Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle

Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle

Background: Qaidam cattle are local breeds that habitats in northwest China. It has many excellent characteristics, such as high cold and roughage tolerance, low oxygen adaptability, and tender meat quality. Copy number variation (CNV) can induce phenotypic changes in animals by a variety of effects...

Full description

Bibliographic Details
Main Authors: Shaoke Guo, Xiaoyun Wu, Jie Pei, Xingdong Wang, Pengjia Bao, Lin Xiong, Min Chu, Chunnian Liang, Ping Yan, Xian Guo
Format: Article
Language:English
Published: Elsevier 2021-11-01
Series:Electronic Journal of Biotechnology
Subjects:
Cold adaptation
Copy number variable regions
Copy number variation
High-altitude adaptation
Hypoxia
Low oxygen adaptation
Online Access:http://www.sciencedirect.com/science/article/pii/S0717345821000397
id doaj-89f3d7d39d054577b684816e3b0cd638
record_format Article
spelling doaj-89f3d7d39d054577b684816e3b0cd6382021-08-28T04:41:27ZengElsevierElectronic Journal of Biotechnology0717-34582021-11-0154816Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattleShaoke Guo0Xiaoyun Wu1Jie Pei2Xingdong Wang3Pengjia Bao4Lin Xiong5Min Chu6Chunnian Liang7Ping Yan8Xian Guo9Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaCorresponding authors.; Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaCorresponding authors.; Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaBackground: Qaidam cattle are local breeds that habitats in northwest China. It has many excellent characteristics, such as high cold and roughage tolerance, low oxygen adaptability, and tender meat quality. Copy number variation (CNV) can induce phenotypic changes in animals by a variety of effects, and thus affects the biological functions of the animals. To explore the molecular mechanism of its adaptation to extreme cold weather and muscle fat development, the CNV variations in the genome of three Qaidam cattle were detected by whole-genome sequencing, in this study. Results: A total of 16,743 CNVs and 9498 copy number variable regions (CNVRs) were obtained after the screening, which accounts for 2.18% of the bovine genome. The CNVR length detected ranged from 0.3 KB to 10.77 KB, with a total length of 58.17 MB and an average length of 6.12 KB/ CNVR. Through functional enrichment of CNVR related genes, LDHB, and ME1 genes were screened as the key genes for Qaidam cattle to adapt to the cold and low oxygen environments, whereas KIT and FGF18 genes might be related to the coat color and growth. In the CNVR overlapped with QTLs, variation in CAPN1 and CAST genes might be closely related to the tender meat quality of Qaidam cattle. Conclusions: Therefore, this study provides new genetic insights on the environmental adaptability and important economic traits of Qaidam cattle.How to cite: Guo S, Wu X, Pei J, et al. Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle. Electron J Biotechnol 2021;54. https://doi.org/10.1016/j.ejbt.2021.07.006http://www.sciencedirect.com/science/article/pii/S0717345821000397Cold adaptationCopy number variable regionsCopy number variationHigh-altitude adaptationHypoxiaLow oxygen adaptation
collection DOAJ
language English
format Article
sources DOAJ
author Shaoke Guo
Xiaoyun Wu
Jie Pei
Xingdong Wang
Pengjia Bao
Lin Xiong
Min Chu
Chunnian Liang
Ping Yan
Xian Guo
spellingShingle Shaoke Guo
Xiaoyun Wu
Jie Pei
Xingdong Wang
Pengjia Bao
Lin Xiong
Min Chu
Chunnian Liang
Ping Yan
Xian Guo
Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle
Electronic Journal of Biotechnology
Cold adaptation
Copy number variable regions
Copy number variation
High-altitude adaptation
Hypoxia
Low oxygen adaptation
author_facet Shaoke Guo
Xiaoyun Wu
Jie Pei
Xingdong Wang
Pengjia Bao
Lin Xiong
Min Chu
Chunnian Liang
Ping Yan
Xian Guo
author_sort Shaoke Guo
title Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle
title_short Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle
title_full Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle
title_fullStr Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle
title_full_unstemmed Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle
title_sort genome-wide cnv analysis reveals variants associated with high-altitude adaptation and meat traits in qaidam cattle
publisher Elsevier
series Electronic Journal of Biotechnology
issn 0717-3458
publishDate 2021-11-01
description Background: Qaidam cattle are local breeds that habitats in northwest China. It has many excellent characteristics, such as high cold and roughage tolerance, low oxygen adaptability, and tender meat quality. Copy number variation (CNV) can induce phenotypic changes in animals by a variety of effects, and thus affects the biological functions of the animals. To explore the molecular mechanism of its adaptation to extreme cold weather and muscle fat development, the CNV variations in the genome of three Qaidam cattle were detected by whole-genome sequencing, in this study. Results: A total of 16,743 CNVs and 9498 copy number variable regions (CNVRs) were obtained after the screening, which accounts for 2.18% of the bovine genome. The CNVR length detected ranged from 0.3 KB to 10.77 KB, with a total length of 58.17 MB and an average length of 6.12 KB/ CNVR. Through functional enrichment of CNVR related genes, LDHB, and ME1 genes were screened as the key genes for Qaidam cattle to adapt to the cold and low oxygen environments, whereas KIT and FGF18 genes might be related to the coat color and growth. In the CNVR overlapped with QTLs, variation in CAPN1 and CAST genes might be closely related to the tender meat quality of Qaidam cattle. Conclusions: Therefore, this study provides new genetic insights on the environmental adaptability and important economic traits of Qaidam cattle.How to cite: Guo S, Wu X, Pei J, et al. Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle. Electron J Biotechnol 2021;54. https://doi.org/10.1016/j.ejbt.2021.07.006
topic Cold adaptation
Copy number variable regions
Copy number variation
High-altitude adaptation
Hypoxia
Low oxygen adaptation
url http://www.sciencedirect.com/science/article/pii/S0717345821000397
work_keys_str_mv AT shaokeguo genomewidecnvanalysisrevealsvariantsassociatedwithhighaltitudeadaptationandmeattraitsinqaidamcattle
AT xiaoyunwu genomewidecnvanalysisrevealsvariantsassociatedwithhighaltitudeadaptationandmeattraitsinqaidamcattle
AT jiepei genomewidecnvanalysisrevealsvariantsassociatedwithhighaltitudeadaptationandmeattraitsinqaidamcattle
AT xingdongwang genomewidecnvanalysisrevealsvariantsassociatedwithhighaltitudeadaptationandmeattraitsinqaidamcattle
AT pengjiabao genomewidecnvanalysisrevealsvariantsassociatedwithhighaltitudeadaptationandmeattraitsinqaidamcattle
AT linxiong genomewidecnvanalysisrevealsvariantsassociatedwithhighaltitudeadaptationandmeattraitsinqaidamcattle
AT minchu genomewidecnvanalysisrevealsvariantsassociatedwithhighaltitudeadaptationandmeattraitsinqaidamcattle
AT chunnianliang genomewidecnvanalysisrevealsvariantsassociatedwithhighaltitudeadaptationandmeattraitsinqaidamcattle
AT pingyan genomewidecnvanalysisrevealsvariantsassociatedwithhighaltitudeadaptationandmeattraitsinqaidamcattle
AT xianguo genomewidecnvanalysisrevealsvariantsassociatedwithhighaltitudeadaptationandmeattraitsinqaidamcattle
_version_ 1721187869276504064

Similar Items