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

Xiaotong Liu; Wenting Chen; Bingjian Huang; Xinrui Wang; Yongdong Peng; Xinhao Zhang; Wenqiong Chai; Muhammad Zahoor Khan; Changfa Wang

doi:10.3389/fvets.2023.1334434

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

Front Vet Sci. 2024 Jan 11:10:1334434. doi: 10.3389/fvets.2023.1334434. eCollection 2023.

Authors

Xiaotong Liu¹, Wenting Chen¹, Bingjian Huang¹, Xinrui Wang¹, Yongdong Peng¹, Xinhao Zhang¹, Wenqiong Chai¹, Muhammad Zahoor Khan¹, Changfa Wang¹

Affiliation

¹ Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China.

Abstract

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.

Keywords: copy number variation; genome; herbivorous livestock; molecular markers; phenotypes.

Publication types

Review

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by the National Key R&D Program of China (grant number 2022YFD1600103), The Shandong Province Modern Agricultural Technology System Donkey Industrial Innovation Team (grant no. SDAIT-27), Livestock and Poultry Breeding Industry Project of the Ministry of Agriculture and Rural Affairs (grant number 19211162), The National Natural Science Foundation of China (grant no. 31671287), The Open Project of Liaocheng University Animal Husbandry Discipline (grant no. 319312101-14), The Open Project of Shandong Collaborative Innovation Center for Donkey Industry Technology (grant no. 3193308), Research on Donkey Pregnancy Improvement (grant no. K20LC0901), and Liaocheng University scientific research fund (grant no. 318052025).