Cargando…
Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs
SIMPLE SUMMARY: Copy number variation (CNV) is a type of variant that may influence meat quality of, for example intramuscular fat (IMF). In this study, a genome-wide association study (GWAS) was then performed between CNVs and IMF in a pig F2 resource population. A total of 19 CNVRs were found to b...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9179479/ https://www.ncbi.nlm.nih.gov/pubmed/35681846 http://dx.doi.org/10.3390/ani12111382 |
_version_ | 1784723286089793536 |
---|---|
author | Wei, Xia Shu, Ze Wang, Ligang Zhang, Tian Zhang, Longchao Hou, Xinhua Yan, Hua Wang, Lixian |
author_facet | Wei, Xia Shu, Ze Wang, Ligang Zhang, Tian Zhang, Longchao Hou, Xinhua Yan, Hua Wang, Lixian |
author_sort | Wei, Xia |
collection | PubMed |
description | SIMPLE SUMMARY: Copy number variation (CNV) is a type of variant that may influence meat quality of, for example intramuscular fat (IMF). In this study, a genome-wide association study (GWAS) was then performed between CNVs and IMF in a pig F2 resource population. A total of 19 CNVRs were found to be significantly associated with IMF. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings. ABSTRACT: Intramuscular fat (IMF) is a key meat quality trait. Research on the genetic mechanisms of IMF decomposition is valuable for both pork quality improvement and the treatment of obesity and type 2 diabetes. Copy number variations (CNVs) are a type of variant that may influence meat quality. In this study, a total of 1185 CNV regions (CNVRs) including 393 duplicated CNVRs, 432 deleted CNVRs, and 361 CNVRs with both duplicated and deleted status were identified in a pig F2 resource population using next-generation sequencing data. A genome-wide association study (GWAS) was then performed between CNVs and IMF, and a total of 19 CNVRs were found to be significantly associated with IMF. QTL colocation analysis indicated that 3 of the 19 CNVRs overlapped with known QTLs. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. Sequence alignment and Alphafold2 structure prediction results indicated that the two alternative splices of PELP1 have a 23 AA sequence variation and a helix-fold structure variation. This region is located in the region of interaction between PELP1 and other proteins which have been reported to be significantly associated with fat deposition or insulin resistance. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. In conclusion, we found some CNVRs, especially CNV150, located in PELP1 that affect IMF. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings. |
format | Online Article Text |
id | pubmed-9179479 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-91794792022-06-10 Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs Wei, Xia Shu, Ze Wang, Ligang Zhang, Tian Zhang, Longchao Hou, Xinhua Yan, Hua Wang, Lixian Animals (Basel) Article SIMPLE SUMMARY: Copy number variation (CNV) is a type of variant that may influence meat quality of, for example intramuscular fat (IMF). In this study, a genome-wide association study (GWAS) was then performed between CNVs and IMF in a pig F2 resource population. A total of 19 CNVRs were found to be significantly associated with IMF. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings. ABSTRACT: Intramuscular fat (IMF) is a key meat quality trait. Research on the genetic mechanisms of IMF decomposition is valuable for both pork quality improvement and the treatment of obesity and type 2 diabetes. Copy number variations (CNVs) are a type of variant that may influence meat quality. In this study, a total of 1185 CNV regions (CNVRs) including 393 duplicated CNVRs, 432 deleted CNVRs, and 361 CNVRs with both duplicated and deleted status were identified in a pig F2 resource population using next-generation sequencing data. A genome-wide association study (GWAS) was then performed between CNVs and IMF, and a total of 19 CNVRs were found to be significantly associated with IMF. QTL colocation analysis indicated that 3 of the 19 CNVRs overlapped with known QTLs. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. Sequence alignment and Alphafold2 structure prediction results indicated that the two alternative splices of PELP1 have a 23 AA sequence variation and a helix-fold structure variation. This region is located in the region of interaction between PELP1 and other proteins which have been reported to be significantly associated with fat deposition or insulin resistance. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. In conclusion, we found some CNVRs, especially CNV150, located in PELP1 that affect IMF. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings. MDPI 2022-05-27 /pmc/articles/PMC9179479/ /pubmed/35681846 http://dx.doi.org/10.3390/ani12111382 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Wei, Xia Shu, Ze Wang, Ligang Zhang, Tian Zhang, Longchao Hou, Xinhua Yan, Hua Wang, Lixian Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs |
title | Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs |
title_full | Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs |
title_fullStr | Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs |
title_full_unstemmed | Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs |
title_short | Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs |
title_sort | copy number variations contribute to intramuscular fat content differences by affecting the expression of pelp1 alternative splices in pigs |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9179479/ https://www.ncbi.nlm.nih.gov/pubmed/35681846 http://dx.doi.org/10.3390/ani12111382 |
work_keys_str_mv | AT weixia copynumbervariationscontributetointramuscularfatcontentdifferencesbyaffectingtheexpressionofpelp1alternativesplicesinpigs AT shuze copynumbervariationscontributetointramuscularfatcontentdifferencesbyaffectingtheexpressionofpelp1alternativesplicesinpigs AT wangligang copynumbervariationscontributetointramuscularfatcontentdifferencesbyaffectingtheexpressionofpelp1alternativesplicesinpigs AT zhangtian copynumbervariationscontributetointramuscularfatcontentdifferencesbyaffectingtheexpressionofpelp1alternativesplicesinpigs AT zhanglongchao copynumbervariationscontributetointramuscularfatcontentdifferencesbyaffectingtheexpressionofpelp1alternativesplicesinpigs AT houxinhua copynumbervariationscontributetointramuscularfatcontentdifferencesbyaffectingtheexpressionofpelp1alternativesplicesinpigs AT yanhua copynumbervariationscontributetointramuscularfatcontentdifferencesbyaffectingtheexpressionofpelp1alternativesplicesinpigs AT wanglixian copynumbervariationscontributetointramuscularfatcontentdifferencesbyaffectingtheexpressionofpelp1alternativesplicesinpigs |