牛断奶前后瘤胃长链非编码 RNA 的研究。

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

机构信息

Department of Animal and Avian Sciences, University of Maryland, 8127 Regents Drive, MD, 20742, College Park, USA.

Animal Genomics and Improvement Laboratory, USDA-ARS, Building 306, BARC-East, MD, 20705, Beltsville, USA.

出版信息

BMC Genomics. 2022 Jul 22;23(1):531. doi: 10.1186/s12864-022-08758-4.

DOI:10.1186/s12864-022-08758-4

PMID:35869425

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9308236/

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.

摘要

背景

本研究旨在从奶牛的瘤胃组织中鉴定长链非编码 RNA（lncRNA），探讨其表达和保守水平等特征，并揭示 lncRNA 与复杂性状之间的潜在联系，这些联系可能表明在断奶期过渡期间，瘤胃 lncRNA 具有重要的功能影响。

结果

共采集了六头奶牛的瘤胃组织样本，分别在断奶前后各采集了三个重复样本。提取总 RNA 并进行测序，基于大小、编码潜能、序列同源性和已知蛋白结构域发现 lncRNA。结果分别在断奶前和断奶后鉴定出 404 个和 234 个瘤胃 lncRNA，但仅有 9 个在两种条件下共享，其中 395 个 lncRNA 仅在断奶前组织中发现，225 个仅在断奶后样本中发现。有趣的是，在两种断奶条件下，这 9 个共同的 lncRNA 均没有差异表达。lncRNA 的平均长度较短、表达水平较低且保守评分低于基因组整体，这与一般 lncRNA 的特征一致。通过整合断奶前和断奶后瘤胃 lncRNA 与牛的大规模全基因组关联研究（GWAS）结果，我们报告了 lncRNA 在具有经济重要性的性状中显著富集，包括生产、繁殖、健康和体型表型。

结论

大多数瘤胃 lncRNA 仅在两种断奶条件之一中特异性表达，表明 lncRNA 在瘤胃发育和断奶过渡中具有功能作用。值得注意的是，断奶前和断奶后的 lncRNA 均与奶牛的多种复杂性状显著富集，这表明瘤胃 lncRNA 对奶牛成年阶段的性能很重要。应该进一步研究这些关系，以更好地了解 lncRNA 在瘤胃发育和奶牛性能中的具体作用。