Genomic prediction based on a joint reference population for the Xinjiang Brown cattle

Menghua Zhang; Lei Xu; Haibo Lu; Hanpeng Luo; Jinghang Zhou; Dan Wang; Xiaoxue Zhang; Xixia Huang; Yachun Wang

doi:10.3389/fgene.2024.1394636

Genomic prediction based on a joint reference population for the Xinjiang Brown cattle

Front Genet. 2024 Apr 26:15:1394636. doi: 10.3389/fgene.2024.1394636. eCollection 2024.

Authors

Menghua Zhang¹, Lei Xu¹, Haibo Lu², Hanpeng Luo², Jinghang Zhou³, Dan Wang¹, Xiaoxue Zhang¹, Xixia Huang¹, Yachun Wang²

Affiliations

¹ College of Animal Science, Xinjiang Agricultural University, Urumqi, China.
² Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
³ Shijiazhuang Molbreeding Biotechnology Co., Ltd., Shijiazhuang, China.

Abstract

Introduction: Xinjiang Brown cattle constitute the largest breed of cattle in Xinjiang. Therefore, it is crucial to establish a genomic evaluation system, especially for those with low levels of breed improvement. Methods: This study aimed to establish a cross breed joint reference population by analyzing the genetic structure of 485 Xinjiang Brown cattle and 2,633 Chinese Holstein cattle (Illumina GeneSeek GGP bovine 150 K chip). The Bayes method single-step genome-wide best linear unbiased prediction was used to conduct a genomic evaluation of the joint reference population for the milk traits of Xinjiang Brown cattle. The reference population of Chinese Holstein cattle was randomly divided into groups to construct the joint reference population. By comparing the prediction accuracy, estimation bias, and inflation coefficient of the validation population, the optimal number of joint reference populations was determined. Results and Discussion: The results indicated a distinct genetic structure difference between the two breeds of adult cows, and both breeds should be considered when constructing multi-breed joint reference and validation populations. The reliability range of genome prediction of milk traits in the joint reference population was 0.142-0.465. Initially, it was determined that the inclusion of 600 and 900 Chinese Holstein cattle in the joint reference population positively impacted the genomic prediction of Xinjiang Brown cattle to certain extent. It was feasible to incorporate the Chinese Holstein into Xinjiang Brown cattle population to form a joint reference population for multi-breed genomic evaluation. However, for different Xinjiang Brown cattle populations, a fixed number of Chinese Holstein cattle cannot be directly added during multi-breed genomic selection. Pre-evaluation analysis based on the genetic structure, kinship, and other factors of the current population is required to ensure the authenticity and reliability of genomic predictions and improve estimation accuracy.

Keywords: Xinjiang Brown cattle; bayes; genomic prediction; multi-breed; single-step GBLUP.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work was funded by the Xinjiang Uygur Autonomous Region Science and technology Aid Xinjiang Project (Grant No. 2018E02052), The Xinjiang Uygur Autonomous Region University Scientific Research Project (Grant No. XJEDU 2017I005) and National Modern Agriculture Industrial System Project (Grant No. CARS-36).