0.051) | 0.291(0.051) | - |
| CPV (%) | 8.06 | 3.37 | 3.97 | 2.92 | 6.08 | 11.17 | |
| ESW48 | beta (SE) | −0.286 (0.051) | 0.228 (0.056) | 0.297 (0.053) | −0.195 (0.055) | 0.285(0.056) | - |
| CPV (%) | 7.31 | 2.33 | 4.26 | 1.71 | 4.93 | 8.45 | |
| ESW52 | beta (SE) | −0.321 (0.051) | 0.220(0.056) | 0.292 (0.053) | −0.179 (0.055) | 0.298(0.055) | - |
| CPV (%) | 7.51 | 2.21 | 3.86 | 1.31 | 7.77 | 18.54 | |
| ESW56 | beta (SE) | −0.333 (0.050) | 0.251 (0.053) | 0.297 (0.021) | −0.124 (0.053) | 0.269(0.053) | - |
| CPV (%) | 6.8 | 2.81 | 4.13 | 0.52 | 7.44 | 15.25 | |
| ESW60 | beta (SE) | −0.368 (0.054) | 0.276 (0.052) | 0.295 (0.049) | −0.215 (0.051) | 0.291(0.052) | - |
| CPV (%) | 6.64 | 3.53 | 4.11 | 2.01 | 5.74 | 13.77 | |
| ESW66 | beta (SE) | −0.388 (0.046) | 0.252 (0.055) | 0.316 (0.052) | −0.234 (0.053) | 0.316(0.054) | - |
| CPV (%) | 8.73 | 2.86 | 4.82 | 2.37 | 5.86 | 10.15 | |
| ESW72 | beta (SE) | −0.382 (0.047) | 0.252 (0.056) | −0.332 (0.053) | −0.211 (0.055) | 0.292(0.056) | - |
| CPV (%) | 8.12 | 2.92 | 5.19 | 1.94 | 6.90 | 15.14 | |
| EST40 | beta (SE) | −0.361(0.054) | 0.245(0.052) | 0.236(0.05) | −0.158(0.051) | 0.198(0.053) | - |
| CPV (%) | 5.33 | 2.78 | 2.67 | 1.07 | 3.98 | 5.56 | |
| EST44 | beta (SE) | −0.313(0.049) | 0.211(0.051) | 0.225(0.048) | −0.236(0.049) | 0.222(0.049) | - |
| CPV (%) | 4.87 | 2.01 | 2.27 | 2.48 | 3.42 | 6.15 | |
| EST48 | beta (SE) | −0.291(0.053) | 0.19(0.054) | 0.2(0.052) | −0.141(0.053) | 0.199(0.053) | - |
| CPV (%) | 4.22 | 1.62 | 1.86 | 0.86 | 4.55 | 5.44 | |
| EST52 | beta (SE) | −0.308(0.051) | 0.2(0.054) | 0.196(0.05) | −0.141(0.052) | 0.168(0.052) | - |
| CPV (%) | 4.63 | 1.75 | 1.77 | 0.81 | 4.18 | 5.51 | |
| EST56 | beta (SE) | −0.312(0.047) | 0.222(0.05) | 0.234(0.048) | −0.19(0.049) | 0.181(0.05) | - |
| CPV (%) | 4.81 | 2.21 | 2.68 | 1.65 | 5.33 | 5.61 | |
| EST60 | beta (SE) | −0.387(0.051) | 0.245(0.053) | 0.267(0.05) | −0.25(0.051) | 0.212(0.052) | - |
| CPV (%) | 7.01 | 2.72 | 3.42 | 2.84 | 4.21 | 6.92 | |
| EST66 | beta (SE) | −0.269(0.047) | 0.203(0.052) | 0.201(0.048) | −0.178(0.049) | 0.171(0.05) | - |
| CPV (%) | 3.49 | 1.74 | 1.87 | 1.33 | 4.63 | 4.12 | |
| EST72 | beta (SE) | −0.339(0.05) | 0.165(0.054) | 0.237(0.05) | −0.25(0.051) | 0.217(0.052) | - |
| CPV (%) | 5.86 | 1.21 | 2.77 | 3.04 | 4.02 | 5.35 | |
| ESS32 | beta (SE) | −0.253(0.048) | 0.172(0.049) | 0.129(0.047) | −0.128(0.047) | 0.126(0.048) | - |
| CPV (%) | 3.18 | 1.28 | 0.74 | 0.73 | 2.65 | 2.95 | |
| ESS40 | beta (SE) | −0.361(0.05) | 0.245(0.05) | 0.264(0.048) | −0.193(0.049) | 0.267(0.05) | - |
| CPV (%) | 6.56 | 2.80 | 3.55 | 1.73 | 4.82 | 6.59 | |
| ESS44 | beta (SE) | −0.285(0.046) | 0.189(0.049) | 0.185(0.047) | −0.165(0.048) | 0.187(0.048) | - |
| CPV (%) | 4.04 | 1.57 | 1.63 | 1.21 | 2.43 | 4.11 | |
| ESS48 | beta (SE) | −0.286(0.051) | 0.152(0.054) | 0.149(0.051) | −0.129(0.052) | 0.183(0.052) | - |
| CPV (%) | 4.16 | 0.96 | 1.04 | 0.78 | 3.56 | 4.22 | |
| ESS52 | beta (SE) | −0.321(0.051) | 0.169(0.054) | 0.241(0.05) | −0.17(0.052) | 0.224(0.052) | - |
| CPV (%) | 5.30 | 1.20 | 2.97 | 1.39 | 5.62 | 5.26 | |
| ESS56 | beta (SE) | −0.333(0.05) | 0.217(0.052) | 0.207(0.05) | −0.142(0.051) | 0.21(0.052) | - |
| CPV (%) | 5.64 | 2.18 | 2.13 | 0.92 | 6.10 | 5.56 | |
| ESS60 | beta (SE) | −0.368(0.054) | 0.303(0.06) | 0.318(0.055) | −0.233(0.058) | 0.227(0.058) | - |
| CPV (%) | 6.70 | 4.09 | 4.68 | 2.29 | 11.52 | 16.12 | |
| ESS66 | beta (SE) | −0.388(0.046) | 0.226(0.052) | 0.25(0.048) | −0.229(0.049) | 0.304(0.049) | - |
| CPV (%) | 7.59 | 2.31 | 3.15 | 2.43 | 5.86 | 6.06 | |
| ESS72 | beta (SE) | −0.382(0.047) | 0.26(0.053) | 0.271(0.049) | −0.239(0.051) | 0.235(0.051) | - |
| CPV (%) | 7.35 | 3.06 | 3.62 | 2.70 | 5.16 | 6.75 | |
EA effect allele (minor allele), AA alternative allele (major allele), MAF minor allele frequency, CPV contribution to phenotypic variance (%), ESW32, ESW40, ESW44, ESW48, ESW52, ESW56, ESW60 eggshell weights of 32, 40, 44, 48, 52, 56, 60, 66, 72 weeks of age
aEstimated allelic substitution effect per copy of the effect allele (EA); SE standard error of the beta bBeta means the effect size of minor alleles. Positive/negative effect size value means that the substitution of major allele to minor allele can lead to heavier/lighter yolk or ovary weight