A new chicken 55K SNP genotyping array

• Published in: BMC genomics Vol. 20; no. 1; pp. 410 - 12
• Main Authors: Liu, Ranran, Xing, Siyuan, Wang, Jie, Zheng, Maiqing, Cui, Huanxian, Crooijmans, Richard P M A, Li, Qinghe, Zhao, Guiping, Wen, Jie
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 22-05-2019; BioMed Central; BMC
• Subjects: Animal husbandry; Animals; Arrays; Bioinformatics; Breeding; Chicken; Chicken breeds; Chickens; Chickens - genetics; Commercial line; Density; DNA microarrays; Farms; Gene frequency; Genes; Genetic analysis; Genetic aspects; Genetic Markers; Genetic research; Genome; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomics; Genomics - methods; Genotyping; Genotyping array; Growth rate; Identification and classification; Innovations; Livestock breeding; Meat; Meat - analysis; Meat industry; Methodology; Multiple criterion; Oligonucleotide Array Sequence Analysis; Phenotype; Polymorphism, Single Nucleotide; Population studies; Poultry; Poultry breeding; Single nucleotide polymorphisms; Single-nucleotide polymorphism; SNP; China; Commercial line; Genotyping array; Chicken; SNP
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-019-5736-8

China has the richest local chicken breeding resources in the world and is the world's second largest producer of meat-type chickens. Development of a moderate-density SNP array for genetic analysis of chickens and breeding of meat-type chickens taking utility of those resources is urgently needed for conventional farms, breeding industry, and research areas.
Eight representative local breeds or commercial broiler lines with 3 pools of 48 individuals within each breed/line were sequenced and supplied the major SNPs resource. There were 7.09 million - 9.41 million SNPs detected in each breed/line. After filtering using multiple criteria such as preferred incorporation of trait-related SNPs and uniformity of distribution across the genome, 52.18 K SNPs were selected in the final array. It consists of: (i) 19.22 K SNPs from the genomes of yellow-feathered, cyan-shank partridge and white-feathered chickens; (ii) 5.98 K SNPs related to economic traits from the Illumina 60 K SNP Bead Chip, which were found as significant associated SNPs with 15 traits in a Beijing-You crossed Cobb F2 resource population by genome-wide association study analysis; (iii) 7.63 K SNPs from 861 candidate genes of economic traits; (iv) the 0.94 K SNPs related to residual feed intake; and (v) 18.41 K from chicken SNPdb. The polymorphisms of 9 extra local breeds and 3 commercial lines were examined with this array, and 40 K - 47 K SNPs were polymorphic (with minor allele frequency > 0.05) in those breeds. The MDS result showed that those breeds can be clearly distinguished by this newly developed genotyping array.
We successfully developed a 55K genotyping array by using SNPs segregated from typical local breeds and commercial lines. Compared to the existing Affy 600 K and Illumina 60 K arrays, there were 21,41 K new SNPs included on our Affy 55K array. The results of the 55K genotyping data can therefore be imputed to high-density SNPs genotyping data. The array offers a wide range of potential applications such as genomic selection breeding, GWAS of interested traits, and investigation of diversity of different chicken breeds.