Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis

As a companion and hunting dog, height, length, length to height ratio (LHR) and body-weight are the vital economic traits for Jindo dog. Human selection and targeted breeding have produced an extraordinary diversity in these traits. Therefore, the identification of causative markers, genes and path...

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Autores principales:	Sunirmal Sheet, Jong-Seok Kim, Min-Jeong Ko, Na-Yeon Kim, Young-Jo Lim, Mi-Rim Park, Seung-Jin Lee, Jeong-Min Kim, Seok-Il Oh, Bong-Hwan Choi
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	indigenous breed Jindo height body-weight length GWAS Veterinary medicine SF600-1100 Zoology QL1-991
Acceso en línea:	https://doaj.org/article/a5e46d7a8ba04d8c90f38eca63f61ae0
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spelling	oai:doaj.org-article:a5e46d7a8ba04d8c90f38eca63f61ae02021-11-25T16:16:42ZInsight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis10.3390/ani111131362076-2615https://doaj.org/article/a5e46d7a8ba04d8c90f38eca63f61ae02021-11-01T00:00:00Zhttps://www.mdpi.com/2076-2615/11/11/3136https://doaj.org/toc/2076-2615As a companion and hunting dog, height, length, length to height ratio (LHR) and body-weight are the vital economic traits for Jindo dog. Human selection and targeted breeding have produced an extraordinary diversity in these traits. Therefore, the identification of causative markers, genes and pathways that help us to understand the genetic basis of this variability is essential for their selection purposes. Here, we performed a genome-wide association study (GWAS) combined with enrichment analysis on 757 dogs using 118,879 SNPs. The genomic heritability (h<sup>2</sup>) was 0.33 for height and 0.28 for weight trait in Jindo. At <i>p</i>-value < 5 × 10<sup>−5</sup>, ten, six, thirteen and eleven SNPs on different chromosomes were significantly associated with height, length, LHR and body-weight traits, respectively. Based on our results, <i>HHIP</i>, <i>LCORL</i> and <i>NCAPG</i> for height, <i>IGFI</i> and <i>FGFR3</i> for length, <i>DLK1</i> and <i>EFEMP1</i> for LHR and <i>PTPN2</i>, <i>IGFI</i> and <i>RASAL2</i> for weight can be the potential candidate genes because of the significant SNPs located in their intronic or upstream regions. The gene-set enrichment analysis highlighted here nine and seven overlapping significant (<i>p</i> < 0.05) gene ontology (GO) terms and pathways among traits. Interestingly, the highlighted pathways were related to hormone synthesis, secretion and signalling were generally involved in the metabolism, growth and development process. Our data provide an insight into the significant genes and pathways if verified further, which will have a significant effect on the breeding of the Jindo dog’s population.Sunirmal SheetJong-Seok KimMin-Jeong KoNa-Yeon KimYoung-Jo LimMi-Rim ParkSeung-Jin LeeJeong-Min KimSeok-Il OhBong-Hwan ChoiMDPI AGarticleindigenous breedJindoheightbody-weightlengthGWASVeterinary medicineSF600-1100ZoologyQL1-991ENAnimals, Vol 11, Iss 3136, p 3136 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	indigenous breed Jindo height body-weight length GWAS Veterinary medicine SF600-1100 Zoology QL1-991
spellingShingle	indigenous breed Jindo height body-weight length GWAS Veterinary medicine SF600-1100 Zoology QL1-991 Sunirmal Sheet Jong-Seok Kim Min-Jeong Ko Na-Yeon Kim Young-Jo Lim Mi-Rim Park Seung-Jin Lee Jeong-Min Kim Seok-Il Oh Bong-Hwan Choi Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis
description	As a companion and hunting dog, height, length, length to height ratio (LHR) and body-weight are the vital economic traits for Jindo dog. Human selection and targeted breeding have produced an extraordinary diversity in these traits. Therefore, the identification of causative markers, genes and pathways that help us to understand the genetic basis of this variability is essential for their selection purposes. Here, we performed a genome-wide association study (GWAS) combined with enrichment analysis on 757 dogs using 118,879 SNPs. The genomic heritability (h<sup>2</sup>) was 0.33 for height and 0.28 for weight trait in Jindo. At <i>p</i>-value < 5 × 10<sup>−5</sup>, ten, six, thirteen and eleven SNPs on different chromosomes were significantly associated with height, length, LHR and body-weight traits, respectively. Based on our results, <i>HHIP</i>, <i>LCORL</i> and <i>NCAPG</i> for height, <i>IGFI</i> and <i>FGFR3</i> for length, <i>DLK1</i> and <i>EFEMP1</i> for LHR and <i>PTPN2</i>, <i>IGFI</i> and <i>RASAL2</i> for weight can be the potential candidate genes because of the significant SNPs located in their intronic or upstream regions. The gene-set enrichment analysis highlighted here nine and seven overlapping significant (<i>p</i> < 0.05) gene ontology (GO) terms and pathways among traits. Interestingly, the highlighted pathways were related to hormone synthesis, secretion and signalling were generally involved in the metabolism, growth and development process. Our data provide an insight into the significant genes and pathways if verified further, which will have a significant effect on the breeding of the Jindo dog’s population.
format	article
author	Sunirmal Sheet Jong-Seok Kim Min-Jeong Ko Na-Yeon Kim Young-Jo Lim Mi-Rim Park Seung-Jin Lee Jeong-Min Kim Seok-Il Oh Bong-Hwan Choi
author_facet	Sunirmal Sheet Jong-Seok Kim Min-Jeong Ko Na-Yeon Kim Young-Jo Lim Mi-Rim Park Seung-Jin Lee Jeong-Min Kim Seok-Il Oh Bong-Hwan Choi
author_sort	Sunirmal Sheet
title	Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis
title_short	Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis
title_full	Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis
title_fullStr	Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis
title_full_unstemmed	Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis
title_sort	insight into the candidate genes and enriched pathways associated with height, length, length to height ratio and body-weight of korean indigenous breed, jindo dog using gene set enrichment-based gwas analysis
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/a5e46d7a8ba04d8c90f38eca63f61ae0
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Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis

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