Composite breeds are widely used in the beef industry. Composites allow producers to combine desirable traits from the progenitor breeds and simplify herd management, without repeated crossbreeding and maintenance of purebreds. In this study, genomic information was used to evaluate the genetic composition and characteristics of a three-breed beef cattle composite. This composite population referred to as Composite Gene Combination (CGC) consisted of 50% Red Angus, 25% Charolais, 25% Tarentaise. A total of 248 animals were used in this study CGC (n=79), Red Angus (n=61), Charolais (n=79) and Tarentaise (n=29). All animals were genotyped with 777k HD panel. Principal component and ADMIXTURE analyses were carried out to evaluate the genetic structure of CGC animals. The ADMIXTURE revealed the proportion of Tarentaise increased to approximately 57% while Charolais decreased to approximately 5%, and Red Angus decreased to 38% across generations. To evaluate these changes in the genomic composition across different breeds and in CGC across generations runs of homozygosity (ROH) were conducted. This analysis showed Red Angus to have the highest total length of ROH segments per animal with a mean of 349.92 Mb and lowest in CGC with a mean of 141.10 Mb. Furthermore, it showed the formation of new haplotypes in CGC around the sixth generation. Selection signatures were evaluated through Fst and HapFlk analyses. Several selection sweeps in CGC were identified especially in chromosomes 5 and 14 which have previously been reported to be associated with coat color and growth traits. The study supports our previous findings that progenitor combinations are not stable over generations and that either direct or natural selection plays a role in modifying the progenitor proportions. Furthermore, the results showed that Tarentaise contributed useful attributes to the composite in a cool semi-arid environment and suggests a re-exploration of this breed’s role may be warranted.

中文翻译：

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复合肉牛群体的遗传结构

复合品种广泛应用于牛肉行业。复合材料使生产者能够结合祖先品种的理想性状并简化畜群管理，而无需重复杂交和维持纯种。在这项研究中，基因组信息用于评估三种肉牛组合的遗传组成和特征。这个复合种群被称为复合基因组合 (CGC)，由 50% 红安格斯牛、25% 夏洛莱牛、25% 塔朗泰牛组成。本研究中总共使用了 248 只动物，CGC（n=79）、红安格斯（n=61）、夏洛莱牛（n=79）和塔朗泰斯（Tarentaise）（n=29）。所有动物均使用 777k HD panel 进行基因分型。进行主成分和 ADMIXTURE 分析以评估 CGC 动物的遗传结构。ADMIXTURE 显示，塔伦泰牛的比例增加至约 57%，夏洛莱牛的比例下降至约 5%，红安格斯牛的比例下降至 38%。为了评估不同品种的基因组组成和各代的 CGC 中的这些变化，进行了纯合性 (ROH) 运行。该分析显示，红安格斯每只动物的 ROH 片段总长度最高，平均值为 349.92 Mb，CGC 片段总长度最低，平均值为 141.10 Mb。此外，它显示了在第六代左右CGC中新单倍型的形成。通过 Fst 和 HapFlk 分析评估选择特征。CGC 中的几个选择扫描尤其是在 5 号和 14 号染色体中被识别出来，此前曾报道这些染色体与毛色和生长性状有关。这项研究支持了我们之前的发现，即祖细胞组合在世代中并不稳定，直接选择或自然选择在改变祖细胞比例方面发挥着作用。此外，结果表明，Tarentaise 在凉爽的半干旱环境中为复合材料提供了有用的属性，并表明可能有必要重新探索该品种的作用。