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Genome-wide association analysis reveals 6 copy number variations associated with the number of cervical vertebrae in Pekin ducks

As a critical developmental stage in vertebrates, the vertebral column formation process is under strict control; however, we observed variations in the number of cervical vertebrae in duck populations in our previous study. Here, we further explored the variations in the number of vertebrae in two...

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Autores principales: Xu, Yaxi, Hu, Jian, Fan, Wenlei, Liu, Hehe, Zhang, Yunsheng, Guo, Zhanbao, Huang, Wei, Liu, Xiaolin, Hou, Shuisheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9685309/
https://www.ncbi.nlm.nih.gov/pubmed/36438573
http://dx.doi.org/10.3389/fcell.2022.1041088
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author Xu, Yaxi
Hu, Jian
Fan, Wenlei
Liu, Hehe
Zhang, Yunsheng
Guo, Zhanbao
Huang, Wei
Liu, Xiaolin
Hou, Shuisheng
author_facet Xu, Yaxi
Hu, Jian
Fan, Wenlei
Liu, Hehe
Zhang, Yunsheng
Guo, Zhanbao
Huang, Wei
Liu, Xiaolin
Hou, Shuisheng
author_sort Xu, Yaxi
collection PubMed
description As a critical developmental stage in vertebrates, the vertebral column formation process is under strict control; however, we observed variations in the number of cervical vertebrae in duck populations in our previous study. Here, we further explored the variations in the number of vertebrae in two duck populations: 421 Pekin duck × mallard F2 ducks and 850 Pekin ducks. Using resequencing data of 125 Pekin ducks with different numbers of cervical vertebrae and 352 Pekin duck × mallard F2 ducks with different numbers of thoracic vertebrae, we detected whole-genome copy number variations (CNVs) and implemented a genome-wide association study (GWAS) to identify the genetic variants related to the traits. The findings verified the existence of variations in the number of cervical vertebrae in duck populations. The number of cervical vertebrae in most ducks was 15, while that in a small number of the ducks was 14 or 16. The number of cervical vertebrae had a positive influence on the neck production, and one cervical vertebra addition could increase 11 g or 2 cm of duck neck. Genome-wide CNV association analysis identified six CNVs associated with the number of cervical vertebrae, and the associated CNV regions covered 15 genes which included WNT10A and WNT6. These findings improve our understanding of the variations in the number of vertebrae in ducks and lay a foundation for future duck breeding.
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spelling pubmed-96853092022-11-25 Genome-wide association analysis reveals 6 copy number variations associated with the number of cervical vertebrae in Pekin ducks Xu, Yaxi Hu, Jian Fan, Wenlei Liu, Hehe Zhang, Yunsheng Guo, Zhanbao Huang, Wei Liu, Xiaolin Hou, Shuisheng Front Cell Dev Biol Cell and Developmental Biology As a critical developmental stage in vertebrates, the vertebral column formation process is under strict control; however, we observed variations in the number of cervical vertebrae in duck populations in our previous study. Here, we further explored the variations in the number of vertebrae in two duck populations: 421 Pekin duck × mallard F2 ducks and 850 Pekin ducks. Using resequencing data of 125 Pekin ducks with different numbers of cervical vertebrae and 352 Pekin duck × mallard F2 ducks with different numbers of thoracic vertebrae, we detected whole-genome copy number variations (CNVs) and implemented a genome-wide association study (GWAS) to identify the genetic variants related to the traits. The findings verified the existence of variations in the number of cervical vertebrae in duck populations. The number of cervical vertebrae in most ducks was 15, while that in a small number of the ducks was 14 or 16. The number of cervical vertebrae had a positive influence on the neck production, and one cervical vertebra addition could increase 11 g or 2 cm of duck neck. Genome-wide CNV association analysis identified six CNVs associated with the number of cervical vertebrae, and the associated CNV regions covered 15 genes which included WNT10A and WNT6. These findings improve our understanding of the variations in the number of vertebrae in ducks and lay a foundation for future duck breeding. Frontiers Media S.A. 2022-11-10 /pmc/articles/PMC9685309/ /pubmed/36438573 http://dx.doi.org/10.3389/fcell.2022.1041088 Text en Copyright © 2022 Xu, Hu, Fan, Liu, Zhang, Guo, Huang, Liu and Hou. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cell and Developmental Biology
Xu, Yaxi
Hu, Jian
Fan, Wenlei
Liu, Hehe
Zhang, Yunsheng
Guo, Zhanbao
Huang, Wei
Liu, Xiaolin
Hou, Shuisheng
Genome-wide association analysis reveals 6 copy number variations associated with the number of cervical vertebrae in Pekin ducks
title Genome-wide association analysis reveals 6 copy number variations associated with the number of cervical vertebrae in Pekin ducks
title_full Genome-wide association analysis reveals 6 copy number variations associated with the number of cervical vertebrae in Pekin ducks
title_fullStr Genome-wide association analysis reveals 6 copy number variations associated with the number of cervical vertebrae in Pekin ducks
title_full_unstemmed Genome-wide association analysis reveals 6 copy number variations associated with the number of cervical vertebrae in Pekin ducks
title_short Genome-wide association analysis reveals 6 copy number variations associated with the number of cervical vertebrae in Pekin ducks
title_sort genome-wide association analysis reveals 6 copy number variations associated with the number of cervical vertebrae in pekin ducks
topic Cell and Developmental Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9685309/
https://www.ncbi.nlm.nih.gov/pubmed/36438573
http://dx.doi.org/10.3389/fcell.2022.1041088
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