Table 1.
Phenotypic descriptive statistics and genetic analysis of the oviduct.
Fig 1.
Manhattan (left) and Q–Q plots (right) of the observed P -values for oviduct traits.
The Manhattan plot shows P values for the association of SNPs (y-axis) plotted against their chromosomal positions (x-axis). The black and green lines depict genome-wide significant (8.43 × 10−7) and suggestive significant (1.69 × 10−5) thresholds, respectively. For the Q–Q plot, the x-axis indicates the expected −log10-transformed P values, and the y-axis shows the observed −log10-transformed P-values. The genomic inflation factors (λ) are shown at the top left of the Q–Q plots.
Fig 2.
Venn diagram illustrating SNPs on GGA1 that are associated significantly with OW and OL.
Table 2.
Number and distribution of significant SNPs for oviduct traits.
Fig 3.
Linkage analysis of the SNPs on GGA1, GGA4, GGA8, and GGA2 Plots A, B, C, and D show the linkage analysis for the SNPs on GGA1, GGA4, GGA8, and GGA2, respectively.
Table 3.
Contributions of five mutations and genomic regions to oviduct trait.
Fig 4.
Genotype effect plot of rs318027552 for oviduct traits and egg quality.
Plots A and B describe the OL and OW phenotypes, respectively, of the three genotypes at rs318027552. Plots C, D, and E describe the phenotypes of egg quality phenotypes, including albumen height, albumen weight, and eggshell weight, respectively, of the three genotypes at rs318027552.
Fig 5.
Genome partitioning of OW using a joint analysis.
A. The estimated proportion of variance captured by each chromosome relative to its size. Solid lines are shown for linear regressions. The characters in circles are the chromosome numbers. B. Contributions of the GWAS SNPs partitioned by chromosome. The whole bars indicate the estimates of variance explained by each chromosome, of which the three gray bars represent the same values for the three leading loci.