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Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs

Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. Dingyuan pig, as a native pig breed in China, low selection leads to obvious genetic and phenotypic differences in the population. Individuals with extreme fat content in the population a...

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Autores principales: Zhang, Pan, Li, Qinggang, Wu, Yijing, Zhang, Yawen, Zhang, Bo, Zhang, Hao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8857214/
https://www.ncbi.nlm.nih.gov/pubmed/35181733
http://dx.doi.org/10.1038/s41598-022-06868-3
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author Zhang, Pan
Li, Qinggang
Wu, Yijing
Zhang, Yawen
Zhang, Bo
Zhang, Hao
author_facet Zhang, Pan
Li, Qinggang
Wu, Yijing
Zhang, Yawen
Zhang, Bo
Zhang, Hao
author_sort Zhang, Pan
collection PubMed
description Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. Dingyuan pig, as a native pig breed in China, low selection leads to obvious genetic and phenotypic differences in the population. Individuals with extreme fat content in the population are ideal models for studying the mechanism of fat deposition. In this study, we used RNA-Seq and tandem mass tags-based (TMT) proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and IMF deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high and low back fat thickness (HBF, LBF) groups, 85 DEGs and 12 DAPs were obtained in the high and low intramuscular fat (HIMF, LIMF) groups. The functional analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in carbohydrates, amino acids, and fatty acids metabolism, whereas the IMF groups were involved in the insulin pathway, longevity, and some disease-related pathways. We found 40 candidate genes that might tissue-specifically lipids deposition for subcutaneous and intramuscular fat. Our research provides theoretical reference materials for the improvement of fat deposition traits of local pig breeds in my country.
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spelling pubmed-88572142022-02-22 Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs Zhang, Pan Li, Qinggang Wu, Yijing Zhang, Yawen Zhang, Bo Zhang, Hao Sci Rep Article Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. Dingyuan pig, as a native pig breed in China, low selection leads to obvious genetic and phenotypic differences in the population. Individuals with extreme fat content in the population are ideal models for studying the mechanism of fat deposition. In this study, we used RNA-Seq and tandem mass tags-based (TMT) proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and IMF deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high and low back fat thickness (HBF, LBF) groups, 85 DEGs and 12 DAPs were obtained in the high and low intramuscular fat (HIMF, LIMF) groups. The functional analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in carbohydrates, amino acids, and fatty acids metabolism, whereas the IMF groups were involved in the insulin pathway, longevity, and some disease-related pathways. We found 40 candidate genes that might tissue-specifically lipids deposition for subcutaneous and intramuscular fat. Our research provides theoretical reference materials for the improvement of fat deposition traits of local pig breeds in my country. Nature Publishing Group UK 2022-02-18 /pmc/articles/PMC8857214/ /pubmed/35181733 http://dx.doi.org/10.1038/s41598-022-06868-3 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Zhang, Pan
Li, Qinggang
Wu, Yijing
Zhang, Yawen
Zhang, Bo
Zhang, Hao
Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs
title Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs
title_full Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs
title_fullStr Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs
title_full_unstemmed Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs
title_short Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs
title_sort identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in dingyuan pigs
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8857214/
https://www.ncbi.nlm.nih.gov/pubmed/35181733
http://dx.doi.org/10.1038/s41598-022-06868-3
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