Cargando…

Runs of Homozygosity Revealed Reproductive Traits of Hu Sheep

Hu sheep, a famous breed in the Taihu Basin, has the advantages of non-seasonal estrus, multiple fetuses, coarse feeding tolerance, and suitability for house feeding. Runs of homozygosity (ROHs) were found to be an effective tool to detect the animal population structure and economic traits. The det...

Descripción completa

Detalles Bibliográficos
Autores principales: Li, Yuzhe, Chen, Zitao, Fang, Yifei, Cao, Caiyun, Zhang, Zhe, Pan, Yuchun, Wang, Qishan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9601733/
https://www.ncbi.nlm.nih.gov/pubmed/36292733
http://dx.doi.org/10.3390/genes13101848
_version_ 1784817138899353600
author Li, Yuzhe
Chen, Zitao
Fang, Yifei
Cao, Caiyun
Zhang, Zhe
Pan, Yuchun
Wang, Qishan
author_facet Li, Yuzhe
Chen, Zitao
Fang, Yifei
Cao, Caiyun
Zhang, Zhe
Pan, Yuchun
Wang, Qishan
author_sort Li, Yuzhe
collection PubMed
description Hu sheep, a famous breed in the Taihu Basin, has the advantages of non-seasonal estrus, multiple fetuses, coarse feeding tolerance, and suitability for house feeding. Runs of homozygosity (ROHs) were found to be an effective tool to detect the animal population structure and economic traits. The detection of ROHs is beneficial for reducing the incidence of inbreeding as well as identifying harmful variants in the genome. However, there is a lack of systemic reports on ruminants in previous studies of ROHs. Here, we sequenced 108 Hu sheep, detected ROHs in Hu sheep to calculate their inbreeding coefficient, and selected genes of Hu sheep breeds within the ROH islands which are relevant to agricultural economic characteristics. Then, we compared the characteristics of the occurrences of SNPs between Hu sheep and other sheep breeds, and also investigated the distribution of the frequencies of SNPs within specific gene regions of Hu sheep breeds to select their breed-specific genes. Furthermore, we performed a comparative genome and transcriptome analysis in human and sheep breeds to identify important reproduction-related genes. In this way, we found some significant SNPs, and mapped these with a set of interesting candidate genes which are related to the productive value of livestock (FGF9, BMPR1B, EFNB3, MICU2, GFRA3), healthy characteristics (LGSN, EPHA5, ALOX15B), and breed specificity (FGF9, SAP18, MICU2). These results in our study describe various production traits of Hu sheep from a genetic perspective, and provide insights into the genetic management and complementary understanding of Hu sheep.
format Online
Article
Text
id pubmed-9601733
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-96017332022-10-27 Runs of Homozygosity Revealed Reproductive Traits of Hu Sheep Li, Yuzhe Chen, Zitao Fang, Yifei Cao, Caiyun Zhang, Zhe Pan, Yuchun Wang, Qishan Genes (Basel) Article Hu sheep, a famous breed in the Taihu Basin, has the advantages of non-seasonal estrus, multiple fetuses, coarse feeding tolerance, and suitability for house feeding. Runs of homozygosity (ROHs) were found to be an effective tool to detect the animal population structure and economic traits. The detection of ROHs is beneficial for reducing the incidence of inbreeding as well as identifying harmful variants in the genome. However, there is a lack of systemic reports on ruminants in previous studies of ROHs. Here, we sequenced 108 Hu sheep, detected ROHs in Hu sheep to calculate their inbreeding coefficient, and selected genes of Hu sheep breeds within the ROH islands which are relevant to agricultural economic characteristics. Then, we compared the characteristics of the occurrences of SNPs between Hu sheep and other sheep breeds, and also investigated the distribution of the frequencies of SNPs within specific gene regions of Hu sheep breeds to select their breed-specific genes. Furthermore, we performed a comparative genome and transcriptome analysis in human and sheep breeds to identify important reproduction-related genes. In this way, we found some significant SNPs, and mapped these with a set of interesting candidate genes which are related to the productive value of livestock (FGF9, BMPR1B, EFNB3, MICU2, GFRA3), healthy characteristics (LGSN, EPHA5, ALOX15B), and breed specificity (FGF9, SAP18, MICU2). These results in our study describe various production traits of Hu sheep from a genetic perspective, and provide insights into the genetic management and complementary understanding of Hu sheep. MDPI 2022-10-13 /pmc/articles/PMC9601733/ /pubmed/36292733 http://dx.doi.org/10.3390/genes13101848 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
Li, Yuzhe
Chen, Zitao
Fang, Yifei
Cao, Caiyun
Zhang, Zhe
Pan, Yuchun
Wang, Qishan
Runs of Homozygosity Revealed Reproductive Traits of Hu Sheep
title Runs of Homozygosity Revealed Reproductive Traits of Hu Sheep
title_full Runs of Homozygosity Revealed Reproductive Traits of Hu Sheep
title_fullStr Runs of Homozygosity Revealed Reproductive Traits of Hu Sheep
title_full_unstemmed Runs of Homozygosity Revealed Reproductive Traits of Hu Sheep
title_short Runs of Homozygosity Revealed Reproductive Traits of Hu Sheep
title_sort runs of homozygosity revealed reproductive traits of hu sheep
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9601733/
https://www.ncbi.nlm.nih.gov/pubmed/36292733
http://dx.doi.org/10.3390/genes13101848
work_keys_str_mv AT liyuzhe runsofhomozygosityrevealedreproductivetraitsofhusheep
AT chenzitao runsofhomozygosityrevealedreproductivetraitsofhusheep
AT fangyifei runsofhomozygosityrevealedreproductivetraitsofhusheep
AT caocaiyun runsofhomozygosityrevealedreproductivetraitsofhusheep
AT zhangzhe runsofhomozygosityrevealedreproductivetraitsofhusheep
AT panyuchun runsofhomozygosityrevealedreproductivetraitsofhusheep
AT wangqishan runsofhomozygosityrevealedreproductivetraitsofhusheep