Cargando…

Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony

BACKGROUND: Body size is considered as one of the most fundamental properties of an organism. Due to intensive breeding and artificial selection throughout the domestication history, horses exhibit striking variations for heights at withers and body sizes. Debao pony (DBP), a famous Chinese horse, i...

Descripción completa

Detalles Bibliográficos
Autores principales: Asadollahpour Nanaei, Hojjat, Esmailizadeh, Ali, Ayatollahi Mehrgardi, Ahmad, Han, Jianlin, Wu, Dong-Dong, Li, Yan, Zhang, Ya-Ping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7370493/
https://www.ncbi.nlm.nih.gov/pubmed/32689947
http://dx.doi.org/10.1186/s12864-020-06887-2
_version_ 1783560988741599232
author Asadollahpour Nanaei, Hojjat
Esmailizadeh, Ali
Ayatollahi Mehrgardi, Ahmad
Han, Jianlin
Wu, Dong-Dong
Li, Yan
Zhang, Ya-Ping
author_facet Asadollahpour Nanaei, Hojjat
Esmailizadeh, Ali
Ayatollahi Mehrgardi, Ahmad
Han, Jianlin
Wu, Dong-Dong
Li, Yan
Zhang, Ya-Ping
author_sort Asadollahpour Nanaei, Hojjat
collection PubMed
description BACKGROUND: Body size is considered as one of the most fundamental properties of an organism. Due to intensive breeding and artificial selection throughout the domestication history, horses exhibit striking variations for heights at withers and body sizes. Debao pony (DBP), a famous Chinese horse, is known for its small body size and lives in Guangxi mountains of southern China. In this study, we employed comparative population genomics to study the genetic basis underlying the small body size of DBP breed based on the whole genome sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (F(ST)), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (θπ), and further analyzed the results to find genomic regions under selection for body size-related traits. RESULTS: A number of protein-coding genes in windows with the top 1% values of F(ST) (367 genes), XP-CLR (681 genes), and log(2) (θπ ratio) (332 genes) were identified. The most significant signal of positive selection was mapped to the NELL1 gene, probably underlies the body size and development traits, and may also have been selected for short stature in the DBP population. In addition, some other loci on different chromosomes were identified to be potentially involved in the development of body size. CONCLUSIONS: Results of our study identified some positively selected genes across the horse genome, which are possibly involved in body size traits. These novel candidate genes may be useful targets for clarifying our understanding of the molecular basis of body size and as such they should be of great interest for future research into the genetic architecture of relevant traits in horse breeding program.
format Online
Article
Text
id pubmed-7370493
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-73704932020-07-21 Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony Asadollahpour Nanaei, Hojjat Esmailizadeh, Ali Ayatollahi Mehrgardi, Ahmad Han, Jianlin Wu, Dong-Dong Li, Yan Zhang, Ya-Ping BMC Genomics Research Article BACKGROUND: Body size is considered as one of the most fundamental properties of an organism. Due to intensive breeding and artificial selection throughout the domestication history, horses exhibit striking variations for heights at withers and body sizes. Debao pony (DBP), a famous Chinese horse, is known for its small body size and lives in Guangxi mountains of southern China. In this study, we employed comparative population genomics to study the genetic basis underlying the small body size of DBP breed based on the whole genome sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (F(ST)), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (θπ), and further analyzed the results to find genomic regions under selection for body size-related traits. RESULTS: A number of protein-coding genes in windows with the top 1% values of F(ST) (367 genes), XP-CLR (681 genes), and log(2) (θπ ratio) (332 genes) were identified. The most significant signal of positive selection was mapped to the NELL1 gene, probably underlies the body size and development traits, and may also have been selected for short stature in the DBP population. In addition, some other loci on different chromosomes were identified to be potentially involved in the development of body size. CONCLUSIONS: Results of our study identified some positively selected genes across the horse genome, which are possibly involved in body size traits. These novel candidate genes may be useful targets for clarifying our understanding of the molecular basis of body size and as such they should be of great interest for future research into the genetic architecture of relevant traits in horse breeding program. BioMed Central 2020-07-20 /pmc/articles/PMC7370493/ /pubmed/32689947 http://dx.doi.org/10.1186/s12864-020-06887-2 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Asadollahpour Nanaei, Hojjat
Esmailizadeh, Ali
Ayatollahi Mehrgardi, Ahmad
Han, Jianlin
Wu, Dong-Dong
Li, Yan
Zhang, Ya-Ping
Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony
title Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony
title_full Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony
title_fullStr Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony
title_full_unstemmed Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony
title_short Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony
title_sort comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in chinese pony
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7370493/
https://www.ncbi.nlm.nih.gov/pubmed/32689947
http://dx.doi.org/10.1186/s12864-020-06887-2
work_keys_str_mv AT asadollahpournanaeihojjat comparativepopulationgenomicanalysisuncoversnovelgenomicfootprintsandgenesassociatedwithsmallbodysizeinchinesepony
AT esmailizadehali comparativepopulationgenomicanalysisuncoversnovelgenomicfootprintsandgenesassociatedwithsmallbodysizeinchinesepony
AT ayatollahimehrgardiahmad comparativepopulationgenomicanalysisuncoversnovelgenomicfootprintsandgenesassociatedwithsmallbodysizeinchinesepony
AT hanjianlin comparativepopulationgenomicanalysisuncoversnovelgenomicfootprintsandgenesassociatedwithsmallbodysizeinchinesepony
AT wudongdong comparativepopulationgenomicanalysisuncoversnovelgenomicfootprintsandgenesassociatedwithsmallbodysizeinchinesepony
AT liyan comparativepopulationgenomicanalysisuncoversnovelgenomicfootprintsandgenesassociatedwithsmallbodysizeinchinesepony
AT zhangyaping comparativepopulationgenomicanalysisuncoversnovelgenomicfootprintsandgenesassociatedwithsmallbodysizeinchinesepony