Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon

Abstract Pig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding abled us to develop “Nanchukmacdon” a pig breeds with an enhanced variety of meat and...

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Autores principales:	Devender Arora, Krishnamoorthy Srikanth, Jongin Lee, Daehwan Lee, Nayoung Park, Suyeon Wy, Hyeonji Kim, Jong-Eun Park, Han-Ha Chai, Dajeong Lim, In-Cheol Cho, Jaebum Kim, Woncheoul Park
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0c25a1249ecd4cceb064b997c6ebc0c7
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spelling	oai:doaj.org-article:0c25a1249ecd4cceb064b997c6ebc0c72021-12-02T13:26:58ZIntegration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon10.1038/s41598-021-86683-42045-2322https://doaj.org/article/0c25a1249ecd4cceb064b997c6ebc0c72021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86683-4https://doaj.org/toc/2045-2322Abstract Pig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding abled us to develop “Nanchukmacdon” a pig breeds with an enhanced variety of meat and high fertility rate. To identify genomic regions under selection we performed whole-genome resequencing, transcriptome, and whole-genome bisulfite sequencing from Nanchukmacdon muscles samples and used published data for three other breeds such as Landrace, Duroc, Jeju native pig and analyzed the functional characterization of candidate genes. In this study, we present a comprehensive approach to identify candidate genes by using multi-omics approaches. We performed two different methods XP-EHH, XP-CLR to identify traces of artificial selection for traits of economic importance. Moreover, RNAseq analysis was done to identify differentially expressed genes in the crossed breed population. Several genes (UGT8, ZGRF1, NDUFA10, EBF3, ELN, UBE2L6, NCALD, MELK, SERP2, GDPD5, and FHL2) were identified as selective sweep and differentially expressed in muscles related pathways. Furthermore, nucleotide diversity analysis revealed low genetic diversity in Nanchukmacdon for identified genes in comparison to related breeds and whole-genome bisulfite sequencing data shows the critical role of DNA methylation pattern in identified genes that leads to enhanced variety of meat. This work demonstrates a way to identify the molecular signature and lays a foundation for future genomic enabled pig breeding.Devender AroraKrishnamoorthy SrikanthJongin LeeDaehwan LeeNayoung ParkSuyeon WyHyeonji KimJong-Eun ParkHan-Ha ChaiDajeong LimIn-Cheol ChoJaebum KimWoncheoul ParkNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Devender Arora Krishnamoorthy Srikanth Jongin Lee Daehwan Lee Nayoung Park Suyeon Wy Hyeonji Kim Jong-Eun Park Han-Ha Chai Dajeong Lim In-Cheol Cho Jaebum Kim Woncheoul Park Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon
description	Abstract Pig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding abled us to develop “Nanchukmacdon” a pig breeds with an enhanced variety of meat and high fertility rate. To identify genomic regions under selection we performed whole-genome resequencing, transcriptome, and whole-genome bisulfite sequencing from Nanchukmacdon muscles samples and used published data for three other breeds such as Landrace, Duroc, Jeju native pig and analyzed the functional characterization of candidate genes. In this study, we present a comprehensive approach to identify candidate genes by using multi-omics approaches. We performed two different methods XP-EHH, XP-CLR to identify traces of artificial selection for traits of economic importance. Moreover, RNAseq analysis was done to identify differentially expressed genes in the crossed breed population. Several genes (UGT8, ZGRF1, NDUFA10, EBF3, ELN, UBE2L6, NCALD, MELK, SERP2, GDPD5, and FHL2) were identified as selective sweep and differentially expressed in muscles related pathways. Furthermore, nucleotide diversity analysis revealed low genetic diversity in Nanchukmacdon for identified genes in comparison to related breeds and whole-genome bisulfite sequencing data shows the critical role of DNA methylation pattern in identified genes that leads to enhanced variety of meat. This work demonstrates a way to identify the molecular signature and lays a foundation for future genomic enabled pig breeding.
format	article
author	Devender Arora Krishnamoorthy Srikanth Jongin Lee Daehwan Lee Nayoung Park Suyeon Wy Hyeonji Kim Jong-Eun Park Han-Ha Chai Dajeong Lim In-Cheol Cho Jaebum Kim Woncheoul Park
author_facet	Devender Arora Krishnamoorthy Srikanth Jongin Lee Daehwan Lee Nayoung Park Suyeon Wy Hyeonji Kim Jong-Eun Park Han-Ha Chai Dajeong Lim In-Cheol Cho Jaebum Kim Woncheoul Park
author_sort	Devender Arora
title	Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon
title_short	Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon
title_full	Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon
title_fullStr	Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon
title_full_unstemmed	Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon
title_sort	integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in nanchukmacdon
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/0c25a1249ecd4cceb064b997c6ebc0c7
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Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon

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