Wolf M, Yin T, Neumann G B, Kokuć P, Brockmann G A, König S
Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany.
Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt Universität zu Berlin, Berlin, Germany.
J Anim Breed Genet. 2025 Sep;142(5):560-570. doi: 10.1111/jbg.12929. Epub 2025 Feb 1.
The aims of the present study were to perform single-step genomic predictions in the dual-purpose German Black Pied cattle (DSN) breed considering a DSN specific SNP chip (DSN_200 K), and to use the corresponding estimated breeding values (EBV) in ongoing optimum genetic contribution (OGC) selection. All results were compared with the application of the commercial Illumina BovineSNP50 BeadChip (50 K). The traits of interest in the present study (due to the differing breeding history of these traits in the past) included 305-day lactation protein percentage (Pro%) of 9029 DSN cows, fat-to-protein ratio (FPR) from the first test-day of 8773 DSN cows, and stature (STAT) measured in cm of 4409 DSN cows. The DSN cows represented the calving years 2008-2019. Genotyping of 2797 DSN animals was conducted using both the DSN_200 K and the 50 K. From the genotyped animals, a subset of 1800 cows had phenotypic records for all three traits FPR, Pro% and STAT. Heritabilities from the single-step genetic parameter estimations were quite large for Pro% (0.69) and STAT (0.78), but small for FPR (0.11). The choice of the SNP chip only had minor effects on variance components, heritabilities and EBVs. Furthermore, genetic parameters were very similar from genetic-statistical models additionally considering a linear regression on pedigree-based inbreeding coefficients. OGC selection was applied to a pool of 1125 pre-selected bull sires (BS) and bull dams (BD). A more relaxed genetic relationship constraint was associated with favourable effects on the average EBVs for Pro%, FPR and STAT, and a declining number of selected BS. The gains in genetic merit were marginal when relaxing the constraint at 0.06 for the genetic relationships or higher. The same associations were found for an overall breeding index (I-DSN), considering the three traits with equal weights. Consequently, we suggested OGC applications with a genetic relationship constraint of 0.06, which contributed to genetic gain in I-DSN of 17.9%, and to increased diversity due to an increased number of BS, when compared to the current practical elite animal selection scheme. A large number of finally selected BS and BD was identical when either using EBV from the DSN_200 K or from the 50 K. From such perspective, we only see marginal extra value for the specific DSN SNP-chip application.
本研究的目的是在兼用型德国黑 pied 牛（DSN）品种中，使用 DSN 特异性 SNP 芯片（DSN_200K）进行单步基因组预测，并在正在进行的最优遗传贡献（OGC）选择中使用相应的估计育种值（EBV）。所有结果都与商业 Illumina BovineSNP50 BeadChip（50K）的应用进行了比较。本研究中感兴趣的性状（由于这些性状过去的育种历史不同）包括 9029 头 DSN 奶牛的 305 天泌乳期蛋白质百分比（Pro%）、8773 头 DSN 奶牛首次检测日的脂肪与蛋白质比率（FPR）以及 4409 头 DSN 奶牛以厘米为单位测量的体高（STAT）。DSN 奶牛代表 2008 - 2019 年的产犊年份。使用 DSN_200K 和 50K 对 2797 头 DSN 动物进行基因分型。在基因分型的动物中，有 1800 头奶牛具有 FPR、Pro%和 STAT 这三个性状的表型记录。单步遗传参数估计得出的遗传力，Pro%（0.69）和 STAT（0.78）相当大，但 FPR（0.11）较小。SNP 芯片的选择对方差分量、遗传力和 EBVs 的影响较小。此外，考虑基于系谱的近亲繁殖系数进行线性回归的遗传统计模型得出的遗传参数非常相似。OGC 选择应用于 1125 头预先选择的公牛（BS）和公牛母亲（BD）。遗传关系约束较为宽松对 Pro%、FPR 和 STAT 的平均 EBVs 有有利影响，并且所选公牛数量减少。当将遗传关系约束放宽到 0.06 或更高时，遗传价值的提升幅度很小。对于综合育种指数（I - DSN），在同等权重考虑这三个性状时也发现了相同的关联。因此，我们建议遗传关系约束为 0.06 的 OGC 应用，与当前实际的精英动物选择方案相比，这有助于 I - DSN 的遗传增益达到 17.9%，并由于公牛数量增加而提高了多样性。当使用来自 DSN_200K 或 50K 的 EBV 时，最终选择的大量公牛和公牛母亲是相同的。从这个角度来看，我们只看到特定 DSN SNP 芯片应用的边际额外价值。
