Genome-wide association study and a post replication analysis revealed a promising genomic region and candidate genes for chicken eggshell blueness

Abstract

The eggshell blueness is an interesting object for chicken genetic studies and blue-shelled chicken industry, especially after the discovery of the causative mutation of chicken blue eggshell. In the present study, genome wide association study (GWAS) was conducted in Chinese Dongxiang blue-shelled chicken underlying four traits of blue eggshell pigments: quantity of biliverdin (QB), quantity of protoporphyrin (QP), quantity of total pigment (QT), and color density trait (CD). A total of 139 individuals were randomly collected for GWAS. We detected two SNPs in genome-wise significance and 35 in suggestive significance, 24 out of the 37 SNP were located either within intron/exon or near 15 genes in a range of ~1.17 Mb on GGA21. For further confirmation of the identified SNP loci by GWAS, the follow-up replication studies were performed in two populations. A total of 146 individuals of the second generation derived from the former GWAS population, as well as 280 individuals from an alternative independent population were employed for genotyping by MALDI-TOF MS in a genotype-phenotype association study. Eighteen SNPs evenly distributed on the GGA21 significant region were successfully genotyped in the two populations, of which 4 and 6 SNP loci were shown significantly associated with QB, QT and QP in the two repeat populations, respectively. Further, the SNPs were narrowed down to a region of ~ 653.819 Kb on GGA21 that harbors five candidate genes: AJAP1, TNFRSF9, C1ORF174, CAMTA1, and CEP104. Shell gland of chickens laying dark and light blue eggshell was chosen for detection of mRNA expression of the five candidate genes. The results showed differential expression levels of these genes in the two groups. The specific function of these genes has not yet been defined clearly in chickens and further in-depth studies are needed to explore the new functional role in chicken eggshell blueness.

Fig 1

Manhattan plot (left) and quantile-quantile plot (right) of the observed P-values for QB (A), QP (B), QT (C) and CD (D). In Manhattan plot, the red and gray horizontal lines indicate the genome-wise significance threshold [-log10 (5.135E-07)] and suggestive significance threshold [-log10 (1.027E-05)], respectively.

Fig 2. The haplotype blocks and linkage disequilibrium.

(A) the N146 population, (B) the N280 population. The darker shading indicates higher linkage disequilibrium and the number within rhombus was D' value.

Fig 3. Expression levels of the five candidate genes AJAP1, CAMTA1, CEP104, TNFRSF9, and C1ORF174 in dark and light blue-shelled chickens.

(A) the N146 population, (B) the N280 population. Note error bars represent the mean ± SE. * denote the difference of expression level with significant difference (P < 0.05). ** denote the difference of expression level with significant difference (P < 0.01).