Egg‐type ducks and meat‐type ducks are predominantly commercial or indigenous and have been subjected to artificial directional selection. These two duck types differ substantially in body shape, production performance and reproductivity. However, the genetic changes associated with phenotypic differences remain unclear. Here, we compared the two duck types at the genomic and transcriptomic levels. We identified a large number of SNPs and genes in genomic divergent regions in terms of F_ST and θπ values. The corresponding genes were mainly enriched in embryonic development function and metabolic pathway. RNA‐seq analysis also revealed differential gene expression in the liver and gonads. The differentially expressed genes were functionally associated with signal transmission and substance metabolism respectively. Furthermore, we found that seven genes were related to differentiation between the two types by both g genome and transcriptome analysis and were plausible candidate genes. These genes were annotated to GO categories of cell development and disease immunity. These findings will enable a better understanding of the artificial selection history of meat and egg ducks and provide a valuable resource for future research on the breeding of these two lineages.

中文翻译：

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联合分析策略揭示了蛋鸭和肉鸭之间人工选择相关的遗传变化

蛋鸭和肉鸭主要是商业性的或本土的，并且已经过人工定向的选择。这两种鸭子类型在体形，生产性能和繁殖力上有很大不同。但是，与表型差异相关的遗传变化仍不清楚。在这里，我们在基因组和转录组水平上比较了两种鸭的类型。我们从F _ST和θπ的角度确定了基因组分歧区域中的大量SNP和基因价值观。相应的基因主要丰富了胚胎发育功能和代谢途径。RNA-seq分析还揭示了肝脏和性腺中的差异基因表达。差异表达的基因在功能上分别与信号传递和物质代谢相关。此外，通过g基因组和转录组分析，我们发现七个基因与两种类型的分化有关，并且是可能的候选基因。这些基因被注释为细胞发育和疾病免疫的GO类别。这些发现将使人们能够更好地了解肉鸭蛋的人工选择历史，并为今后对这两个血统的繁殖进行研究提供宝贵的资源。