Journal Article

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

Van Damme, Renaud, Liang, Chunnian, Ayalew, Wondossen, Tessema, Tesfaye Sisay, Naboulsi, Rakan, Chu, Min, Bongcam-Rudloff, Erik, Tarekegn, Getinet Mekuriaw, Ping, Yan, Xiaoyun, Wu

2024

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Adaptability / Adaptation / Adaptation (Physiology) / Adaptation, Physiological - genetics / Agricultural and Veterinary Sciences / Agricultural research / Altitude / Animal and Dairy Science / Animal Genetics and Genomics / Animal populations / Animals / Biomedical and Life Sciences / Breeding / Breeding methods / Cattle / Cattle - genetics / Copy number / Copy number variation / Copy number variations / Disease resistance / DNA Copy Number Variations / DNA sequencing / Economic importance / Environmental aspects / Ethiopia / Ethiopian cattle / Evolution & development / Gene sequencing / Genetic analysis / Genetic aspects / Genetic diversity / Genetic transformation / Genome / Genomes / Genomic analysis / Heat stress / Heat tolerance / High altitude / High-altitude environments / Husdjursvetenskap / Lantbruksvetenskap och veterinärmedicin / Life Sciences / Methods / Microarrays / Microbial Genetics and Genomics / Nucleotide sequencing / Physiological aspects / Plant Genetics and Genomics / Polymerase chain reaction / Population (statistical) / Population genetics / Proteomics / Quantitative trait loci / Software / Statistical analysis / Superoxide dismutase / Whole Genome Sequencing