Animal Genomics, Institute of Agricultural Science, ETH Zürich, 8092, Zürich, Switzerland.
BMC Genomics. 2019 Sep 3;20(1):695. doi: 10.1186/s12864-019-6066-6.
Little is known about the genetic architecture of economically important traits in Brown Swiss cattle because only few genome-wide association studies (GWAS) have been carried out in this breed. Moreover, most GWAS have been performed for single traits, thus not providing detailed insights into potentially existing pleiotropic effects of trait-associated loci.
To compile a comprehensive catalogue of large-effect quantitative trait loci (QTL) segregating in Brown Swiss cattle, we carried out association tests between partially imputed genotypes at 598,016 SNPs and daughter-derived phenotypes for more than 50 economically important traits, including milk production, growth and carcass quality, body conformation, reproduction and calving traits in 4578 artificial insemination bulls from two cohorts of Brown Swiss cattle (Austrian-German and Swiss populations). Across-cohort multi-trait meta-analyses of the results from the single-trait GWAS revealed 25 quantitative trait loci (QTL; P < 8.36 × 10) for economically relevant traits on 17 Bos taurus autosomes (BTA). Evidence of pleiotropy was detected at five QTL located on BTA5, 6, 17, 21 and 25. Of these, two QTL at BTA6:90,486,780 and BTA25:1,455,150 affect a diverse range of economically important traits, including traits related to body conformation, calving, longevity and milking speed. Furthermore, the QTL at BTA6:90,486,780 seems to be a target of ongoing selection as evidenced by an integrated haplotype score of 2.49 and significant changes in allele frequency over the past 25 years, whereas either no or only weak evidence of selection was detected at all other QTL.
Our findings provide a comprehensive overview of QTL segregating in Brown Swiss cattle. Detected QTL explain between 2 and 10% of the variation in the estimated breeding values and thus may be considered as the most important QTL segregating in the Brown Swiss cattle breed. Multi-trait association testing boosts the power to detect pleiotropic QTL and assesses the full spectrum of phenotypes that are affected by trait-associated variants.
由于在瑞士褐牛中进行的全基因组关联研究（GWAS）较少，因此人们对其经济重要性状的遗传结构知之甚少。此外，大多数 GWAS 都是针对单一性状进行的，因此无法深入了解与性状相关的基因座中可能存在的多效性效应。
为了编制瑞士褐牛中分离的大效应数量性状基因座（QTL）的综合目录，我们对 598016 个 SNP 的部分估算基因型与两个瑞士褐牛群体（奥地利-德国和瑞士群体）的 4578 头人工授精公牛的 50 多个经济重要性状（包括产奶量、生长和胴体品质、体型、繁殖和产犊性状）的女儿衍生表型进行了关联测试。对单性状 GWAS 结果的跨群体多性状荟萃分析揭示了 17 条牛巴氏杆菌染色体（BTA）上与经济相关性状相关的 25 个数量性状基因座（QTL；P < 8.36×10）。在位于 BTA5、6、17、21 和 25 上的五个 QTL 中检测到了多效性的证据。其中，位于 BTA6:90,486,780 和 BTA25:1,455,150 的两个 QTL 影响了一系列广泛的经济重要性状，包括与体型、产犊、寿命和挤奶速度相关的性状。此外，BTA6:90,486,780 上的 QTL 似乎是正在选择的目标，因为整合的单倍型评分为 2.49，并且过去 25 年中等位基因频率发生了显著变化，而在所有其他 QTL 中则没有或只有微弱的选择证据。
我们的研究结果提供了瑞士褐牛中分离的 QTL 的综合概述。检测到的 QTL 解释了估计育种值中 2%至 10%的变异，因此可以被认为是瑞士褐牛品种中分离的最重要的 QTL。多性状关联测试提高了检测多效性 QTL 的能力，并评估了受性状相关变异影响的全部表型。
