RNA sequencing reveals lncRNA-mediated non-mendelian inheritance of feather growth change in chickens

Abstract

Background Long non-coding RNAs (lncRNAs) play an essential role in biological processes. However, the expression patterns of lncRNAs that regulate the non-Mendelian inheritance feather phenotypes remain unknown. Objective This study aimed to compare the expression profiles of lncRNAs in the follicles of the late-feathering cocks (LC) and late-feathering hens (LH) that followed genetic rules and the early-feathering hen (EH) and early-feathering cock (EC) that did not conform to the genetic laws. Methods We performed RNA sequencing and investigated the differentially expressed lncRNAs (DElncRNAs) between the early- and late-feathering chickens, which function by cis-acting or participate in the competing endogenous RNA (ceRNA) network. Results A total of 53 upregulated and 43 downregulated lncRNAs were identified in EC vs. LC, and 58 upregulated and 109 downregulated lncRNAs were identified in EH vs. LH. The target mRNAs regulated by lncRNAs in cis were enriched in the pentose phosphate pathway, TGF-β signaling pathway and Jak-STAT signaling pathway in EC vs. LC and were associated with the TGF-β signaling pathway, Wnt signaling pathway, p53 signaling pathway and Jak-STAT signaling pathway in EH vs. LH. In addition, the lncRNA-mediated ceRNA regulatory pathways of hair follicle formation were mainly enriched in the TGF-β signaling pathway, Wnt signaling pathway, melanogenesis, and calcium signaling pathways. The levels of ENSGALG00000047626 were significantly higher in the late-feathering chickens than in the early-feathering chickens, which regulated the expression of SSTR2 by gga-miR-1649-5p. Conclusion This study provides a novel molecular mechanism of lncRNA’s response to the feather rate that does not conform to the genetic laws in chickens.

The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications

“…Some signaling pathways and genes were commonly found in previous investigations of birds, such as the TYR gene in chicken [52], the crested ibis [53], and ducks [54]. The melanogenesis pathway found in PSGs of the Temminck's tragopan was also been identi ed in other birds [32,37,38,[55][56][57], such as the chicken based on transcriptome [57] and genomic SNP data [32]. The WNT10A gene was identi ed in melanogenesis pathway in PSGs of the Temminck's tragopan, and a previous study showed that miR-193b might participate in the adjustment of coat color in the skin tissue of Cashmere goats by targeting WNT10A and GNAI2 [58].…”