Figures 1 and 2 show examples of the deformed and normal beaks of BJY chickens. According to our previous investigations, a frequency of beak deformity (normally the lower mandible crossed left or right randomly) of 1 to 3% was found in several indigenous chickens, including Silkies, Huxu, and Beijing-You (BJY) chickens. However, for most bird species, especially for poultry, crossed beaks represent a malformation or an abnormality. For example, crossbill species like Loxia are characterized by the mandibles with crossed beaks, which is an adaptation enabling them to extract seeds from the cones they live on. It also has differentuses because of its diversity in shape between bird species. In a similar way to lips and teeth in mammals, the beak functions in birds primarily for feeding and drinking. The beak is an external anatomical structure of birds, which consists of an upper and a lower mandible. Potentially useful candidate genes and pathways for beak deformity were identified, which should be the subject of further functional characterization. The pathway-based association study highlighted the association of six pathways with beak deformity, including the calcium signaling pathway. Four high-confidence genes, LOC421892, TDRD3, RET, and STMN1, were identified as the most promising candidate genes underlying this complex trait in view of their positions, functions, and overlaps with previous studies. The single SNP-based association study identified one associated SNP with 5% genome-wide significance and seven suggestively associated SNPs. The P-value was corrected by a Bonferroni adjustment based on linkage disequilibrium pruning. As a result, 95 individuals and 429,539 SNPs were obtained after quality control. A total of 48 birds with deformed beaks (case) and 48 normal birds (control) were genotyped using Affymetrix 600 K HD genotyping arrays.
In this study, single SNP- and pathway-based genome-wide association studies (GWASs) were performed using ROADTRIPS and SNP ratio test (SRT), respectively. Although previous studies shed some light on the genetic regulation of this complex trait, the genetic basis of this malformation remains incompletely understood.
Beak deformity severely impairs the birds’ growth and welfare. Beak deformity, typically expressed as the crossing of upper and lower mandibles, is found in several indigenous chicken breeds, including the Beijing-You chickens studied here.
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