RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep

Abstract Genetic basis of fat deposition in sheep tail have not been completely elucidated yet. Understanding the genetic mechanisms controlling fat-tail size can improve breeding strategies to modulate fat deposition. RNA sequencing has made it possible to discover genetic variants that may underli...

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Autores principales:	Mohammad Reza Bakhtiarizadeh, Ali A. Alamouti
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/754316a2beca4670ab631c11464cc44c
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spelling	oai:doaj.org-article:754316a2beca4670ab631c11464cc44c2021-12-02T18:50:55ZRNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep10.1038/s41598-020-70527-82045-2322https://doaj.org/article/754316a2beca4670ab631c11464cc44c2020-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-70527-8https://doaj.org/toc/2045-2322Abstract Genetic basis of fat deposition in sheep tail have not been completely elucidated yet. Understanding the genetic mechanisms controlling fat-tail size can improve breeding strategies to modulate fat deposition. RNA sequencing has made it possible to discover genetic variants that may underlie various phenotypic differences. Hence, to identify genetic variants that are important for describing different fat-tail phenotypes in sheep, RNA sequencing was used for single nucleotide polymorphism (SNP) calling in two Iranian sheep breeds (Lori-Bakhtiari, fat-tailed; n = 4, vs Zel, thin-tailed; n = 4). Using a stringent pipeline, a total of 112,344 known SNPs were genotyped, of which 30,550 and 42,906 SNPs were shared by at least two Lori-Bakhtiari and Zel, respectively. Comparing these SNPs showed 2,774 (including 209 missense and 25 deleterious SNPs) and 10,470 (including 1,054 missense and 116 deleterious SNPs) breed-specific SNPs in Lori-Bakhtiari and Zel sheep, respectively. Potential breed-specific SNPs were detected by considering those located in QTL regions associated with fatness or reported as important candidates in previous similar studies. Of the breed-specific SNPs, 724 and 2,905 were located in the QTL regions. Functional enrichment analysis of the affected genes revealed several enriched gene ontologies and KEGG pathways related to fat metabolism. Based on the results, several affected genes were proposed to be strongly linked with fat deposition such as DGAT2, ACSL1, ACACA, ADIPOQ, ACLY, FASN, CPT2, SCD, ADCY6, PER3, CSF1R, SLC22A4, GFPT1, CDS2, BMP6, ACSS2, ELOVL6, HOXA10 and FABP4. Moreover, several SNPs were found in the candidate genes related to fatty acid oxidation introducing them as promising candidates responsible for lower fat content in tail of Zel. Our findings provided new insights into the genetic mechanisms of fat deposition in sheep, which can serve to designing appropriate breeding programs.Mohammad Reza BakhtiarizadehAli A. AlamoutiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-13 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mohammad Reza Bakhtiarizadeh Ali A. Alamouti RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep
description	Abstract Genetic basis of fat deposition in sheep tail have not been completely elucidated yet. Understanding the genetic mechanisms controlling fat-tail size can improve breeding strategies to modulate fat deposition. RNA sequencing has made it possible to discover genetic variants that may underlie various phenotypic differences. Hence, to identify genetic variants that are important for describing different fat-tail phenotypes in sheep, RNA sequencing was used for single nucleotide polymorphism (SNP) calling in two Iranian sheep breeds (Lori-Bakhtiari, fat-tailed; n = 4, vs Zel, thin-tailed; n = 4). Using a stringent pipeline, a total of 112,344 known SNPs were genotyped, of which 30,550 and 42,906 SNPs were shared by at least two Lori-Bakhtiari and Zel, respectively. Comparing these SNPs showed 2,774 (including 209 missense and 25 deleterious SNPs) and 10,470 (including 1,054 missense and 116 deleterious SNPs) breed-specific SNPs in Lori-Bakhtiari and Zel sheep, respectively. Potential breed-specific SNPs were detected by considering those located in QTL regions associated with fatness or reported as important candidates in previous similar studies. Of the breed-specific SNPs, 724 and 2,905 were located in the QTL regions. Functional enrichment analysis of the affected genes revealed several enriched gene ontologies and KEGG pathways related to fat metabolism. Based on the results, several affected genes were proposed to be strongly linked with fat deposition such as DGAT2, ACSL1, ACACA, ADIPOQ, ACLY, FASN, CPT2, SCD, ADCY6, PER3, CSF1R, SLC22A4, GFPT1, CDS2, BMP6, ACSS2, ELOVL6, HOXA10 and FABP4. Moreover, several SNPs were found in the candidate genes related to fatty acid oxidation introducing them as promising candidates responsible for lower fat content in tail of Zel. Our findings provided new insights into the genetic mechanisms of fat deposition in sheep, which can serve to designing appropriate breeding programs.
format	article
author	Mohammad Reza Bakhtiarizadeh Ali A. Alamouti
author_facet	Mohammad Reza Bakhtiarizadeh Ali A. Alamouti
author_sort	Mohammad Reza Bakhtiarizadeh
title	RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep
title_short	RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep
title_full	RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep
title_fullStr	RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep
title_full_unstemmed	RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep
title_sort	rna-seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/754316a2beca4670ab631c11464cc44c
work_keys_str_mv	AT mohammadrezabakhtiarizadeh rnaseqbasedgeneticvariantdiscoveryprovidesnewinsightsintocontrollingfatdepositioninthetailofsheep AT aliaalamouti rnaseqbasedgeneticvariantdiscoveryprovidesnewinsightsintocontrollingfatdepositioninthetailofsheep
_version_	1718377454340407296

RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep

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