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Genomic Structural Diversity in Local Goats: Analysis of Copy-Number Variations. | LitMetric

AI Article Synopsis

  • Copy-number variations (CNVs) are significant structural changes in mammalian genomes, and this study observed CNVs in four local Sicilian goat breeds using SNP array data from 120 individuals.
  • A total of 702 CNVs were detected in 107 goats, which were consolidated into 75 CNV regions, covering about 1.2% of the goat genome.
  • Functional analysis of these CNVs revealed 139 associated genes related to traits like coat color, behavior, immune response, reproduction, and olfactory receptors, paving the way for future research on genetic variations and their impact on phenotypic traits.

Article Abstract

Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes, and are present as deletions, insertions, or duplications. Only few studies have been conducted in goats on CNVs derived from SNP array data, and many local breeds still remain uncharacterized, e.g., the Sicilian goat dairy breeds. In this study, CNV detection was performed, starting from the genotypic data of 120 individuals, belonging to four local breeds (Argentata dell'Etna, Derivata di Siria, Girgentana, and Messinese), genotyped with the Illumina GoatSNP50 BeadChip array. Overall, 702 CNVs were identified in 107 individuals using PennCNV software based on the hidden Markov model algorithm. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair, while 85 CNVs remained unique. The part of the genome covered by CNV events was 35.21 Mb (1.2% of the goat genome length). Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs that are involved in local adaptations, such as coat colour ( and ), mild behaviour (), immune response ( and ), reproduction ( and ), and olfactory receptors (). This study provides insights into the genomic variations for these Sicilian dairy goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341319PMC
http://dx.doi.org/10.3390/ani10061040DOI Listing

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