USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT 59301, USA.
USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA.
J Anim Sci. 2022 Sep 1;100(9). doi: 10.1093/jas/skac230.
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, and 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%, whereas 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.
复合品种在牛肉行业中被广泛应用。复合品种可以让生产者将祖代品种的优良性状结合起来，并简化牛群管理，而无需重复杂交和维持纯种。在这项研究中，我们利用基因组信息来评估一个三品种肉牛复合品种的遗传组成和特征。这个复合种群被称为复合基因组合（CGC），由 50%的红安格斯牛、25%的夏洛莱牛和 25%的塔郎坦牛组成。这项研究共使用了 248 头动物：CGC（n=79）、红安格斯牛（n=61）、夏洛莱牛（n=79）和塔郎坦牛（n=29）。所有动物均采用 777k HD 面板进行基因分型。进行主成分和 ADMIXTURE 分析，以评估 CGC 动物的遗传结构。ADMIXTURE 结果表明，塔郎坦牛的比例增加到了约 57%，而夏洛莱牛减少到了约 5%，红安格斯牛减少到了 38%。为了评估不同品种和不同世代的 CGC 基因组组成的这些变化，进行了纯合片段（ROH）分析。该分析表明，红安格斯牛的每个动物的 ROH 片段总长度最高，平均为 349.92Mb，而 CGC 的平均长度最低，为 141.10Mb。此外，该分析还表明在第六代时 CGC 形成了新的单倍型。通过 Fst 和 HapFlk 分析评估了选择信号。在 CGC 中鉴定出了几个选择清扫，特别是在先前报道与毛色和生长性状相关的染色体 5 和 14 上。该研究支持我们之前的发现，即祖代组合在几代之后并不稳定，直接或自然选择在改变祖代比例方面发挥了作用。此外，结果表明，塔郎坦牛在凉爽的半干旱环境中为复合品种贡献了有用的性状，并提示可能需要重新探索该品种的作用。
