Meat quality and composition traits have become valuable in modern pork production; however, genetic improvement has been slow due to high phenotyping costs. Combining genomic information with multi-trait indirect selection based on cheaper indicator traits is an alternative for continued cost-effective genetic improvement. Data from an ongoing breeding program were used in this study. Phenotypic and genomic information was collected on three-way crossbred and purebred Duroc animals belonging to 28 half-sib families. We applied different methods to assess the value of using purebred and crossbred information (both genomic and phenotypic) to predict expensive-to-record traits measured on crossbred individuals. Estimation of multi-trait variance components set the basis for comparing the different scenarios, together with a fourfold cross-validation approach to validate the phenotyping schemes under four genotyping strategies. The benefit of including genomic information for multi-trait prediction depended on the breeding goal trait, the indicator traits included, and the source of genomic information. While some traits benefitted significantly from genotyping crossbreds (e.g., loin intramuscular fat content, backfat depth, and belly weight), multi-trait prediction was advantageous for some traits even in the absence of genomic information (e.g., loin muscle weight, subjective color, and subjective firmness). Our results show the value of using different sources of phenotypic and genomic information. For most of the traits studied, including crossbred genomic information was more beneficial than performing multi-trait prediction. Thus, we recommend including crossbred individuals in the reference population when these are phenotyped for the breeding objective.

中文翻译：

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猪肉品质和胴体成分遗传改良的基因分型和表型分析策略

肉质和成分特征在现代猪肉生产中变得有价值；然而，由于表型分析成本高，遗传改良一直很缓慢。将基因组信息与基于更便宜的指标性状的多性状间接选择相结合是持续具有成本效益的遗传改良的替代方案。本研究使用了来自正在进行的育种计划的数据。收集了属于 28 个半同胞家族的三向杂交和纯种杜洛克动物的表型和基因组信息。我们应用了不同的方法来评估使用纯种和杂交信息（基因组和表型）来预测对杂交个体测量的昂贵记录性状的价值。多特征方差分量的估计为比较不同情景奠定了基础，连同四重交叉验证方法来验证四种基因分型策略下的表型方案。将基因组信息纳入多性状预测的好处取决于育种目标性状、包括的指标性状和基因组信息的来源。虽然一些性状显着受益于基因分型杂交（例如，腰肌内脂肪含量、背膘深度和腹部重量），但即使在没有基因组信息的情况下（例如，腰肌重量、主观颜色、和主观坚定）。我们的结果显示了使用不同来源的表型和基因组信息的价值。对于所研究的大多数性状，包括杂交基因组信息比进行多性状预测更有益。因此，