Functional characterization of Copy Number Variations regions in Djallonké sheep

Fernández, I.; Tapsoba, Arnaud S. R.; Traoré, Amadou; Menéndez‐Arias, Nuria A.

doi:10.1111/jbg.12542

Cited by 13 publications

(9 citation statements)

References 48 publications

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“…The number of CNVs and CNVRs identified in this study was not directly comparable with other previously reported papers due to differences in the used algorithms, technologies, filter criteria, and numbers of tested samples and breeds [ 42 ]. Although the use of SNP arrays is, nowadays, a standard method, they vary in density and number of markers, ranging from 50K [ 2 , 3 , 4 ] to 600K [ 43 , 44 , 45 ]; for example, Ma et al [ 44 ], analyzing 48 Chinese sheep with the 600K SNP array, identified a higher number of CNVRs (1296) with a smaller size (about 96 Kb) compared with ours.…”

Section: Discussioncontrasting

confidence: 77%

Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Gerlando

Mastrangelo

Tolone

et al. 2022

Animals

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Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome.

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Section: Discussioncontrasting

confidence: 77%

Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Gerlando

Mastrangelo

Tolone

et al. 2022

Animals

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“…Coelho Ladeira detected 216 CNVRs from 491 Santa Inês individuals using the the 50 K SNP array 13 . Different results across studies may be due to different algorithms used for each study, quality control procidures,numbers of individuals and breed chrachteristics 50 .…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds

Taghizadeh

Gholizadeh

Rahimi-Mianji

et al. 2022

Sci Rep

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Copy number variants (CNVs) are a type of genetic polymorphism which contribute to phenotypic variation in several species, including livestock. In this study, we used genomic data of 192 animals from 3 Iranian sheep breeds including 96 Baluchi sheep and 47 Lori-Bakhtiari sheep as fat-tailed breeds and 47 Zel sheep as thin-tailed sheep breed genotyped with Illumina OvineSNP50K Beadchip arrays. Also, for association test, 70 samples of Valle del Belice sheep were added to the association test as thin-tailed sheep breed. PennCNV and CNVRuler software were, respectively, used to study the copy number variation and genomic association analyses. We detected 573 and 242 CNVs in the fat and thin tailed breeds, respectively. In terms of CNV regions (CNVRs), these represented 328 and 187 CNVRs that were within or overlapping with 790 known Ovine genes. The CNVRs covered approximately 73.85 Mb of the sheep genome with average length 146.88 kb, and corresponded to 2.6% of the autosomal genome sequence. Five CNVRs were randomly chosen for validation, of which 4 were experimentally confirmed using Real time qPCR. Functional enrichment analysis showed that genes harbouring CNVs in thin-tailed sheep were involved in the adaptive immune response, regulation of reactive oxygen species biosynthetic process and response to starvation. In fat-tailed breeds these genes were involved in cellular protein modification process, regulation of heart rate, intestinal absorption, olfactory receptor activity and ATP binding. Association test identified one copy gained CNVR on chromosomes 6 harbouring two protein-coding genes HGFAC and LRPAP1. Our findings provide information about genomic structural changes and their association to the interested traits including fat deposition and environmental compatibility in sheep.

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“…In the past twenty years, a large number of CNVs have been revealed and identi ed by using array comparative genome hybridization (aCGH) chips and high-density SNP chips in domestic animals, such as cattle, sheep, goats, horses, dogs, chickens, turkeys and ducks. Meanwhile, numerous CNV-covered genes have been shown to be associated with coat color, growth, fertility and production [1,2], immune response [3][4][5][6][7], olfactory transduction [8][9][10][11], molecular function [12,13], lipid metabolism [4,9,[14][15][16]] and environmental adaptability [17]. Compared with aCGH and SNP chips, the sensitivity of which is mainly limited by the density of the probes, whole genome resequencing can be used to detect new and rare CNVs.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Analysis of CNVs in Three Populations of Tibetan Sheep using Whole-genome Resequencing

Zhang

et al. 2021

Preprint

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Background: Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptations in the Qinghai-Tibetan Plateau.Results: A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected in three Tibetan sheep populations. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis at each CNVR showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between HTS and VTS, and RUNX1 and LOC101111988 were significantly differentiated between VTS and OTS. Meaningfully, the duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in QTP, which deserves further research in detail.Conclusions: In this study, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.

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Functional characterization of Copy Number Variations regions in Djallonké sheep

Cited by 13 publications

References 48 publications

Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds

Genome-wide Analysis of CNVs in Three Populations of Tibetan Sheep using Whole-genome Resequencing

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