Genome wide association study on feed conversion ratio using imputed sequence data in chickens

• Published in: Animal bioscience Vol. 32; no. 4; pp. 494 - 500
• Main Authors: Wang, Jiaying, Yuan, Xiaolong, Ye, Shaopan, Huang, Shuwen, He, Yingting, Zhang, Hao, Li, Jiaqi, Zhang, Xiquan, Zhang, Zhe
• Format: Journal Article
• Language: English
• Published: Korea (South) Asian - Australasian Association of Animal Production Societies 01.04.2019; Asian-Australasian Association of Animal Production Societies (AAAP) and Korean Society of Animal Science and Technology (KSAST); Asian-Australasian Association of Animal Production Societies; 아세아·태평양축산학회
• Subjects: Calcium binding proteins; Calmodulin; Chicken; Chickens; DNA binding proteins; Feed Conversion Ratio; Feed utilization efficiency; Genes; Genetic polymorphisms; Genetic research; Genome-wide association studies; Genome-wide Association Study (GWAS); Genomes; Genomics; Hydrolases; Imputed Whole Sequence Data; Legal fees; Manufacturing costs; Membrane proteins; Poultry industry; Quantitative genetics; Single nucleotide polymorphisms; Transcription (Genetics); Ubiquitin; 축산학; China; Chicken; Feed Conversion Ratio; Genome-wide Association Study (GWAS); Imputed Whole Sequence Data
• ISSN: 1011-2367; 2765-0189; 1976-5517; 2765-0235
• DOI: 10.5713/ajas.18.0319

Feed consumption contributes a large percentage for total production costs in the poultry industry. Detecting genes associated with feeding traits will be of benefit to improve our understanding of the molecular determinants for feed efficiency. The objective of this study was to identify candidate genes associated with feed conversion ratio (FCR) via genome-wide association study (GWAS) using sequence data imputed from single nucleotide polymorphism (SNP) panel in a Chinese indigenous chicken population. A total of 435 Chinese indigenous chickens were phenotyped for FCR and were genotyped using a 600K SNP genotyping array. Twenty-four birds were selected for sequencing, and the 600K SNP panel data were imputed to whole sequence data with the 24 birds as the reference. The GWAS were performed with GEMMA software. After quality control, 8,626,020 SNPs were used for sequence based GWAS, in which ten significant genomic regions were detected to be associated with FCR. Ten candidate genes, ubiquitin specific peptidase 44, leukotriene A4 hydrolase, ETS transcription factor, R-spondin 2, inhibitor of apoptosis protein 3, sosondowah ankyrin repeat domain family member D, calmodulin regulated spectrin associated protein family member 2, zinc finger and BTB domain containing 41, potassium sodium-activated channel subfamily T member 2, and member of RAS oncogene family were annotated. Several of them were within or near the reported FCR quantitative trait loci, and others were newly reported. Results from this study provide valuable prior information on chicken genomic breeding programs, and potentially improve our understanding of the molecular mechanism for feeding traits.