Table 3. Genome-wide association analyses for yolk weight (YW) and follicle weight (FW).
| Traits | SNP ID | Chr | Position | Candidate genes /Nearest Gene | Location | Minor/Majorallele | MAF | N | Effect size a (s.e.m.) | CPV(%) | P value |
|---|---|---|---|---|---|---|---|---|---|---|---|
| FYW | rs313187645 | 5 | 40106943 | DOT1L | intron | A/G | 0.307 | 1,494 | 0.293(0.047) | 3.47 | 5.00E-10 |
| FYW | rs312299419 | 5 | 40167320 | STON2 | intron | T/G | 0.277 | 1,494 | -0.294(0.049) | 3.34 | 2.16E-09 |
| FYW | rs314422825 | 5 | 40194495 | STON2 | exon(missense) | A/G | 0.333 | 1,494 | -0.269(0.046) | 3.18 | 4.61E-09 |
| FYW | rs315568325 | 5 | 42130216 | GALC | downstream_1,172bp | T/C | 0.288 | 1,494 | -0.266(0.048) | 2.80 | 4.08E-08 |
| YW40 | rs16187384 | 23 | 1456741 | RPA2 | Intron | A/G | 0.493 | 1,476 | -0.241(0.044) | 2.77 | 3.76E-08 |
| YW48 | rs313116098 | 1 | 173851584 | BRCA2/ZAR1 | exon/downstream_2,140bp | A/G | 0.298 | 1,226 | 0.242(0.049) | 2.48 | 8.61E-07 |
| YW56 | rs316715137 | 3 | 22975753 | EML4/KCNG3 | intron/downstream_267kb | A/G | 0.291 | 1,348 | -0.263(0.049) | 2.61 | 7.79E-08 |
| YW56 | rs314923267 | 3 | 22971805 | EML4/ KCNG3 | intron/downstream_267kb | T/C | 0.277 | 1,348 | 0.256(0.051) | 2.40 | 6.57E-07 |
| YW66 | rs312474469 | 28 | 3667179 | ELL | intron | T/C | 0.177 | 1,304 | 0.289(0.057) | 2.49 | 4.91E-07 |
| YW66 | rs315213484 | 28 | 3665094 | ELL | upstream_1,134bp | A/C | 0.178 | 1,304 | 0.286(0.057) | 2.47 | 6.95E-07 |
| YW72 | rs312274422 | 3 | 79252286 | ENSGALG00000028314 | downstream_80,003bp | T/G | 0.280 | 1,253 | -0.278(0.050) | 2.79 | 3.53E-08 |
| YW72 | rs312873273 | 17 | 1366852 | RGS3 | intron | C/G | 0.213 | 1,253 | -0.298(0.058) | 2.89 | 3.73E-07 |
| FW | rs14920313 | 1 | 172060693 | DCLK1/SPG20 | intron/upstream_7.3kb | T/C | 0.249 | 1,450 | -0.261(0.051) | 2.60 | 1.09E-07 |
| FW | rs14920355 | 1 | 172084219 | DCLK1 | intron | T/C | 0.246 | 1,450 | -0.257(0.051) | 2.42 | 3.00E-08 |
| FW | rs313140585 | 1 | 172453837 | NBEA/STARD13 | intron/upstream_47.7kb | T/C | 0.277 | 1,450 | -0.242(0.048) | 2.50 | 3.88E-07 |
Abbreviations: Chr = chromosome; CPV = contribution to phenotype variance; FW = follicle weight; FYW = first yolk weight; MAF = minor allele frequency; N = number of samples; SNP = single nucleotide polymorphism; YW40,48,56,66, and 72 = yolk weights of 40,48,56,66,and 72 weeks, respectively.
a Effect size means the effect 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.