Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #390318

Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Investigation of rumen long noncoding RNA before and after weaning in cattle

item MARCEAU, ALEXIS - University Of Maryland
item GAO, YAHUI - University Of Maryland
item Baldwin, Ransom - Randy
item Li, Congjun - Cj
item JIANG, JICAI - North Carolina State University
item MA, LI - University Of Maryland
item Liu, Ge - George

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/12/2022
Publication Date: 7/22/2022
Citation: Marceau, A., Gao, Y., Baldwin, R.L., Li, C., Jiang, J., Ma, L., Liu, G. 2022. Investigation of rumen long noncoding RNA before and after weaning in cattle. BMC Genomics. 23:531.

Interpretive Summary: Long non-coding RNAs (lncRNAs) play important roles in controlling gene expression. We identified and compared rumen lncRNAs before and after weaning, revealing their functional roles in rumen development and transition of weaning. These results fill our knowledge gaps and provide the foundation for incorporating new knowledge into the future animal breeding program. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: Background: This study aims to identify lncRNA from the rumen tissue in dairy cattle, explore their features including expression and conservation levels, and reveal potential links between lncRNA and complex traits that may indicate important functional impacts of rumen lncRNA during the transition of the weaning period. Results: A total of six cattle rumen samples were taken with three replicates from before and after weaning periods, respectively. Total RNAs were extracted and sequenced with lncRNA discovered based on size, coding potential, sequence homology, and known protein domains. As a result, 404 and 234 rumen lncRNAs were identified before and after weaning, respectively. However, only nine of them were shared under two conditions, with 395 lncRNAs found only in pre-weaning tissues and 225 only in post-weaning samples. Interestingly, none of the nine common lncRNAs were differentially expressed between the two weaning conditions. LncRNA averaged shorter length, lower expression, and lower conservation scores when compared to the genome overall, which is consistent with general lncRNA characteristics. By integrating rumen lncRNA before and after weaning with large-scale GWAS results in cattle, we reported significant enrichment of both pre- and after-weaning lncRNA with traits of economic importance including production, reproduction, health, and body conformation phenotypes. Conclusions: The majority of rumen lncRNAs are uniquely expressed in one of the two weaning conditions, indicating a functional role of lncRNA in rumen development and transition of weaning. Notably, both pre- and post-weaning lncRNA showed significant enrichment with a wide variety of dairy traits, suggesting the importance of rumen lncRNA for cattle performance in the adult stage. These relationships should be further investigated to better understand the specific roles lncRNAs are playing in rumen development and cattle performance.