BACKGROUND Genome wide association studies (GWAS) were conducted on 7,853,211 imputed whole genome sequence variants in a population of 3354 to 3984 animals from multiple beef cattle breeds for five carcass merit traits including hot carcass weight (HCW), average backfat thickness (AFAT), rib eye area (REA), lean meat yield (LMY) and carcass marbling score (CMAR). Based on the GWAS results, genetic architectures of the carcass merit traits in beef cattle were elucidated. RESULTS The distributions of DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants conformed to a scaled inverse chi-squared distribution to a greater extent. At a threshold of P-value < 10-5, 51, 33, 46, 40, and 38 lead DNA variants on multiple chromosomes were significantly associated with HCW, AFAT, REA, LMY, and CMAR, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on HCW, AFAT, REA, and LMY were found on chromosome 6. On average, missense variants, 3'UTR variants, 5'UTR variants, and other regulatory region variants exhibited larger allele substitution effects on the traits in comparison to other functional classes. The amounts of additive genetic variance explained per DNA variant were smaller for intergenic and intron variants on all the traits whereas synonymous variants, missense variants, 3'UTR variants, 5'UTR variants, downstream and upstream gene variants, and other regulatory region variants captured a greater amount of additive genetic variance per sequence variant for one or more carcass merit traits investigated. In total, 26 enriched cellular and molecular functions were identified with lipid metabolisms, small molecular biochemistry, and carbohydrate metabolism being the most significant for the carcass merit traits. CONCLUSIONS The GWAS results have shown that the carcass merit traits are controlled by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory, synonymous, and missense functional classes have relatively larger impacts per sequence variant on the variation of carcass merit traits. The genetic architecture as revealed by the GWAS will improve our understanding on genetic controls of carcass merit traits in beef cattle.

中文翻译：

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通过推算全基因组序列变异的全基因组关联研究揭示肉牛数量性状的遗传结构：II：胴体优点性状。


背景 全基因组关联研究 (GWAS) 对来自多个肉牛品种的 3354 至 3984 只动物的 7,853,211 个推算全基因组序列变异进行了五种胴体优点性状，包括热胴体重量 (HCW)、平均背膘厚度 (AFAT)、肋眼面积 (REA)、瘦肉率 (LMY) 和胴体大理石花纹评分 (CMAR)。根据 GWAS 结果，阐明了肉牛胴体优点性状的遗传结构。结果所有性状的DNA变异等位基因替代效应的分布近似于钟形分布，而由单个DNA变异解释的加性遗传方差的分布在更大程度上符合比例反卡方分布。在 P 值 < 阈值下，多条染色体上的 10-5、51、33、46、40 和 38 个先导 DNA 变异分别与 HCW、AFAT、REA、LMY 和 CMAR 显着相关。此外，在 6 号染色体上发现了对 HCW、AFAT、REA 和 LMY 具有潜在多效性影响的先导 DNA 变异。平均而言，错义变异、3'UTR 变异、5'UTR 变异和其他调控区变异表现出更大的等位基因与其他功能类别相比，对性状的替代效应。对于所有性状的基因间和内含子变异，每个 DNA 变异解释的加性遗传变异量较小，而同义变异、错义变异、3'UTR 变异、5'UTR 变异、下游和上游基因变异以及捕获的其他调控区变异对于所研究的一个或多个胴体优点性状，每个序列变体具有更大量的附加遗传变异。 总共鉴定出 26 种丰富的细胞和分子功能，其中脂质代谢、小分子生物化学和碳水化合物代谢对胴体品质性状最重要。结论 GWAS 结果表明，胴体品质性状受少数影响较大的 DNA 变异和许多影响较小的 DNA 变异控制。调节、同义和错义功能类别中的核苷酸多态性对于每个序列变异对胴体优点性状的变化具有相对较大的影响。 GWAS 揭示的遗传结构将提高我们对肉牛胴体品质性状遗传控制的理解。