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ORIGINAL RESEARCH article

Front. Genet.
Sec. Livestock Genomics
Volume 15 - 2024 | doi: 10.3389/fgene.2024.1435793

Identification of Heilongjiang Crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data

Provisionally accepted
Shuang Li Shuang Li 1,2Li Liu Li Liu 1*Zulfiqar Ahmed Zulfiqar Ahmed 3Wang Fuwen Wang Fuwen 2Chuzhao Lei Chuzhao Lei 2*Fang Sun Fang Sun 1*
  • 1 Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang Province, China
  • 2 College of Animal Science and Technology, Northwest A&F University, Xianyang, China
  • 3 Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot, Azad Kashmir, Pakistan

The final, formatted version of the article will be published soon.

    To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands. This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls. Results showed that a total of 14,427,729 biallelic SNPs were discovered, with the majority located in intergenic and intron regions and a small percentage in exon regions, impacting protein function. Population genetic analyses including Principal Component Analysis (PCA), Neighbor-Joining (NJ) tree, and ADMIXTURE identified Angus, Holstein, and Mishima as the main ancestors of Crossbred beef cattle. In genetic diversity analysis, nucleotide diversity, linkage disequilibrium, and inbreeding coefficient analysis reveal that the genetic diversity of Crossbred beef cattle is at a moderate level, and a higher inbreeding coefficient indicates the need for careful breeding management. In addition, some genes related to economic traits are identified through the identification of Runs of Homozygosity (ROH) islands and important fragments from ancestors. Overall, this comprehensive genomic characterization supports the targeted improvement of economically important traits in Crossbred beef cattle, facilitating advanced breeding strategies.

    Keywords: Heilongjiang Crossbred beef cattle, functional gene, genetic diversity, population genetic structure, Whole genome

    Received: 21 May 2024; Accepted: 08 Jul 2024.

    Copyright: © 2024 Li, Liu, Ahmed, Fuwen, Lei and Sun. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Li Liu, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang Province, China
    Chuzhao Lei, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
    Fang Sun, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang Province, China

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