Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection.
Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection.
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DOI：
10.1093/gigascience/giad016
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发表时间：
2023-03-20
期刊：
影响因子：
9.2
通讯作者：
中科院分区：
文献类型：
--
作者：
短期的、强烈的人工选择促使家畜的表型发生快速变化，并在它们的基因组上留下印记。然而，这种选择反应的遗传基础知之甚少。为了更好地解决这一问题，我们采用了北京鸭Z2纯系，其中胸肌重量增加了近3倍，经过10代的育种。我们从头组装了一个高质量的参考基因组的雌性北京鸭的这个线（GCA_003850225.1），并确定了8.60万个遗传变异的119个个体之间的10代的育种群体。我们在第一代和第十代之间鉴定了53个选定区域，93.8%的鉴定变异富集在调控区和非编码区。整合选择标记和全基因组关联方法，我们发现包含UTP25和FBRSL1的2个覆盖0.36 Mb的区域最有可能有助于乳房肌肉重量的改善。这两个基因座的主效等位基因频率随世代的增加而逐渐增加，其趋势相同。此外，我们发现，包含整个EXOC 4基因的拷贝数变异区域可以解释1.9%的胸肌重量变异，这表明神经系统可能在经济性状改善中发挥作用。我们的研究不仅提供了深入的人工选择下的基因组动力学的见解，但也提供了资源，基因组学使鸭子育种的改进。
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.
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影响因子：
3.7
作者：
Fulcher, F. Kent;Smith, Bethany T.;Russ, Misty;Patel, Yashomati M.
通讯作者：
Patel, Yashomati M.
影响因子：
12.3
作者：
Akdemir KC;Chin L
通讯作者：
Chin L
影响因子：
4.4
作者：
Farslow JC;Lipinski KJ;Packard LB;Edgley ML;Taylor J;Flibotte S;Moerman DG;Katju V;Bergthorsson U
通讯作者：
Bergthorsson U
影响因子：
4.5
作者：
Ghosh S;Qu Z;Das PJ;Fang E;Juras R;Cothran EG;McDonell S;Kenney DG;Lear TL;Adelson DL;Chowdhary BP;Raudsepp T
通讯作者：
Raudsepp T
影响因子：
4.4
作者：
Dunnington, EA;Siegel, PB
通讯作者：
Siegel, PB