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.

Exploring the genetic architecture of feed efficiency traits in chickens

“…Li et al 38 showed that additive model and the combined additive and dominance models produced the majority of significant SNPs in feed-related traits. Recently, Darwish et al 39 demonstrated for eggshell blueness chickens that the contribution of genotypic effects of some SNPs were further divided into additive and dominant effects depending on the trait.…”

Genetic effect on free amino acid contents of egg yolk and albumen using five different chicken genotypes under floor rearing system

“…Using varieties of chicken genotypes, significant effects on genetic differences were found in yolk and albumen free amino acid contents. Until now, genome-wide association study (GWAS) and quantitative trait locus (QTL) mappings have been performed for egg traits such as egg weight, eggshell color, yolk size, and albumen height for identifying genetic variants [10][11][12][13][14]. However, there are few reports of GWAS and QTL studies for egg yolk and albumen amino acid traits so far [17].…”

“…Egg traits such as egg weight, eggshell color, yolk size, albumen height [10][11][12][13][14], and ingredients of yolk and albumen [15][16][17] are fairly influenced by genetic factors. Therefore, eggs from several breeds may express a large variation in the appearance of eggs and contents of yolk and albumen caused by differences in genetic background.…”

Parâmetros genéticos de características de produção e qualidade de ovos em linhagens nacionais de galinhas caipiras

“…A cor azul da casca dos ovos exibe uma herança autossômica dominante e os ovos postos por aves homozigotas são mais azuis do que os ovos de heterozigotos . O gene autossômico dominante relacionado à cor azul da casca do ovo foi denominado Oocyan (locus O) e mapeado no braço curto do cromossomo 1 a uma distância de 2,3 cM do vírus endógeno da leucose aviária (ALEV1) (Bartlett et al, 1996;Bitgood et al, 2000 (Darwish et al, 2019;.…”

“…Darwish et al (2019) identificaram uma região de 653,819 Kb no cromossomo 21 da galinha que está associada com características de intensidade da cor da casca do ovo. Esta região genômica contém os genes candidatos AJAP1, C1ORF174, CAMTA1, CEP104 e TNFRSF9, que foram significativamente associados a galinhas de ovos com casca azul escuro e azul claro.…”