Wang Kejun, Hua Guoying, Li Jingyi, Yang Yu, Zhang Chenxi, Yang Lan, Hu Xiaoyu, Scheben Armin, Wu Yanan, Gong Ping, Zhang Shuangjie, Fan Yanfeng, Zeng Tao, Lu Lizhi, Gong Yanzhang, Jiang Ruirui, Sun Guirong, Tian Yadong, Kang Xiangtao, Hu Haifei, Li Wenting
Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and Technology Henan Agricultural University Zhengzhou China.
The Shennong Laboratory Zhengzhou China.
Imeta. 2023 Dec 17;3(1):e154. doi: 10.1002/imt2.154. eCollection 2024 Feb.
Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan-genome constructed using five genome assemblies capturing ∼40.98 Mb new sequences. This pan-genome together with high-depth sequencing data (∼46.5×) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchoring in a gene body or regulatory region are linked to duck's domestication and improvement. By combining quantitative genetics with molecular experiments, we, for the first time, unraveled a 6945 bp Gypsy insertion as a functional mutation of the major gene associated with duck bodyweight. This Gypsy insertion, to our knowledge, explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). In addition, we also examined another 6634 bp Gypsy insertion in intron, which triggers a novel transcript of , thereby contributing to the development of white plumage. Our findings highlight the importance of using a pan-genome as a reference in genomics studies and illuminate the impact of transposons in trait formation and livestock breeding.
结构变异（SVs）是驯化和改良性状的主要来源。我们展示了首个利用五个基因组组装构建的鸭泛基因组，捕获了约40.98 Mb的新序列。该泛基因组与高深度测序数据（约46.5×）一起鉴定出101,041个SVs，其中很大一部分源自转座元件（TE）活性。许多定位于基因体或调控区域的TE衍生SVs与鸭的驯化和改良有关。通过将数量遗传学与分子实验相结合，我们首次揭示了一个6945 bp的吉普赛插入序列是与鸭体重相关的主要基因的功能突变。据我们所知，这种吉普赛插入对鸟类体重的影响最大（占表型变异的27.61%）。此外，我们还研究了内含子中另一个6634 bp的吉普赛插入序列，它引发了一个新的转录本，从而促进了白羽的发育。我们的研究结果突出了在基因组学研究中使用泛基因组作为参考的重要性，并阐明了转座子在性状形成和家畜育种中的影响。
