Porcine milk is a complex fluid, containing a myriad of immunological, biochemical, and cellular components, made to satisfy the nutritional requirements of the neonate. Whole milk contains many different cell types, including mammary epithelial cells, neutrophils, macrophages, and lymphocytes, as well nanoparticles, such as milk exosomes. To-date, only a limited number of livestock transcriptomic studies have reported sequencing of milk. Moreover, those studies focused only on sequencing somatic cells as a proxy for the mammary gland with the goal of investigating differences in the lactation process. Recent studies have indicated that RNA originating from multiple cell types present in milk can withstand harsh environments, such as the digestive system, and transmit regulatory molecules from maternal to neonate. Transcriptomic profiling of porcine whole milk, which is reflective of the combined cell populations, could help elucidate these mechanisms. To this end, total RNA from colostrum and mature milk samples were sequenced from 65 sows at differing parities. A stringent bioinformatic pipeline was used to identify and characterize 70,841 transcripts. The 70,841 identified transcripts included 42,733 previously annotated transcripts and 28,108 novel transcripts. Differential gene expression analysis was conducted using a generalized linear model coupled with the Lancaster method for P-value aggregation across transcripts. In total, 1667 differentially expressed genes (DEG) were identified for the milk type main effect, and 33 DEG were identified for the milk type x parity interaction. Several gene ontology (GO) terms related to immune response were significant for the milk type main effect, supporting the well-known fact that immunoglobulins and immune cells are transferred to the neonate via colostrum. This is the first study to perform global transcriptome analysis from whole milk samples in sows from different parities. Our results provide important information and insight into synthesis of milk proteins and innate immunity and potential targets for future improvement of swine lactation and piglet development.

中文翻译：

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不同胎次猪初乳和成熟乳转录谱的表征及比较分析

猪奶是一种复杂的液体，含有多种免疫、生化和细胞成分，旨在满足新生儿的营养需求。全脂牛奶含有许多不同的细胞类型，包括乳腺上皮细胞、中性粒细胞、巨噬细胞和淋巴细胞，以及纳米粒子，例如牛奶外泌体。迄今为止，只有有限数量的家畜转录组研究报告了牛奶的测序。此外，这些研究仅侧重于对作为乳腺替代物的体细胞进行测序，目的是研究哺乳过程中的差异。最近的研究表明，源自牛奶中多种细胞类型的 RNA 可以承受消化系统等恶劣环境，并将调节分子从母体传递给新生儿。猪全脂乳的转录组学分析反映了组合细胞群的情况，可以帮助阐明这些机制。为此，我们对 65 头不同胎次母猪的初乳和成熟乳样本中的总 RNA 进行了测序。使用严格的生物信息学流程来识别和表征 70,841 个转录本。70,841 个已识别的转录本包括 42,733 个先前注释的转录本和 28,108 个新颖的转录本。使用广义线性模型结合 Lancaster 方法进行转录本间 P 值聚合，进行差异基因表达分析。总共，鉴定出 1667 个差异表达基因 (DEG) 与牛奶类型主效应相关，并鉴定出 33 个差异表达基因与牛奶类型 x 胎次相互作用相关。与免疫反应相关的几个基因本体论 (GO) 术语对于乳型主效应具有重要意义，支持免疫球蛋白和免疫细胞通过初乳转移到新生儿这一众所周知的事实。这是第一项对不同胎次母猪的全脂奶样本进行全局转录组分析的研究。我们的结果为乳蛋白合成和先天免疫以及未来改善猪泌乳和仔猪发育的潜在目标提供了重要信息和见解。