Junqueira V S, Cardoso F F, Oliveira M M, Sollero B P, Silva F F, Lopes P S
Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Minas Gerais (MG), Brazil.
Empresa Brasileira de Pesquisa Agropecuária, Centro de Pesquisa de Pecuária dos Campos Sul-Brasileiros, Bagé, Rio Grande do Sul (RS), Brazil.
J Anim Breed Genet. 2017 Feb;134(1):14-26. doi: 10.1111/jbg.12239. Epub 2016 Sep 22.
The selection of genetically superior individuals is conditional upon accurate breeding value predictions which, in turn, are highly depend on how precisely relationship is represented by pedigree. For that purpose, the numerator relationship matrix is essential as a priori information in mixed model equations. The presence of pedigree errors and/or the lack of relationship information affect the genetic gain because it reduces the correlation between the true and estimated breeding values. Thus, this study aimed to evaluate the effects of correcting the pedigree relationships using single-nucleotide polymorphism (SNP) markers on genetic evaluation accuracies for resistance of beef cattle to ticks. Tick count data from Hereford and Braford cattle breeds were used as phenotype. Genotyping was carried out using a high-density panel (BovineHD - Illumina bead chip with 777 962 SNPs) for sires and the Illumina BovineSNP50 panel (54 609 SNPs) for their progenies. The relationship between the parents and progenies of genotyped animals was evaluated, and mismatches were based on the Mendelian conflicts counts. Variance components and genetic parameters estimates were obtained using a Bayesian approach via Gibbs sampling, and the breeding values were predicted assuming a repeatability model. A total of 460 corrections in relationship definitions were made (Table 1) corresponding to 1018 (9.5%) tick count records. Among these changes, 97.17% (447) were related to the sire's information, and 2.8% (13) were related to the dam's information. We observed 27.2% (236/868) of Mendelian conflicts for sire-progeny genotyped pairs and 14.3% (13/91) for dam-progeny genotyped pairs. We performed 2174 new definitions of half-siblings according to the correlation coefficient between the coancestry and molecular coancestry matrices. It was observed that higher-quality genetic relationships did not result in significant differences of variance components estimates; however, they resulted in more accurate breeding values predictions. Using SNPs to assess conflicts between parents and progenies increases certainty in relationships and consequently the accuracy of breeding value predictions of candidate animals for selection. Thus, higher genetic gains are expected when compared to the traditional non-corrected relationship matrix.
选择遗传上更优秀的个体取决于准确的育种值预测,而准确的育种值预测又高度依赖于系谱对亲缘关系的精确表示。为此,分子亲缘关系矩阵作为混合模型方程中的先验信息至关重要。系谱错误的存在和/或亲缘关系信息的缺乏会影响遗传进展,因为这会降低真实育种值与估计育种值之间的相关性。因此,本研究旨在评估使用单核苷酸多态性(SNP)标记校正系谱关系对肉牛蜱抗性遗传评估准确性的影响。来自赫里福德和布拉福德牛品种的蜱计数数据用作表型。对公牛使用高密度芯片(具有777962个SNP的牛HD - Illumina芯片)进行基因分型,对其后代使用Illumina牛SNP50芯片(54609个SNP)。评估了基因分型动物亲子代之间的关系,并根据孟德尔冲突计数确定错配情况。通过吉布斯抽样使用贝叶斯方法获得方差分量和遗传参数估计值,并在重复力模型下预测育种值。共进行了460次关系定义校正(表1),对应1018条(9.5%)蜱计数记录。在这些变化中,97.17%(447次)与公牛信息相关,2.8%(13次)与母牛信息相关。我们观察到,公牛 - 后代基因分型对的孟德尔冲突率为27.2%(236/868),母牛 - 后代基因分型对的孟德尔冲突率为14.3%(13/91)。根据同祖系数矩阵和分子同祖系数矩阵之间的相关系数,我们进行了2174次半同胞关系的新定义。结果发现,更高质量的遗传关系并未导致方差分量估计值有显著差异;然而,它们导致育种值预测更准确。使用SNP评估亲子代之间的冲突可增加亲缘关系的确定性,从而提高候选选择动物育种值预测的准确性。因此,与传统的未校正关系矩阵相比,有望获得更高的遗传进展。