A Prospective Screening of Gene Copy Number Variation in Brazilian Admixed Population Sample

Jimenez, Dianny Elizabeth; Lins, Tulio Cesar de Lima; Taveira, Priscilla Orosco; Pereira, Rinaldo Wellerson

doi:10.4172/2161-1041.1000125

Cited by 3 publications

(3 citation statements)

References 43 publications

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“…The exact mutation and inheritance patterns of CNVs are, however not fully understood (Zhang L. et al, 2014 ). It has been proposed that forces such as recombination, selection, and mutations are the primry factors driving the genomic architecture of large variations (Jimenez, 2014 ), with CNVs comprising a mechanism by which the genome responds to selection pressures subseqeunt to genomic instability induced by such pressures (Redon et al, 2006 ). CNVRs correlations and breed type distribution observed in this study, further augment this theory exhibiting an external pressure acting on regions within the genome involved in specific functions (Table 3 ).…”

Section: Discussionmentioning

confidence: 99%

“…The formation and fixation of CNVRs within the genome has not been fully explored. It has been proposed that forces such as recombination, selection and mutations are the primary factors driving the genomic architecture of large variations (Jimenez, 2014 ). Their fixation within the genome indicates an advantage that necessitates DNA repair mechanisms to not remove them from the genome.…”

Section: Introductionmentioning

confidence: 99%

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Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations

2018

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Copy number variations (CNVs) comprise deletions, duplications, and insertions found within the genome larger than 50 bp in size. CNVs are thought to be primary role-players in breed formation and adaptation. South Africa boasts a diverse ecology with harsh environmental conditions and a broad spectrum of parasites and diseases that pose challenges to livestock production. This has led to the development of composite cattle breeds which combine the hardiness of Sanga breeds and the production potential of the Taurine breeds. The prevalence of CNVs within these respective breeds of cattle and the prevalence of CNV regions (CNVRs) in their diversity, adaptation and production is however not understood. This study therefore aimed to ascertain the prevalence, diversity, and correlations of CNVRs within cattle breeds used in South Africa. Illumina Bovine SNP50 data and PennCNV were utilized to identify CNVRs within the genome of 287 animals from seven cattle breeds representing Sanga, Taurine, Composite, and cross breeds. Three hundred and fifty six CNVRs of between 36 kb to 4.1 Mb in size were identified. The null hypothesis that one CNVR loci is independent of another was tested using the GENEPOP software. One hunded and two and seven of the CNVRs in the Taurine and Sanga/Composite cattle breeds demonstrated a significant (p ≤ 0.05) association. PANTHER overrepresentation analyses of correlated CNVRs demonstrated significant enrichment of a number of biological processes, molecular functions, cellular components, and protein classes. CNVR genetic variation between and within breed group was measured using phiPT which allows intra-individual variation to be suppressed and hence proved suitable for measuring binary CNVR presence/absence data. Estimate PhiPT within and between breed variance was 2.722 and 0.518 respectively. Pairwise population PhiPT values corresponded with breed type, with Taurine Holstein and Angus breeds demonstrating no between breed CNVR variation. Phylogenetic trees were drawn. CNVRs primarily clustered animals of the same breed type together. This study successfully identified, characterized, and analyzed 356 CNVRs within seven cattle breeds. CNVR correlations were evident, with many more correlations being present among the exotic Taurine breeds. CNVR genetic diversity of Sanga, Taurine and Composite breeds was ascertained with breed types exposed to similar selection pressures demonstrating analogous incidences of CNVRs.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations

2018

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“…Admixture may generate spurious associations in CNV population genetic studies, although Jimenez et al . () demonstrated no statistical correlation between variation and genetic ancestry and proposed forces such as recombination, selection and mutations as possibly being the factors driving the genomic architecture of large variations in populations. However, the authors did recommend further studies of CNVs in admixed populations to expand this discussion.…”

Section: Challenges and Feasibility Of Cnv Studies In African Cattlementioning

confidence: 97%

Tropically adapted cattle of Africa: perspectives on potential role of copy number variations

et al. 2015

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Africa is host to diverse and locally adapted cattle breeds that are expected to survive the harsh and extreme tropical environments associated with diseases and parasite infections, heat stress and episodes of feed and water scarcity. Genomic copy number variations (CNVs) are considered to be primary role players in cattle breed formation and adaptation where isolation and genetic drift together with subsequent mutations have created an enormous diversity of local populations. CNVs are modifications in DNA structure comprising deletions, duplications and insertions that are >1 kb in size. Despite attracting much attention, the frequency and pattern of bovine CNV events, especially in African cattle breeds, are for the most part largely unknown. Characterization of genetic variation in the indigenous cattle of Africa will be a vital step toward dissecting the molecular mechanisms underlying phenotypic variation and local adaptation. This review therefore aims to describe the current knowledge regarding bovine CNVs and the implications and potentials they encompass for dissecting genetic adaptation and the genotypic skeleton of tropical African cattle populations.

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Cattle Conservation in the 21st Century: A Mini Review

Bolaji¹,

Ajasa²,

Ahmed³

et al. 2021

OJAS

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Cattle are arguably the most important livestock species. Since the beginning of this century, the loss of genetic diversity within this species has been a major concern as this could have serious consequences on the ability of this species to respond to future production constraints. Genetic diversity has traditionally been accessed from pedigree, however, with the advances in molecular genetics new opportunities have emerged. We examined different methods for accessing genetic diversity and estimating genetic diversity parameters at the genomic level. We also examined criteria and strategies for the conservation of animal genetic resources. Finally, we examined genomic studies on some endangered cattle breeds.

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A Prospective Screening of Gene Copy Number Variation in Brazilian Admixed Population Sample

Cited by 3 publications

References 43 publications

Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations

Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations

Tropically adapted cattle of Africa: perspectives on potential role of copy number variations

Cattle Conservation in the 21st Century: A Mini Review

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