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

Abstract

Background: This study aimed to identify long non-coding RNA (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 to 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 than 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 variety of complex traits in dairy cattle, 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 cow performance.

Fig. 1

Filtering of Transcripts in Pre-weaning and Post-Weaning Rumen Tissue Samples. Once a consensus sequence was generated for each sample, a series of filtering steps were used to isolate candidate lncRNA. Steps included removing known protein coding transcripts, removing transcripts possessing coding potential, and those that demonstrated nucleotide and protein sequence homology. In the pre-weaning rumen tissue sample, 404 transcripts remained, and 234 transcripts remained in the post-weaning rumen tissue sample

Fig. 2

Length distribution of candidate lncRNA transcripts. A Length of all candidate lncRNA transcript. The average length of transcripts measured 674 base pairs, indicated by red line. B Zoomed in distribution of length of all candidate lncRNA transcript. Excluding those longer than 2000 base pairs for added clarity.  C Length of pre-weaning transcripts, ranging from 200 to 17809 and averaging 466 nucleotides. D Length of post-weaning transcripts, ranging from 200 to 56626 and averaging 1033 nucleotides

Fig. 3

Expression of lncRNA candidate transcripts. A FPKM values of transcripts expressed in pre-weaning tissue. Expression levels ranged from 0.17 to 46.81 FPKM, averaging 5.24 FPKM. The average length of transcripts was indicated by red line. B FPKM values of transcripts expressed in post-weaning tissue. Expression levels ranged from 0.72 to 106 FPKM, averaging 7.89 FPKM. The average length of transcripts was indicated by red line

Fig. 4

Phastcons scores of pre- and post-weaning conditions at whole genome, intergenic region, and lncRNA levels. A Boxplot of PhastCons scores for all transcripts, all intergenic transcripts, and all lncRNA candidate transcripts. B Violin plot of all six profiles: all preweaning transcripts, preweaning intergenic regions, preweaning lncRNA transcripts, all postweaning transcripts, postweaning intergenic regions, and postweaning lncRNA transcripts

Fig. 5

Scatter plot of lncRNA PhastCons scores. Most lncRNAs show scores well below 0.50 with a small number being well conserved across many species. Pre-weaning scores ranged from 0.000873 to 0.879405, and post-weaning scores ranged from 0.000183 to 0.658853, with an outlier of 0.98854