Single-cell transcriptomic landscape of the sheep rumen provides insights into physiological programming development and adaptation of digestive strategies
Yuan Yuan, 西北工业大学生态环境学院, 陕西 西安 710072, 中国, Daming Sun, Tao Qin, Shengyong Mao, Weiyun Zhu, Yuyang Yin, Jie Huang, Rasmus Heller, Zhipeng Li, Junhua Liu, Qiang Qiu, 南京农业大学动物科技学院反刍动物营养与饲料工程技术研究中心, 江苏 南京 210095, 中国, 南京农业大学动物科技学院国家动物肠道营养国际联合研究中心, 江苏省消化道营养与动物健康重点实验室, 江苏 南京 210095, 中国, 湖州农业科学院, 浙江 湖州 313000, 中国, 吉林农业大学动物科学技术学院, 吉林 长春 130118, 中国
Abstract
As an important evolutionary innovation and unique organ, the rumen has played a crucial role in ruminant adaptation to complex ecological environments. However, the cellular basis of its complex morphology and function remains largely unknown. In this study, we identified eight major cell types from seven representative prenatal and postnatal rumen samples using ~56 600 single-cell transcriptomes. We captured the dynamic changes and high heterogeneity in cellular and molecular profiles before, during, and after the appearance of keratinized stratified squamous epithelium with neatly arranged papillae and functional maturity. Basal cells, keratinocytes, differentiating keratinocytes, terminally differentiated keratinocytes, and special spinous cells provided the cellular basis for rumen epithelium formation. Notably, we obtained clear evidence of two keratinization processes involved in early papillogenesis and papillae keratinization and identified <i>TBX3</i> as a potential marker gene. Importantly, enriched stratum spinosum cells played crucial roles in volatile fatty acid (VFA) metabolism and immune response. Our results provide a comprehensive transcriptional landscape of rumen development at single-cell resolution, as well as valuable insight into the interactions between dietary metabolism and the rumen.