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Influence of population structure on the compilation of the Bonsmara genomic reference population

机译：人口结构对盆地基因组参考人群汇编的影响

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摘要

The most popular beef breed in South Africa is the Bonsmara, a locally developed composite breed adapted to sub-tropical conditions. The establishment ofa genomic reference population is currently ongoing for the application of genomic selection. To date, 583 Bonsmara cattle (388 bulls and 195 cows) have been genotyped with the GeneSeek Genomic Profiler Bovine HD Chip (GGP-HD) 80 K chip, and the population structure of the reference population was studied. The average minor allele frequency for theBonsmara was 0.280 across 56248 autosomal single-nucleotide polymorphisms (SNPs), whereas the observed and expected heterozygosity values were 0.361 and 0.365, respectively. After pruning the data set for SNPs in linkage disequilibrium, 19119 SNPs were retained, averaging 659 SNPs per autosomal chromosome. This generated an average SNP density of 1 SNP per 90 kb. Structure analysis revealed a non-homogenous population with a high level of genetic admixture, which may negatively influence genomic breeding value prediction accuracy. Genotyping ofa further 990 Bonsmara cattle are pending, using the GeneSeek GGP-HD 150 K chip. As more animals will be added to the reference population, the profile of the reference population are expected to change in such away to ensure improved genomic estimated breeding value accuracies.
机译：南非最受欢迎的牛肉品种是Bonsmara，这是一种适应亚热带条件的本地开发的复合品种。建立基因组参考人口目前正在进行适用基因组选择。迄今为止，583辆盆景牛（388公牛和195奶牛）已经与Geneseek基因组分布术牛HD芯片（GGP-HD）80k芯片进行了基因分型，研究了参考人群的人口结构。在56248个常染色体单核苷酸多态性（SNPS）上，禁止禁止的平均次要等位基因频率为0.280，而观察到的和预期的杂合子值分别为0.361和0.365。在修剪连锁不平衡中SNP的数据集后，保留了19119个SNP，平均每种常染色体染色体659个SNP。这产生了每90 kB的平均SNP密度为1 SNP。结构分析显示出具有高水平遗传混合物的非均质群体，其可能对基因组育种值预测准确性产生负面影响。使用Geneseek GGP-HD 150 K芯片，进一步的990牛肉牛的基因分型。随着更多动物将被添加到参考群体中，预计参考人群的轮廓将变为如此，以确保改善的基因组估计的育种价值准确性。

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  • 来源
    《Advances in Animal Biosciences》 |2017年第1期|共1页
  • 作者

    L. Bosman; R. R. van der Westhuizen; C. Visser; E. van Marle-Koster;

  • 作者单位

    Department of Animal and Wildlife Sciences University of Pretoria Private Bag X20 Hatfield 0028 South Africa;

    Department of Animal and Wildlife Sciences University of Pretoria Private Bag X20 Hatfield 0028 South Africa;

    Department of Animal and Wildlife Sciences University of Pretoria Private Bag X20 Hatfield 0028 South Africa;

    Department of Animal and Wildlife Sciences University of Pretoria Private Bag X20 Hatfield 0028 South Africa;

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  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 动物学;
  • 关键词

    admixture; cattle; selection; SNP;

    机译：混合物;牛;选择;SNP;

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