A new chicken 55K SNP genotyping array

BMC Genomics

Qinghe Li¹  Jie Wang¹  Ranran Liu¹  Huanxian Cui¹  Maiqing Zheng¹  Siyuan Xing²  Guiping Zhao³  Jie Wen³  Richard P. M. A. Crooijmans⁴ 

[1]0000 0001 0526 1937, grid.410727.7, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, 100193, Beijing, People’s Republic of China

[2]0000 0001 0526 1937, grid.410727.7, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, 100193, Beijing, People’s Republic of China

[3]0000 0001 0791 5666, grid.4818.5, Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands

[4]0000 0001 0526 1937, grid.410727.7, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, 100193, Beijing, People’s Republic of China

[5]0000 0004 0369 6250, grid.418524.e, State Key Laboratory of Animal Nutrition, Ministry of Agriculture and Rural Affairs, 100193, Beijing, People’s Republic of China

[6]0000 0004 0369 6250, grid.418524.e, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, 100193, Beijing, People’s Republic of China

[7]0000 0001 0791 5666, grid.4818.5, Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands

关键词: Chicken;    Commercial line;    Genotyping array;    SNP;   

DOI  :  10.1186/s12864-019-5736-8

来源: publisher

【 摘 要 】

BackgroundChina 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.ResultsEight 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.ConclusionsWe 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.

【 授权许可】

CC BY