Genome‐wide selective detection of Mile red‐bone goat using next‐generation sequencing technology

He, Yanan; Hong, Qionghua; Zhou, Dong‐Ke; Wang, Shizhi; Yang, Bo; Yuan, Ying; Zhang, Weiyi; Huang, Yongfu; Guang‐Xin, E

doi:10.1002/ece3.8165

Cited by 4 publications

(3 citation statements)

References 42 publications

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“…Yuan and co-authors were the first to utilize resequencing technology to establish a CNV map of Chinese fine-wool sheep and analyzed the overlap of CNVRs with several quantitative trait loci related to economic traits, providing vital insights for the future improvement of fine-wool sheep ( 110 ). Consistently previous studies employed resequencing to analyze the genomic CNVs of Mile red-boned goats and African goats, respectively ( 64 , 65 ). These findings facilitated a deeper understanding of the genetic traits of these animals.…”

Section: Overview Of Screening Methods For Cnvs In Herbivorous Livest...supporting

confidence: 67%

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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Section: Overview Of Screening Methods For Cnvs In Herbivorous Livest...supporting

confidence: 67%

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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“…However, the results of this study showed non-significant differences in genotype and allele frequencies of the identified SNPs and copy number of EDN3 gene among blackboned and non-black-boned sheep. Interestingly, a different bone pigmentation, e.g., red pigmentation, has also been described in goats [103][104][105]. Such pigmentation characteristics might influence carcass quality and standards and, subsequently, consumer preference.…”

Section: Black Bone Color or Hyperpigmentationmentioning

confidence: 99%

Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes

et al. 2022

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Background After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. Review Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. Conclusions Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.

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“…As compared to SNP mutations, the CNV fragments are large in length and cover a wider range of genomes that have broader prospects in studying animal genetics and breeding application. Recently, next-generation genome sequencing technologies have been continuously used to detect the genome-wide CNVs of livestock (8,9). However, numerous genomic studies exploring CNVs in commercial cattle breeds have underestimated the role of native breeds in the adaptation process (10,11).…”

Section: Introductionmentioning

confidence: 99%

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

Liu

Wang

et al. 2023

Front. Vet. Sci.

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Qaidam cattle (CDM) are indigenous breed inhabiting Northwest China. In the present study, we newly sequenced 20 Qaidam cattle to investigate the copy number variants (CNVs) based on the ARS-UMD1.2 reference genome. We generated the CNV region (CNVR) datasets to explore the genomic CNV diversity and population stratification. The other four cattle breeds (Xizang cattle, XZ; Kazakh cattle, HSK; Mongolian cattle, MG; and Yanbian cattle, YB) from the regions of North China embracing 43 genomic sequences were collected and are distinguished from each of the other diverse populations by deletions and duplications. We also observed that the number of duplications was significantly more than deletions in the genome, which may be less harmful to gene formation and function. At the same time, only 1.15% of CNVRs overlapped with the exon region. Population differential CNVRs and functional annotations between the Qaidam cattle population and other cattle breeds revealed the functional genes related to immunity (MUC6), growth (ADAMTSL3), and adaptability (EBF2). Our analysis has provided numerous genomic characteristics of some Chinese cattle breeds, which are valuable as customized biological molecular markers in cattle breeding and production.

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Genome‐wide selective detection of Mile red‐bone goat using next‐generation sequencing technology

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri bution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 4 publications

References 42 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

Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes

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

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