A new chicken 55K SNP genotyping array

  • Ranran Liu (Creator)
  • Siyuan Xing (Chinese Academy of Agricultural Sciences (CAAS) (Creator)
  • Jie Wang (Creator)
  • Maiqing Zheng (Creator)
  • Huanxian Cui (Creator)
  • Richard Crooijmans (Creator)
  • Qinghe Li (Creator)
  • Guiping Zhao (Creator)
  • Jie Wen (Creator)



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. Results 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. Conclusions 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.
Date made available22 Mar 2019
PublisherWageningen University and Research


  • Chicken
  • Commercial line
  • Genotyping array
  • SNP
  • A new chicken 55K SNP genotyping array

    Liu, R., Xing, S., Wang, J., Zheng, M., Cui, H., Crooijmans, R. P. M. A., Li, Q., Zhao, G. & Wen, J., 22 May 2019, In: BMC Genomics. 20, 1, 1 p.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    22 Citations (Scopus)

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