Understanding the relationship between genetic admixture and phenotypic performance is crucial for the optimization of crossbreeding programs. The use of small sets of informative ancestry markers can be a cost-effective option for the estimation of breed composition and for parentage assignment in situations where pedigree recording is difficult. The objectives of this study were to develop small single nucleotide polymorphism (SNP) panels that can accurately estimate the total dairy proportion and assign parentage in both West and East African crossbred dairy cows. Medium- and high-density SNP genotype data (Illumina BovineSNP50 and BovineHD Beadchip) for 4231 animals sampled from African crossbreds, African Bos taurus, European Bos taurus, Bos indicus, and African indigenous populations were used. For estimating breed composition, the absolute differences in allele frequency were calculated between pure ancestral breeds to identify SNPs with the highest discriminating power, and different combinations of SNPs weighted by ancestral origin were tested against estimates based on all available SNPs. For parentage assignment, informative SNPs were selected based on the highest minor allele frequency (MAF) in African crossbred populations assuming two Scenarios: (1) parents were selected among all the animals with known genotypes, and (2) parents were selected only among the animals known to be a parent of at least one progeny. For the medium-density genotype data, SNPs selected for the largest differences in allele frequency between West African indigenous and European Bos taurus breeds performed best for most African crossbred populations and achieved a prediction accuracy (r2) for breed composition of 0.926 to 0.961 with 200 SNPs. For the high-density dataset, a panel with 70% of the SNPs selected on their largest difference in allele frequency between African and European Bos taurus performed best or very near best across all crossbred populations with r2 ranging from 0.978 to 0.984 with 200 SNPs. In all African crossbred populations, unambiguous parentage assignment was possible with ≥ 300 SNPs for the majority of the panels for Scenario 1 and ≥ 200 SNPs for Scenario 2. The identified low-cost SNP assays could overcome incomplete or inaccurate pedigree records in African smallholder systems and allow effective breeding decisions to produce progeny of desired breed composition.

中文翻译：

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用于估计非洲杂交奶牛奶牛品种比例和亲子分配的 SNP panel

了解遗传混合物和表型性能之间的关系对于优化杂交育种计划至关重要。在谱系记录困难的情况下，使用少量信息丰富的祖先标记可能是估计品种组成和亲子关系分配的一种经济有效的选择。本研究的目的是开发小型单核苷酸多态性 (SNP) 组合，能够准确估计西非和东非杂交奶牛的总乳制品比例并分配亲子关系。使用从非洲杂交种、非洲牛、欧洲牛、印度牛和非洲土著种群中采样的 4231 只动物的中密度和高密度 SNP 基因型数据（Illumina BovineSNP50 和 BovineHD Beadchip）。为了估计品种组成，计算了纯祖先品种之间等位基因频率的绝对差异，以识别具有最高区分能力的 SNP，并根据基于所有可用 SNP 的估计值测试了按祖先起源加权的 SNP 的不同组合。对于亲子分配，根据非洲杂交种群中最高次要等位基因频率（MAF）选择信息丰富的 SNP，假设两种情况：（1）在所有具有已知基因型的动物中选择亲本，（2）仅在具有已知基因型的动物中选择亲本。已知是至少一个后代的亲本的动物。对于中等密度基因型数据，为西非本土和欧洲牛牛品种之间等位基因频率差异最大而选择的 SNP 对于大多数非洲杂交种群表现最佳，并且品种组成的预测准确度 (r2) 为 0.926 至 0.961，其中 200 SNP。对于高密度数据集，根据非洲和欧洲牛牛之间等位基因频率最大差异选择的 70% SNP 的面板在所有杂交群体中表现最佳或非常接近最佳，r2 范围为 0.978 至 0.984，具有 200 个 SNP。在所有非洲杂交群体中，对于场景 1 的大多数组，≥ 300 个 SNP，对于场景 2，≥ 200 个 SNP，可以进行明确的亲子分配。所确定的低成本 SNP 测定可以克服非洲小农系统中不完整或不准确的谱系记录并允许有效的育种决策来产生所需品种组成的后代。