Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China.
Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, P. R. China.
PLoS One. 2020 Feb 12;15(2):e0228964. doi: 10.1371/journal.pone.0228964. eCollection 2020.
Jiaji Duck (JJ) is a Muscovy duck species that possesses many superior characteristics, and it has become an important genetic resource in China. However, to date, its genetic characteristics and genetic relationship with other duck breeds have not been explored yet, which greatly limits the utilization of JJ. In the present study, we investigated the genome sequences of 15 individual ducks representing five different duck populations, including JJ, French Muscovy duck (FF), mallard (YD), hong duck (HD) and Beijing duck (BD). Moreover, we investigated the characteristics of JJ-specific single nucleotide polymorphisms (SNPs) and compared the genome sequences of JJ vs. YD and JJ vs. BD using integrated strategies, including mutation detection, selective screening, and Gene Ontology (GO) analysis. More than 40 Gb of clean data were obtained for each population (mean coverage of 13.46 Gb per individual). A total number of 22,481,367 SNPs and 4,156,829 small insertion-deletions (Indels) were identified for the five duck populations, which could be used as molecular markers in breeding and utilization of JJ. Moreover, we identified 1,447,932 JJ-specific SNPs, and found that genes covering at least one JJ-specific SNP mainly involved in protein phosphorylation and dephosphorylation, as well as DNA modification. Phylogenetic tree and principal components analysis (PCA) revealed that the genetic relationship of JJ was closest to FF, while it was farthest to BD. A total of 120 and 111 genes were identified as positive selection genes for JJ vs. BD and JJ vs. YD, respectively. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the positive selection genes for JJ vs. BD ducks mainly involved in pigmentation, muscle contraction and stretch, gland secretion, and immunology, while the positive selection genes obtained from JJ vs. YD ducks mainly involved in embryo development, muscle contraction and stretch, and gland secretion. Taken together, our findings enabled us to better understand the characteristics of JJ and provided a molecular basis for the breeding and hybrid utilization of JJ in the future.
嘉积鸭（JJ）是一种麝香鸭品种，具有许多优良特性，已成为中国重要的遗传资源。然而，迄今为止，其遗传特征及其与其他鸭品种的遗传关系尚未得到研究，这极大地限制了 JJ 的利用。本研究对来自五个不同鸭种群的 15 个个体的基因组序列进行了研究，这些种群包括 JJ、法国麝香鸭（FF）、绿头鸭（YD）、红鸭（HD）和北京鸭（BD）。此外，我们还研究了 JJ 特异性单核苷酸多态性（SNP）的特征，并通过突变检测、选择性筛选和基因本体论（GO）分析等综合策略，比较了 JJ 与 YD 和 JJ 与 BD 的基因组序列。每个群体都获得了超过 40 Gb 的清洁数据（每个个体的平均覆盖度为 13.46 Gb）。共鉴定出 22481367 个 SNP 和 4156829 个小插入-缺失（Indel），可作为 JJ 选育和利用的分子标记。此外，我们还鉴定出 1447932 个 JJ 特异性 SNP，发现至少覆盖一个 JJ 特异性 SNP 的基因主要参与蛋白质磷酸化和去磷酸化以及 DNA 修饰。系统发育树和主成分分析（PCA）表明，JJ 的遗传关系与 FF 最接近，而与 BD 最远。共鉴定出 120 个和 111 个基因分别为 JJ vs. BD 和 JJ vs. YD 的正选择基因。GO 和京都基因与基因组百科全书（KEGG）分析表明，JJ vs. BD 鸭的正选择基因主要涉及色素沉着、肌肉收缩和伸展、腺体分泌和免疫学，而 JJ vs. YD 鸭的正选择基因主要涉及胚胎发育、肌肉收缩和伸展以及腺体分泌。总之，我们的研究结果使我们能够更好地了解 JJ 的特征，并为未来 JJ 的选育和杂交利用提供了分子基础。
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