Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony
Abstract 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...
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doaj-f8589cf73f3c499b905af00bd6db84332020-11-25T02:48:04ZengBMCBMC Genomics1471-21642020-07-0121111010.1186/s12864-020-06887-2Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese ponyHojjat Asadollahpour Nanaei0Ali Esmailizadeh1Ahmad Ayatollahi Mehrgardi2Jianlin Han3Dong-Dong Wu4Yan Li5Ya-Ping Zhang6Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of KermanDepartment of Animal Science, Faculty of Agriculture, Shahid Bahonar University of KermanDepartment of Animal Science, Faculty of Agriculture, Shahid Bahonar University of KermanCAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS)State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of SciencesState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan UniversityState Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of SciencesAbstract 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 log2 (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.http://link.springer.com/article/10.1186/s12864-020-06887-2Body sizeArtificial selectionPopulation genomicsHorseNELL1 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hojjat Asadollahpour Nanaei Ali Esmailizadeh Ahmad Ayatollahi Mehrgardi Jianlin Han Dong-Dong Wu Yan Li Ya-Ping Zhang |
spellingShingle |
Hojjat Asadollahpour Nanaei Ali Esmailizadeh Ahmad Ayatollahi Mehrgardi Jianlin Han Dong-Dong Wu Yan Li Ya-Ping Zhang Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony BMC Genomics Body size Artificial selection Population genomics Horse NELL1 |
author_facet |
Hojjat Asadollahpour Nanaei Ali Esmailizadeh Ahmad Ayatollahi Mehrgardi Jianlin Han Dong-Dong Wu Yan Li Ya-Ping Zhang |
author_sort |
Hojjat Asadollahpour Nanaei |
title |
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_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_sort |
comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in chinese pony |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2020-07-01 |
description |
Abstract 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 log2 (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. |
topic |
Body size Artificial selection Population genomics Horse NELL1 |
url |
http://link.springer.com/article/10.1186/s12864-020-06887-2 |
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