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Insights Into mRNA and Long Non-coding RNA Profiling RNA Sequencing in Uterus of Chickens With Pink and Blue Eggshell Colors

The blue egg is both of biological interest and economic importance for consumers, egg retailers, and scientists. To date, the genetic mechanisms underlying pigment have mainly focused on protein-coding genes. However, the underpinning mechanism of non-coding RNAs on the pigment deposition among dif...

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Autores principales: Chen, Siyu, Chen, Kecheng, Xu, Jiaming, Li, Fangwei, Ding, Jinlong, Ma, Zheng, Li, Gen, Li, Hua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8529033/
https://www.ncbi.nlm.nih.gov/pubmed/34692811
http://dx.doi.org/10.3389/fvets.2021.736387
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author Chen, Siyu
Chen, Kecheng
Xu, Jiaming
Li, Fangwei
Ding, Jinlong
Ma, Zheng
Li, Gen
Li, Hua
author_facet Chen, Siyu
Chen, Kecheng
Xu, Jiaming
Li, Fangwei
Ding, Jinlong
Ma, Zheng
Li, Gen
Li, Hua
author_sort Chen, Siyu
collection PubMed
description The blue egg is both of biological interest and economic importance for consumers, egg retailers, and scientists. To date, the genetic mechanisms underlying pigment have mainly focused on protein-coding genes. However, the underpinning mechanism of non-coding RNAs on the pigment deposition among different eggshell colors remains unknown. In this study, RNA sequencing was employed to profile the uterine gland transcriptome (lncRNA and mRNA) of 15 Changshun blue eggshell layers, to better understand the genetic mechanisms of deposition of blue eggshell color. Results showed that differentially expressed mRNAs, GO terms, and KEGG pathways among pink-eggshell and blue-eggshell chickens were mainly targeting immune- and transporter-related terms with the SLC family, IgJ, CD family, and MTMR genes. Furthermore, the progesterone-mediated oocyte maturation and cortisol synthesis and secretion pathway with targeted gene PGR and Pbx1 were significantly enriched between blue- and pink-eggshell chickens. Integrating analysis of lncRNA and mRNA profiles predicted 4 and 25 lncRNA–gene pairs by antisense and cis analysis. They were relative to immune, nerve, and lipids and amino acid metabolisms, porphyrin, and chlorophyll metabolism with targeted gene FECH and oxidative phosphorylation and cardiac muscle contraction pathways with targeted gene COX6A1. Within blue-eggshell chickens, the GO terms hindbrain tangential cell migration and phosphatidylinositol monophosphate phosphatase activity with targeted gene Plxna2 and MTRM1 were identified. Integrating analysis of lncRNA and mRNA profiles predicted 8 and 22 lncRNA–gene pairs. Most pathways were mainly enriched on lipid-related metabolisms as found in mRNA sequencing. The lncRNAs did exert similar functions in color formation by modulating pigment disposition and immune- and lipid-related metabolisms. Our results provide a catalog of chicken uterine lncRNAs and genes worthy of further studies to understand their roles in the selection for blue eggshell color layers.
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spelling pubmed-85290332021-10-22 Insights Into mRNA and Long Non-coding RNA Profiling RNA Sequencing in Uterus of Chickens With Pink and Blue Eggshell Colors Chen, Siyu Chen, Kecheng Xu, Jiaming Li, Fangwei Ding, Jinlong Ma, Zheng Li, Gen Li, Hua Front Vet Sci Veterinary Science The blue egg is both of biological interest and economic importance for consumers, egg retailers, and scientists. To date, the genetic mechanisms underlying pigment have mainly focused on protein-coding genes. However, the underpinning mechanism of non-coding RNAs on the pigment deposition among different eggshell colors remains unknown. In this study, RNA sequencing was employed to profile the uterine gland transcriptome (lncRNA and mRNA) of 15 Changshun blue eggshell layers, to better understand the genetic mechanisms of deposition of blue eggshell color. Results showed that differentially expressed mRNAs, GO terms, and KEGG pathways among pink-eggshell and blue-eggshell chickens were mainly targeting immune- and transporter-related terms with the SLC family, IgJ, CD family, and MTMR genes. Furthermore, the progesterone-mediated oocyte maturation and cortisol synthesis and secretion pathway with targeted gene PGR and Pbx1 were significantly enriched between blue- and pink-eggshell chickens. Integrating analysis of lncRNA and mRNA profiles predicted 4 and 25 lncRNA–gene pairs by antisense and cis analysis. They were relative to immune, nerve, and lipids and amino acid metabolisms, porphyrin, and chlorophyll metabolism with targeted gene FECH and oxidative phosphorylation and cardiac muscle contraction pathways with targeted gene COX6A1. Within blue-eggshell chickens, the GO terms hindbrain tangential cell migration and phosphatidylinositol monophosphate phosphatase activity with targeted gene Plxna2 and MTRM1 were identified. Integrating analysis of lncRNA and mRNA profiles predicted 8 and 22 lncRNA–gene pairs. Most pathways were mainly enriched on lipid-related metabolisms as found in mRNA sequencing. The lncRNAs did exert similar functions in color formation by modulating pigment disposition and immune- and lipid-related metabolisms. Our results provide a catalog of chicken uterine lncRNAs and genes worthy of further studies to understand their roles in the selection for blue eggshell color layers. Frontiers Media S.A. 2021-10-07 /pmc/articles/PMC8529033/ /pubmed/34692811 http://dx.doi.org/10.3389/fvets.2021.736387 Text en Copyright © 2021 Chen, Chen, Xu, Li, Ding, Ma, Li and Li. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Veterinary Science
Chen, Siyu
Chen, Kecheng
Xu, Jiaming
Li, Fangwei
Ding, Jinlong
Ma, Zheng
Li, Gen
Li, Hua
Insights Into mRNA and Long Non-coding RNA Profiling RNA Sequencing in Uterus of Chickens With Pink and Blue Eggshell Colors
title Insights Into mRNA and Long Non-coding RNA Profiling RNA Sequencing in Uterus of Chickens With Pink and Blue Eggshell Colors
title_full Insights Into mRNA and Long Non-coding RNA Profiling RNA Sequencing in Uterus of Chickens With Pink and Blue Eggshell Colors
title_fullStr Insights Into mRNA and Long Non-coding RNA Profiling RNA Sequencing in Uterus of Chickens With Pink and Blue Eggshell Colors
title_full_unstemmed Insights Into mRNA and Long Non-coding RNA Profiling RNA Sequencing in Uterus of Chickens With Pink and Blue Eggshell Colors
title_short Insights Into mRNA and Long Non-coding RNA Profiling RNA Sequencing in Uterus of Chickens With Pink and Blue Eggshell Colors
title_sort insights into mrna and long non-coding rna profiling rna sequencing in uterus of chickens with pink and blue eggshell colors
topic Veterinary Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8529033/
https://www.ncbi.nlm.nih.gov/pubmed/34692811
http://dx.doi.org/10.3389/fvets.2021.736387
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