Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle

Abstract

Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from the liver, muscle, hypothalamus, pituitary gland and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.

Transcriptome analysis reveals the potential roles of long non-coding RNAs in feed efficiency of chicken

“…Recently, lncRNAs have received much consideration and a growing number of studies have shown that lncRNAs play key roles in various physiological and pathological processes 59 , 60 . Whereas many of the lncRNAs and their functions are known in different species, such as humans and mouse, lncRNA research is in its infancy in domestic animals, especially in chickens 61 .…”

Transcriptome Analysis Reveals the Potential Roles of Long Non-Coding RNAs in Feed Efficiency of Chicken

“…Recently, lncRNAs have received much consideration and a growing number of studies have shown that lncRNAs play key roles in various physiological and pathological processes (Kern et al, 2018;Alexandre et al, 2020). Whereas many of the lncRNAs and their functions are known in different species, such as humans and mouse, lncRNA research is in its infancy in domestic animals, especially in chickens (Zhang et al, 2017).…”

“…Recently, lncRNAs have received much consideration and a growing number of studies have shown that lncRNAs play key roles in various physiological and pathological processes(Kern et al, 2018;Alexandre et al…”

Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species

“…In cattle, 126 lncRNA were reported to be associated with feed efficiency [ 166 ]. Among them, 71 detected lncRNAs (21 were identified in the adrenal gland, 8 in liver, 10 in muscle, 15 in the hypothalamus, and 17 in the pituitary gland) were identified as the key lncRNAs, which have the potential to regulate the expression of mRNA associated with feed efficiency in cattle [ 166 ]. Meanwhile, several of them were detected within the genomic regions of QTL for traits related to feed efficiency, feed intake, and fat deposition [ 166 ].…”

“…Among them, 71 detected lncRNAs (21 were identified in the adrenal gland, 8 in liver, 10 in muscle, 15 in the hypothalamus, and 17 in the pituitary gland) were identified as the key lncRNAs, which have the potential to regulate the expression of mRNA associated with feed efficiency in cattle [ 166 ]. Meanwhile, several of them were detected within the genomic regions of QTL for traits related to feed efficiency, feed intake, and fat deposition [ 166 ]. For example, TCONS_00119451 and TCONS_00119463 were reported to overlap seven QTLs, which include QTL:56461, QTL:20842, QTL:20843, QTL:20844, QTL:20845, QTL:20846, and QTL:20847, associated with RFI; TCONS_00032445, TCONS_00062811, and TCONS_00149966 were reported to overlap the QTLs related to dry matter intake; TCONS_00188391 and TCONS_00190543 were reported to coincide the QTLs associated with feed conversion ratio; and TCONS_00119451 and TCONS_00119463 were reported to overlap eleven QTLs related to fat deposition related traits [ 166 ].…”