State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
Gigascience. 2023 Mar 20;12. doi: 10.1093/gigascience/giad016. Epub 2023 Mar 27.
Short-term, intense artificial selection drives fast phenotypic changes in domestic animals and leaves imprints on their genomes. However, the genetic basis of this selection response is poorly understood. To better address this, we employed the Pekin duck Z2 pure line, in which the breast muscle weight was increased nearly 3-fold after 10 generations of breeding. We denovo assembled a high-quality reference genome of a female Pekin duck of this line (GCA_003850225.1) and identified 8.60 million genetic variants in 119 individuals among 10 generations of the breeding population.
We identified 53 selected regions between the first and tenth generations, and 93.8% of the identified variations were enriched in regulatory and noncoding regions. Integrating the selection signatures and genome-wide association approach, we found that 2 regions covering 0.36 Mb containing UTP25 and FBRSL1 were most likely to contribute to breast muscle weight improvement. The major allele frequencies of these 2 loci increased gradually with each generation following the same trend. Additionally, we found that a copy number variation region containing the entire EXOC4 gene could explain 1.9% of the variance in breast muscle weight, indicating that the nervous system may play a role in economic trait improvement.
Our study not only provides insights into genomic dynamics under intense artificial selection but also provides resources for genomics-enabled improvements in duck breeding.
短期、高强度的人工选择会导致家畜的表型快速变化，并在其基因组上留下印记。然而，这种选择反应的遗传基础还不太清楚。为了更好地解决这个问题，我们利用了北京鸭 Z2 纯系，在 10 代的选育后，其胸肌重量增加了近 3 倍。我们从头组装了这条系的一只雌性北京鸭的高质量参考基因组（GCA_003850225.1），并在 10 代的选育群体中鉴定了 119 个个体中的 860 万个遗传变异。
我们在第 1 代和第 10 代之间鉴定了 53 个选择区域，其中 93.8%的鉴定变异富集在调控和非编码区。整合选择特征和全基因组关联方法，我们发现了 2 个包含 UTP25 和 FBRSL1 的 0.36 Mb 大小的区域最有可能有助于胸肌重量的改善。这两个位点的主要等位基因频率随着每一代的选育而逐渐增加，趋势相同。此外，我们发现一个包含整个 EXOC4 基因的拷贝数变异区域可以解释胸肌重量变异的 1.9%，这表明神经系统可能在经济性状的改善中发挥作用。
我们的研究不仅深入了解了强烈人工选择下的基因组动态，还为鸭的基因组改良提供了资源。
