Non-coding transcriptomic profiles in the sheep mammary gland during different lactation periods

Weihao Chen; Xinyu Gu; Xiaoyang Lv; Xiukai Cao; Zehu Yuan; Shanhe Wang; Wei Sun

doi:10.3389/fvets.2022.983562

Non-coding transcriptomic profiles in the sheep mammary gland during different lactation periods

Front Vet Sci. 2022 Nov 8:9:983562. doi: 10.3389/fvets.2022.983562. eCollection 2022.

Authors

Weihao Chen¹, Xinyu Gu¹, Xiaoyang Lv², Xiukai Cao², Zehu Yuan², Shanhe Wang², Wei Sun^{1

2

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Affiliations

¹ College of Animal Science and Technology, Yangzhou University, Yangzhou, China.
² Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China.
³ International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China.

Abstract

Sheep milk production is a dynamic and multifactorial trait regulated by diverse biological mechanisms. To improve the quality and production of sheep milk, it is necessary to understand the underlying non-coding transcriptomic mechanisms. In this study, ribonucleic acid-sequencing (RNA-seq) was used to profile the expression of microRNAs (miRNAs) and circular RNAs (circRNAs) in the sheep mammary gland at three key lactation time points (perinatal period, PP; early lactation, EL; and peak lactation, PL). A total of 2,369 novel circRNAs and 272 miRNAs were profiled, of which 348, 373, and 36 differentially expressed (DE) circRNAs and 30, 34, and 7 DE miRNAs were detected in the comparison of EL vs. PP, PL vs. PP, and PL vs. EL, respectively. A series of bioinformatics analyses including functional enrichment, machine learning prediction, and competing endogenous RNA (ceRNA) network analyses were conducted to identify subsets of the potential candidate miRNAs (e.g., oar_miR_148a, oar_miR_362, and oar_miR_432) and circRNAs (e.g., novel_circ_0011066, novel_circ_0010460, and novel_circ_0006589) involved in sheep mammary gland development. Taken together, this study offers a window into the dynamics of non-coding transcriptomes that occur during sheep lactation and may provide further insights into miRNA and circRNA that influence sheep mammary gland development.

Keywords: ceRNA; circRNA; lactation; machine learning; mammary gland; miRNA; sheep.