Ahmed R H, Schmidtmann C, Mugambe J, Thaller G
Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Kiel, Germany.
IT Solutions for Animal Production (vit), Verden (Aller), Germany.
Front Genet. 2025 Jun 5;16:1530310. doi: 10.3389/fgene.2025.1530310. eCollection 2025.
Beef on Dairy (BoD) calves are born from the crossing of dairy cows with beef breeds. The genetic architecture of these calves differs significantly from the parent breeds due to heterosis and other dominance effects. Identification of the genomic regions associated with traits in BoD calves and the inheritance pattern of these regions can assist in the selection process. We conducted a genome-wide association study (GWAS) for Belgian blue and Angus crossbreds born from a Holstein dam, incorporating additive and dominance effects to identify genomic regions associated with birth weight, calving difficulty, and gestation length. Additionally, a haplotype-based GWAS was performed to compare the effectiveness of these two different methodologies and to identify the parental origin of the haplotypes based on similar allelic patterns between crossbred and parental breeds.
The heritability estimates for birth weight, calving difficulty, and gestation length were 0.29 (±0.03), 0.36 (±0.04), and 0.09 (±0.03), respectively. Using SNP-based GWAS for birth weight, a genomic region containing the gene on BTA 6 was identified. In addition, the haplotype-based analysis identified three more genes (, , and ) associated with birth weight. Incorporating dominance effects into the GWAS model led to the identification of an additional gene, , related to birth weight. For calving difficulty, SNP-based GWAS in Angus crossbreds revealed a genomic region containing the gene. Most of the haplotypes associated with these traits originated from the three parental breeds, but six unique haplotypes for Angus and Belgian blue were identified.
Based on this study, Haplotype GWAS was found to have superior statistical power in the identification of associated genomic regions in BoD crossbreds. However, for traits such as calving difficulty, SNP-based GWAS proved to be more effective. Both approaches are essential for the identification of genomic regions associated with traits of interest in BoD calves.
乳用型肉牛（BoD）犊牛是通过奶牛与肉牛品种杂交产生的。由于杂种优势和其他显性效应，这些犊牛的遗传结构与亲本品种有显著差异。鉴定与BoD犊牛性状相关的基因组区域以及这些区域的遗传模式有助于选择过程。我们对荷斯坦奶牛所生的比利时蓝牛和安格斯杂交牛进行了全基因组关联研究（GWAS），纳入加性和显性效应，以鉴定与出生体重、产犊难度和妊娠期长度相关的基因组区域。此外，还进行了基于单倍型的GWAS，以比较这两种不同方法的有效性，并根据杂交品种和亲本品种之间相似的等位基因模式确定单倍型的亲本来源。
出生体重、产犊难度和妊娠期长度的遗传力估计值分别为0.29（±0.03）、0.36（±0.04）和0.09（±0.03）。使用基于单核苷酸多态性（SNP）的GWAS分析出生体重，在BTA 6染色体上鉴定出一个包含 基因的基因组区域。此外，基于单倍型的分析又鉴定出另外三个与出生体重相关的基因（ 、 和 ）。将显性效应纳入GWAS模型后，又鉴定出一个与出生体重相关的额外基因 。对于产犊难度，安格斯杂交牛基于SNP的GWAS揭示了一个包含 基因的基因组区域。与这些性状相关的大多数单倍型起源于三个亲本品种，但鉴定出了六个安格斯和比利时蓝牛的独特单倍型。
基于本研究，发现单倍型GWAS在鉴定BoD杂交牛相关基因组区域方面具有更高统计效力。然而，对于产犊难度等性状，基于SNP的GWAS被证明更有效。两种方法对于鉴定与BoD犊牛感兴趣的性状相关的基因组区域都至关重要。
