Genome-wide investigation to assess copy number variants in the Italian local chicken population.

Chicken Conservation Copy number variant Local breed SNP

Journal

Journal of animal science and biotechnology

ISSN: 1674-9782

Titre abrégé: J Anim Sci Biotechnol

Pays: England

ID NLM: 101581293

Informations de publication

Date de publication:
03 Jan 2024

Historique:

received: 17 07 2023

accepted: 01 12 2023

medline: 4 1 2024

pubmed: 4 1 2024

entrez: 3 1 2024

Statut: epublish

Résumé

Copy number variants (CNV) hold significant functional and evolutionary importance. Numerous ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population structure of livestock. High-density chips have enabled the detection of CNV with increased resolution, leading to the identification of even small CNV. This study aimed to identify CNV in local Italian chicken breeds and investigate their distribution across the genome. Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type CNV. The majority of CNV in the investigated breeds were of types 0 and 1, and the minimum length of CNV was significantly larger than that reported in previous studies. Interestingly, a high proportion of the length of chromosome 16 was covered by copy number variation regions (CNVR), with the major histocompatibility complex being the likely cause. Among the genes identified within CNVR, only those present in at least five animals across breeds (n = 95) were discussed to reduce the focus on redundant CNV. Some of these genes have been associated to functional traits in chickens. Notably, several CNVR on different chromosomes harbor genes related to muscle development, tissue-specific biological processes, heat stress resistance, and immune response. Quantitative trait loci (QTL) were also analyzed to investigate potential overlapping with the identified CNVR: 54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size, carcass characteristics, egg production, egg components, fat deposition, and feed intake. The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources.

Sections du résumé

BACKGROUND BACKGROUND

RESULTS RESULTS

Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type CNV. The majority of CNV in the investigated breeds were of types 0 and 1, and the minimum length of CNV was significantly larger than that reported in previous studies. Interestingly, a high proportion of the length of chromosome 16 was covered by copy number variation regions (CNVR), with the major histocompatibility complex being the likely cause. Among the genes identified within CNVR, only those present in at least five animals across breeds (n = 95) were discussed to reduce the focus on redundant CNV. Some of these genes have been associated to functional traits in chickens. Notably, several CNVR on different chromosomes harbor genes related to muscle development, tissue-specific biological processes, heat stress resistance, and immune response. Quantitative trait loci (QTL) were also analyzed to investigate potential overlapping with the identified CNVR: 54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size, carcass characteristics, egg production, egg components, fat deposition, and feed intake.

CONCLUSIONS CONCLUSIONS

The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources.

Identifiants

DOI: 10.1186/s40104-023-00965-7 PMID: 38167097

pubmed: 38167097

doi: 10.1186/s40104-023-00965-7

pii: 10.1186/s40104-023-00965-7

doi:

Types de publication

Journal Article

Langues

eng

Pagination

Subventions

Organisme : Ministero delle Politiche Agricole Alimentari e Forestali

ID : Ministero delle Politiche Agricole Alimentari e Forestali

Informations de copyright

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