Abstract
Artificial selection is often associated with numerous changes in seemingly unrelated phenotypic traits. The genetic mechanisms of correlated phenotypes probably involve pleiotropy or linkage of genes related to such phenotypes. Dongxiang blue-shelled chicken, an indigenous chicken breed of China, has segregated significantly for the dermal hyperpigmentation phenotype. Two lines of the chicken have been divergently selected with respect to comb color for over 20 generations. The red comb line chicken produces significantly higher number of eggs than the dark comb line chicken. The objective of this study was to explore potential mechanisms involved in the relationship between comb color and egg production among chickens. Based on the genome-wide association study results, we identified a genomic region on chromosome 20 involving EDN3 and BMP7, which is associated with hyperpigmentation of chicken comb. Further analyses by selection signatures in the two divergent lines revealed that several candidate genes, including EDN3, BMP7, BPIFB3, and PCK1, closely located on chromosome 20 are involved in the development of neural crest cell and reproductive system. The two genes EDN3 and BMP7 have known roles in regulating both ovarian function and melanogenesis, indicating the pleiotropic effect on hyperpigmentation and egg production in blue-shelled chickens. Association analysis for egg production confirmed the pleiotropic effect of selected loci identified by selection signatures. The study provides insights into phenotypic evolution due to genetic variation across the genome. The information might be useful in the current breeding efforts to develop improved breeds for egg production.
Highlights
Domestication is the strongest type of directional selection, resulting in the accumulation of numerous phenotypic variations in animals
The results revealed that the number of eggs produced by red comb line (RCL) was significantly higher than that by dark comb line (DCL), almost throughout the laying period (P < 0.001) (Figure 2A)
We found that bone morphogenetic protein 7 (BMP7) and bone morphogenetic protein receptor type 2 (BMPR2) are involved in the Gene Ontology (GO) biological process (BP) category “reproductive system development” (GO: 0061458) (P = 6.89 E-4); BMP7 and PCK1 are involved in the “cellular response to steroid hormone stimulus” (GO: 0071383) (P = 1.92E-3) and “cellular response to hormone stimulus” (GO: 0032870) (P = 7.19E-3)
Summary
Domestication is the strongest type of directional selection, resulting in the accumulation of numerous phenotypic variations in animals. During the last two decades, numerous genetic bases of traits accounting for the causative mutation of interesting phenotypes in domestic animals have been deciphered (Andersson and Georges, 2004). It has been reported that vibrant appearance represents the physiognomy and relates to development, health, and Pleiotropism of Genes in Chicken production traits. Such changes in unrelated phenotypes are potentially caused by pleiotropy or linkage between independent genetic architectures (Wright et al, 2010). Spurious pleiotropy is where the causal variants in different genes are in strong linkage disequilibrium (Hodgkin, 1998; Solovieff et al, 2013). Genome-wide association studies (GWASs) on human complex diseases (Solovieff et al, 2013; Pickrell et al, 2016) and livestock traits have revealed that pleiotropy is common in vertebrates (Rosengren Pielberg et al, 2008; Johnsson et al, 2012; Curik et al, 2013; Johnsson et al, 2014)
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