title: Consistency of linkage disequilibrium between Chinese and Nordic Holsteins and genomic prediction for Chinese Holsteins using a joint reference population.
abstract: BACKGROUND
  In China, the reference population of genotyped Holstein cattle is relatively small with to date, 80 bulls and 2091 cows genotyped with the Illumina 54 K chip. Including genotyped Holstein cattle from other countries in the reference population could improve the accuracy of genomic prediction of the Chinese Holstein population. This study investigated the consistency of linkage disequilibrium between adjacent markers between the Chinese and Nordic Holstein populations, and compared the reliability of genomic predictions based on the Chinese reference population only or the combined Chinese and Nordic reference populations.
  
  
  METHODS
  Genomic estimated breeding values of Chinese Holstein cattle were predicted using a single-trait GBLUP model based on the Chinese reference dataset, and using a two-trait GBLUP model based on a joint reference dataset that included both the Chinese and Nordic Holstein data.
  
  
  RESULTS
  The extent of linkage disequilibrium was similar in the Chinese and Nordic Holstein populations and the consistency of linkage disequilibrium between the two populations was very high, with a correlation of 0.97. Genomic prediction using the joint versus the Chinese reference dataset increased reliabilities of genomic predictions of Chinese Holstein bulls in the test data from 0.22, 0.15 and 0.11 to 0.51, 0.47 and 0.36 for milk yield, fat yield and protein yield, respectively. Using five-fold cross-validation, reliabilities of genomic predictions of Chinese cows increased from 0.15, 0.12 and 0.15 to 0.26, 0.17 and 0.20 for milk yield, fat yield and protein yield, respectively.
  
  
  CONCLUSIONS
  The linkage disequilibrium between the two populations was very consistent and using the combined Nordic and Chinese reference dataset substantially increased reliabilities of genomic predictions for Chinese Holstein cattle.
authors.affiliation: Department of Molecular Biology and Genetics, Aarhus University, Tjele DK-8830, Denmark.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhou
authors.forename: Xiangdong
authors.initials: X
authors.lastname: Ding
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.forename: Yachun
authors.initials: Y
authors.lastname: Wang
authors.forename: Mogens S
authors.initials: MS
authors.lastname: Lund
authors.forename: Guosheng
authors.initials: G
authors.lastname: Su
mesh_terms: D000818:Animals; D017849:Animals, Inbred Strains; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D016678:Genome; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D011153:Population / Q000235:genetics; D019655:Quantitative Trait, Heritable