INRAE, INP, UMR 1388 GenPhySE, 31326, Castanet-Tolosan, France.
Institut de l'Elevage, 31321, Castanet-Tolosan, France.
Genet Sel Evol. 2024 Sep 30;56(1):69. doi: 10.1186/s12711-024-00934-2.
The Dohne Merino sheep was introduced to Australia from South Africa in the 1990s. It was primarily used in crosses with the Merino breed sheep to improve on attributes such as reproduction and carcass composition. Since then, this breed has continued to expand in Australia but the number of genotyped and phenotyped purebred individuals remains low, calling into question the accuracy of genomic selection. The Australian Merino, on the other hand, has a substantial reference population in a separate genomic evaluation (MERINOSELECT). Combining these resources could fast track the impact of genomic selection on the smaller breed, but the efficacy of this needs to be investigated. This study was based on a dataset of 53,663 genotypes and more than 2 million phenotypes. Its main objectives were (1) to characterize the genetic structure of Merino and Dohne Merino breeds, (2) to investigate the utility of combining their evaluations in terms of quality of predictions, and (3) to compare several methods of genetic grouping. We used the 'LR-method' (Linear Regression) for these assessments.
We found very low Fst values (below 0.048) between the different Merino lines and Dohne breed considered in our study, indicating very low genetic differentiation. Principal component analysis revealed three distinct groups, identified as purebred Merino, purebred Dohne, and crossbred animals. Considering the whole population in the reference led to the best quality of predictions and the largest increase in accuracy (from 'LR-method') from pedigree to genomic-based evaluations: 0.18, 0.14 and 0.16 for yearling fibre diameter (YFD), yearling greasy fleece weight (YGFW) and yearling liveweight (YWT), respectively. Combined genomic evaluations showed higher accuracies than the evaluation based on the Dohne reference only (accuracies increased by 0.16, 0.06 and 0.07 for YFD, YGFW, and YWT, respectively). For the combined genomic evaluations, metafounder models were more accurate than Unknown Parent Groups models (accuracies increased by 0.04, 0.04 and 0.06 for YFD, YGFW and YWT, respectively).
We found promising results for the future transition of the Dohne breed from pedigree to genomic selection. A combined genomic evaluation, with the MERINOSELECT evaluation in addition to using metafounders, is expected to enhance the quality of genomic predictions for the Dohne Merino breed.
多赛特羊于 20 世纪 90 年代从南非引入澳大利亚。它主要用于与美利奴羊杂交，以提高繁殖力和胴体组成等特性。从那时起，这种品种在澳大利亚继续扩张，但基因型和表型纯种种群数量仍然很低，这使得基因组选择的准确性受到质疑。另一方面，澳大利亚美利奴羊在一个单独的基因组评估（MERINOSELECT）中有大量的参考群体。结合这些资源可以加速基因组选择对较小品种的影响，但需要研究其效果。本研究基于一个包含 53663 个基因型和 200 多万个表型的数据集。其主要目的是：（1）描述美利奴羊和多赛特羊品种的遗传结构，（2）根据预测质量调查组合它们的评估的效用，（3）比较几种遗传分组方法。我们使用“LR 方法”（线性回归）进行这些评估。
我们发现，在所研究的不同美利奴羊系和多赛特羊品种之间，Fst 值非常低（低于 0.048），表明遗传分化很小。主成分分析显示有三个不同的群体，分别鉴定为纯美利奴羊、纯多赛特羊和杂交动物。考虑到参考群体中的所有个体，可获得最佳的预测质量，并从系谱到基于基因组的评估中提高最大的准确性：对周岁纤维直径（YFD）、周岁油性毛重（YGFW）和周岁体重（YWT）的提高分别为 0.18、0.14 和 0.16。综合基因组评估的准确性高于仅基于多赛特参考的评估（对 YFD、YGFW 和 YWT 的准确性分别提高了 0.16、0.06 和 0.07）。对于综合基因组评估，元祖模型比未知亲本群模型更准确（对 YFD、YGFW 和 YWT 的准确性分别提高了 0.04、0.04 和 0.06）。
我们发现多赛特羊从系谱到基因组选择的未来过渡有希望取得成果。结合 MERINOSELECT 评估并使用元祖，综合基因组评估预计将提高多赛特美利奴羊品种的基因组预测质量。
