Consistency of linkage disequilibrium between Chinese and Nordic Holsteins and genomic prediction for Chinese Holsteins using the joint reference population

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

Dokumenter

DOI

  • Lei Zhou, Danmark
  • Xiandong Ding, College of Animal Science and Technology, China Agricultural University, Kina
  • Qin Zhang, College of Animal Science and Technology, China Agricultural University, Kina
  • Yachun Wang, College of Animal Science and Technology, China Agricultural University, Kina
  • Mogens Sandø Lund
  • Guosheng Su
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.
OriginalsprogEngelsk
Artikelnummer7
TidsskriftGenetics Selection Evolution
Vol/bind45
Nummer1
Antal sider7
ISSN0999-193X
DOI
StatusUdgivet - 21 mar. 2013

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