Genome‐wide detection ofCNVs associated with beak deformity in chickens using high‐density 600KSNParrays

Abstract

Beak deformity (crossed beaks) is found in several indigenous chicken breeds including Beijing-You studied here. Birds with deformed beaks have reduced feed intake and poor production performance. Recently, copy number variation (CNV) has been examined in many species and is recognized as a source of genetic variation, especially for disease phenotypes. In this study, to unravel the genetic mechanisms underlying beak deformity, we performed genome-wide CNV detection using Affymetrix chicken high-density 600K data on 48 deformed-beak and 48 normal birds using penncnv. As a result, two and eight CNV regions (CNVRs) covering 0.32 and 2.45 Mb respectively on autosomes were identified in deformed-beak and normal birds respectively. Further RT-qPCR studies validated nine of the 10 CNVRs. The ratios of six CNVRs were significantly different between deformed-beak and normal birds (P < 0.01). Within these six regions, three and 21 known genes were identified in deformed-beak and normal birds respectively. Bioinformatics analysis showed that these genes were enriched in six GO terms and one KEGG pathway. Five candidate genes in the CNVRs were further validated using RT-qPCR. The expression of LRIG2 (leucine rich repeats and immunoglobulin like domains 2) was lower in birds with deformed beaks (P < 0.01). Therefore, the LRIG2 gene could be considered a key factor in view of its known functions and its potential roles in beak deformity. Overall, our results will be helpful for future investigations of the genomic structural variations underlying beak deformity in chickens.

Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

“…Moreover, mutations in RET are also associated with the disorders such as multiple endocrine neoplasia, type IIA, multiple endocrine neoplasia, type IIB, Hirschsprung disease, and medullary thyroid carcinoma [ 44 ]. In addition, its interacting gene, LRIG2 , was also identified as one of the most promising candidate genes underlying this trait in our previous CNV study within the same genotyped data used here [ 45 ]. Thus, the RET and LRIG2 genes might jointly contribute to the development of deformed beaks.…”

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

“…Following the first two genome-wide scans for CNVs in human genome [7,8], a large number of CNV detection studies have been performed, which revealed that CNVs are ubiquitously distributed in genome and can influence the phenotype via regulations of gene expression and gene dosage [9][10][11]. Besides, numerous studies in other species have also shown that CNVs contributed to phenotypic variation of complex diseases and traits [12][13][14][15][16][17][18][19], including MD in chicken [20][21][22]. Two major traditional platforms employed in CNV detection are based on SNP chips, one is known as comparative genomic hybridization (CGH) array, and the other is SNP genotyping array.…”

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing

“…Following the rst two genome-wide scans for CNVs in human genome [7,8], an large number of CNV detection studies have been performed, which revealed that CNVs are ubiquitously distributed in the genome and can in uence the phenotype via regulations of gene expression and gene dosage [9][10][11]. Besides, numerous studies in other species have also shown that CNVs contributed to phenotypic variation of complex diseases and traits [12][13][14][15][16][17][18][19], including MD in chicken [20][21][22]. Two major traditional platforms employed in CNV detection are based on SNP chips, one is known as comparative genomic hybridization (CGH) array, and the other is SNP genotyping array.…”