Whole-genome sequencing of copy number variation analysis in Ethiopian cattle reveals adaptations to diverse environments

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Abstract

Background

Genomic structural variations (GSVs), notably copy number variations (CNVs), significantly shape genetic diversity and facilitate adaptation in cattle populations. Despite their importance, the genome-wide characterization of CNVs in indigenous Ethiopian cattle breeds—Abigar, Fellata, and Gojjam-Highland remains largely unexplored. In this study, we applied a read-depth approach to whole genome sequencing (WGS) data to conduct the first comprehensive analysis of CNVs in these populations.

Results

We identified 3,893 CNV regions (CNVRs) covering 19.15 Mb (0.71% of the cattle genome). These CNVRs ranged from 1.60 kb to 488.0 kb, with an average size of 4.92 kb. These CNVRs included deletions (1713), duplications (1929), and mixed events (251) showing notable differences in distribution among the breeds. Four out of five randomly selected CNVRs were successfully validated using real time polymerase chain reaction (qPCR). Further analyses identified candidate genes associated with high-altitude adaptation ( GBE1 and SOD1), heat stress adaptation ( HSPA13, DNAJC18, and DNAJC8) and resistance to tick infestations ( BoLA and KRT33A). In addition, variance stabilizing transformation ( V _ST ) statistics highlighted population-specific CNVRs, emphasizing the unique genetic signatures of high-altitude adaptation in the Gojjam-Highland cattle breed. Among the detected CNVRs, 4.93% (192 out of 3,893) overlapped with 520 quantitative traits loci (QTLs) associated with six economically important trait categories suggesting that these CNVRs may significantly contribute to the genetic variation underlying these traits.

Conclusions

Our comprehensive analysis reveals significant CNVRs associated with key adaptive traits in Ethiopian cattle breeds highlighting their genetic diversity and resilience. These findings offer valuable insights into the genetic basis of adaptability and can inform sustainable breeding practices and conservation efforts. Future research should prioritize the functional validation of these CNVRs and their integration into breeding programs to enhance traits such as disease resistance and environmental adaptability.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-024-10936-5.

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Most cited references 74

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Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2009)

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk

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BEDTools: a flexible suite of utilities for comparing genomic features

Aaron Quinlan, Ira Hall (2010)

Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools Contact: aaronquinlan@gmail.com; imh4y@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.

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Author and article information

Contributors

Wu Xiaoyun: wuxiaoyun@caas.cn

Getinet Mekuriaw Tarekegn: getinet.tarekegn@sruc.ac.uk

Yan Ping: pingyanlz@163.com

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 15 November 2024

Publication date PMC-release: 15 November 2024

Publication date Collection: 2024

Volume: 25

Electronic Location Identifier: 1088

Affiliations

[1 ]Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, ( https://ror.org/05ckt8b96) Lanzhou, 30050 P.R. China

[2 ]GRID grid.410727.7, ISNI 0000 0001 0526 1937, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, , Chinese Academy of Agricultural Sciences, ; Lanzhou, 730050 P.R. China

[3 ]Institute of Biotechnology, Addis Ababa University, ( https://ror.org/038b8e254) P.O. Box 1176, Addis Ababa, Ethiopia

[4 ]State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, ( https://ror.org/05v9jqt67) Guangzhou, 510642 China

[5 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, Scotland’s Rural College (SRUC), Roslin Institute Building, University of Edinburgh, ; Edinburgh, EH25 9RG UK

[6 ]Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, ( https://ror.org/056d84691) Tomtebodavägen 18A, Stockholm, 17177 Sweden

[7 ]Department of Animal Biosciences, Swedish University of Agricultural Sciences, ( https://ror.org/02yy8x990) Uppsala, 75007 Sweden

[8 ]Institute of Western Agriculture, The Chinese Academy of Agricultural Sciences, ( https://ror.org/0313jb750) Changji, 831100 P.R. China

Article

Publisher ID: 10936

DOI: 10.1186/s12864-024-10936-5

PMC ID: 11566455

PubMed ID: 39548375

SO-VID: 7d7c4d5b-3a65-4db7-b4b2-d1dc6e89c74e

License:

Open Access This 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/.

History

Date received : 4 August 2024

Date accepted : 22 October 2024

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: adaptation,copy number variation,ethiopian cattle,whole-genome sequencing

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ScienceOpen disciplines: Genetics

Keywords: adaptation, copy number variation, ethiopian cattle, whole-genome sequencing

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Whole-genome sequencing of copy number variation analysis in Ethiopian cattle reveals adaptations to diverse environments

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Abstract

Background

Results

Conclusions

Supplementary Information

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Most cited references 74

Trimmomatic: a flexible trimmer for Illumina sequence data

Fast and accurate short read alignment with Burrows–Wheeler transform

BEDTools: a flexible suite of utilities for comparing genomic features

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