Genome-Wide Detection of Copy Number Variations and Their Association With Distinct Phenotypes in the World’s Sheep

Salehian-Dehkordi, Hosein; Xu, Yaxi; Xu, Song-Song; Li, Xin; Luo, Laixin; Liu, Ya-Jing; Wang, Dongfeng; Cao, Yin-Hong; Shen, Min; Gao, Lei; Chen, Zehui; Glessner, Joseph; Lenstra, Johannes A.; Esmailizadeh, Ali; Li, Menghua; Lv, Feng‐Hua

doi:10.3389/fgene.2021.670582

Cited by 14 publications

(28 citation statements)

References 71 publications

(98 reference statements)

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“…The proteins of the LRP1B gene (within CNVR_59, common to all breeds), participate in a wide range of physiological processes, including the regulation of lipid metabolism, neurodevelopment, and transport of nutrients and vitamins [ 52 , 53 ], but also in cell proliferation process, making it a potential candidate gene for the supernumerary nipple phenotype [ 54 ]. The KHDRBS2 gene, within the CNVR_310 with the highest variance, has been associated with fertility and reproductive traits in cattle [ 55 ], goat [ 56 ], and sheep [ 57 ]. Moreover, the FILIP1 gene (CNVR_185), reported by Salehian-Dehkordi et al [ 57 ] has been linked with fertility traits.…”

Section: Discussionmentioning

confidence: 99%

“…The KHDRBS2 gene, within the CNVR_310 with the highest variance, has been associated with fertility and reproductive traits in cattle [ 55 ], goat [ 56 ], and sheep [ 57 ]. Moreover, the FILIP1 gene (CNVR_185), reported by Salehian-Dehkordi et al [ 57 ] has been linked with fertility traits. The ACAD9 gene is a recently identified acyl-CoA dehydrogenase that demonstrates maximum activity with unsaturated long-chain acyl-CoAs [ 58 ].…”

Section: Discussionmentioning

confidence: 99%

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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: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

Gerlando

Mastrangelo

Tolone

et al. 2022

Animals

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“…Fat tail in sheep is an adaptive response to harsh environmental conditions and is a source of energy in adverse environmental conditions such as periods of food shortage and severe cold 48 . Salehian-Dehkordi et al identified various CNV-related genes associated with climatic adaptation and artificial selection in sheep 29 .…”

Section: Discussionmentioning

confidence: 99%

“…Salehian-Dehkordi et al using the genome-wide SNPs detected eight CNVRs associated with fat deposition in the tails in the Large-tailed and Small-tailed Han sheep horboting PPP1R11 and GABBR1 genes to be involved in fat deposition in the tails 29 . Zhu et al using high-density SNP arrays detected genome-wide CNVs in Chinese indigenous sheep with different types of tails and reported CNVRs including genes associated with fat deposition 30 .…”

Section: Introductionmentioning

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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“…Unlike SNPs, which refer to the substitution, deletion or insertion of just a single nucleotide for another, CNVs involve fragmental variation even larger than 1000 bp in size ( Iafrate et al, 2004 ; Feuk et al, 2006 ). Therefore, it has been widely recognized that CNVs have the potential to markedly affect phenotypic traits of domestic animals ( Salehian-Dehkordi et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing

Zhang

et al. 2022

Front. Genet.

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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 adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. 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 egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, 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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Genome-Wide Detection of Copy Number Variations and Their Association With Distinct Phenotypes in the World’s Sheep

Cited by 14 publications

References 71 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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