CNV analysis of <i>VAMP7</i> gene reveals variation associated with growth traits in Chinese cattle

Liu, Xian; Yang, Peng; Sun, Haoming; Zhang, Zijing; Cai, Cuicui; Xu, Jie; Ding, Xiaoting; Wang, Xianwei; Lyu, Shijie; Li, Zhiming; Xu, Zejun; Shi, Qiaoting; Wang, Eryao; Lei, Chuzhao; Chen, Hong; Ru, Baorui; Huang, Yongzhen

doi:10.1080/10495398.2021.2011741

Animal Biotechnology

2022

DOI: 10.1080/10495398.2021.2011741

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CNV analysis of VAMP7 gene reveals variation associated with growth traits in Chinese cattle

Xian Liu¹,

Peng Yang

Haoming Sun

et al.

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2024

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Cited by 2 publications

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Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits

Liu,

Chen,

Huang

et al. 2024

Front. Vet. Sci.

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Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.

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Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits

Liu,

Chen,

Huang

et al. 2024

Front. Vet. Sci.

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Analysis of genomic copy number variations through whole-genome scan in Yunling cattle

Dang,

Zhang,

Gao

et al. 2024

Front. Vet. Sci.

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Yunling cattle is a new breed of beef cattle bred in Yunnan Province, China, which has the advantages of fast growth, excellent meat quality, improved tolerance ability, and important landscape value. Copy number variation (CNV) is a significant source of gene structural variation and plays a crucial role in evolution and phenotypic diversity. Based on the latest reference genome ARS-UCD2.0, this study analyzed the genome-wide distribution of CNVs in Yunling cattle using short-read whole-genome sequencing data (n = 129) and single-molecule long-read sequencing data (n = 1), and a total of 16,507 CNVs were detected. After merging CNVs with overlapping genomic positions, 3,728 CNV regions (CNVRs) were obtained, accounting for 0.61% of the reference genome. The functional analysis indicated significant enrichment of CNVRs in 96 GO terms and 57 KEGG pathways, primarily related to cell adhesion, signal transduction, neuromodulation, and nutritional metabolism. Additionally, 111 CNVRs overlapped with 76 quantitative trait loci (QTLs), including Subcutaneous fat thickness QTL, Longissimus muscle area QTL, and Marbling score QTL. Several CNVR-overlapping genes, including BZW1, AOX1, and LOC100138449, overlap with regions associated with meat color and quality QTLs. Furthermore, Vst analysis showed that PSMB4, ERICH1, SMC2, and PPP4R3A were highly divergent between Yunling and Brahman cattle. In summary, we have constructed the genomic CNV map of Yunling cattle for the first time using whole-genome resequencing. This provides valuable genetic variation resources for the study of the Yunling cattle genome and contributes to the study of economic traits in Yunling cattle.

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CNV analysis of VAMP7 gene reveals variation associated with growth traits in Chinese cattle

Cited by 2 publications

References 34 publications

Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits

Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits

Analysis of genomic copy number variations through whole-genome scan in Yunling cattle

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