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Selection signatures of Fuzhong Buffalo based on whole-genome sequences

BACKGROUND: Fuzhong buffalo, a native breed of Guangxi Zhuang Autonomous Region, is traditionally used as a draft animal to provide farm power in the rice cultivation. In addition, the Fuzhong buffalo also prepared for the bullfighting festival organized by the locals. The detection of the selective...

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Autores principales: Sun, Ting, Huang, Guang-yun, Wang, Zi-hao, Teng, Shao-hua, Cao, Yan-hong, Sun, Jun-li, Hanif, Quratulain, Chen, Ning-bo, Lei, Chu-zhao, Liao, Yu-ying
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
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Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7526191/
https://www.ncbi.nlm.nih.gov/pubmed/32993537
http://dx.doi.org/10.1186/s12864-020-07095-8
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author Sun, Ting
Huang, Guang-yun
Wang, Zi-hao
Teng, Shao-hua
Cao, Yan-hong
Sun, Jun-li
Hanif, Quratulain
Chen, Ning-bo
Lei, Chu-zhao
Liao, Yu-ying
author_facet Sun, Ting
Huang, Guang-yun
Wang, Zi-hao
Teng, Shao-hua
Cao, Yan-hong
Sun, Jun-li
Hanif, Quratulain
Chen, Ning-bo
Lei, Chu-zhao
Liao, Yu-ying
author_sort Sun, Ting
collection PubMed
description BACKGROUND: Fuzhong buffalo, a native breed of Guangxi Zhuang Autonomous Region, is traditionally used as a draft animal to provide farm power in the rice cultivation. In addition, the Fuzhong buffalo also prepared for the bullfighting festival organized by the locals. The detection of the selective signatures in its genome can help in elucidating the selection mechanisms in its stamina and muscle development of a draft animal. RESULTS: In this study, we analyzed 27 whole genomes of buffalo (including 15 Fuzhong buffalo genomes and 12 published buffalo genomes from Upper Yangtze region). The ZHp, ZFst, π-Ratio, and XP-EHH statistics were used to identify the candidate signatures of positive selection in Fuzhong buffalo. Our results detected a set of candidate genes involving in the pathways and GO terms associated with the response to exercise (e.g., ALDOA, STAT3, AKT2, EIF4E2, CACNA2D2, TCF4, CDH2), immunity (e.g., PTPN22, NKX2-3, PIK3R1, ITK, TMEM173), nervous system (e.g., PTPN21, ROBO1, HOMER1, MAGI2, SLC1A3, NRG3, SNAP47, CTNNA2, ADGRL3). In addition, we also identified several genes related to production and growth traits (e.g., PHLPP1, PRKN, MACF1, UCN3, RALGAPA1, PHKB, PKD1L). Our results depicted several pathways, GO terms, and candidate genes to be associated with response to exercise, immunity, nervous system, and growth traits. CONCLUSIONS: The selective sweep analysis of the Fuzhong buffalo demonstrated positive selection pressure on potential target genes involved in behavior, immunity, and growth traits, etc. Our findings provided a valuable resource for future research on buffalo breeding and an insight into the mechanisms of artificial selection.
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spelling pubmed-75261912020-09-30 Selection signatures of Fuzhong Buffalo based on whole-genome sequences Sun, Ting Huang, Guang-yun Wang, Zi-hao Teng, Shao-hua Cao, Yan-hong Sun, Jun-li Hanif, Quratulain Chen, Ning-bo Lei, Chu-zhao Liao, Yu-ying BMC Genomics Research Article BACKGROUND: Fuzhong buffalo, a native breed of Guangxi Zhuang Autonomous Region, is traditionally used as a draft animal to provide farm power in the rice cultivation. In addition, the Fuzhong buffalo also prepared for the bullfighting festival organized by the locals. The detection of the selective signatures in its genome can help in elucidating the selection mechanisms in its stamina and muscle development of a draft animal. RESULTS: In this study, we analyzed 27 whole genomes of buffalo (including 15 Fuzhong buffalo genomes and 12 published buffalo genomes from Upper Yangtze region). The ZHp, ZFst, π-Ratio, and XP-EHH statistics were used to identify the candidate signatures of positive selection in Fuzhong buffalo. Our results detected a set of candidate genes involving in the pathways and GO terms associated with the response to exercise (e.g., ALDOA, STAT3, AKT2, EIF4E2, CACNA2D2, TCF4, CDH2), immunity (e.g., PTPN22, NKX2-3, PIK3R1, ITK, TMEM173), nervous system (e.g., PTPN21, ROBO1, HOMER1, MAGI2, SLC1A3, NRG3, SNAP47, CTNNA2, ADGRL3). In addition, we also identified several genes related to production and growth traits (e.g., PHLPP1, PRKN, MACF1, UCN3, RALGAPA1, PHKB, PKD1L). Our results depicted several pathways, GO terms, and candidate genes to be associated with response to exercise, immunity, nervous system, and growth traits. CONCLUSIONS: The selective sweep analysis of the Fuzhong buffalo demonstrated positive selection pressure on potential target genes involved in behavior, immunity, and growth traits, etc. Our findings provided a valuable resource for future research on buffalo breeding and an insight into the mechanisms of artificial selection. BioMed Central 2020-09-29 /pmc/articles/PMC7526191/ /pubmed/32993537 http://dx.doi.org/10.1186/s12864-020-07095-8 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
Sun, Ting
Huang, Guang-yun
Wang, Zi-hao
Teng, Shao-hua
Cao, Yan-hong
Sun, Jun-li
Hanif, Quratulain
Chen, Ning-bo
Lei, Chu-zhao
Liao, Yu-ying
Selection signatures of Fuzhong Buffalo based on whole-genome sequences
title Selection signatures of Fuzhong Buffalo based on whole-genome sequences
title_full Selection signatures of Fuzhong Buffalo based on whole-genome sequences
title_fullStr Selection signatures of Fuzhong Buffalo based on whole-genome sequences
title_full_unstemmed Selection signatures of Fuzhong Buffalo based on whole-genome sequences
title_short Selection signatures of Fuzhong Buffalo based on whole-genome sequences
title_sort selection signatures of fuzhong buffalo based on whole-genome sequences
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7526191/
https://www.ncbi.nlm.nih.gov/pubmed/32993537
http://dx.doi.org/10.1186/s12864-020-07095-8
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