Diversity of copy number variation in the worldwide goat population

M, Liu; Zhou, Yuan; Bd, Rosen; Tassell, Van; Stella, Alessandra; Tosser‐Klopp, Gwenola; Rupp, Rachel; Palhière, Isabelle; Colli, Licia; Sayre, Brian; Crepaldi, P.; Fang, Lingzhao; Mészáros, Gábor; Chen, H; Liu, Ge

doi:10.1038/s41437-018-0150-6

Cited by 48 publications

(83 citation statements)

References 52 publications

(56 reference statements)

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“…A large proportion of the global CNVR identi ed in this study (65.1 %) are within the CNVR reported by Liu et al [18]. The remaining 34.9 % may comprise false positive CNVR and CNVR that were missed by the PennCNV algorithm used in the other study, considering the limitation of CNV detection using SNP data, which include limited coverage for genome, low resolution, and di culty in detecting novel and rare mutations.…”

Section: Discussionsupporting

confidence: 60%

Detection of copy number variants in African goats using whole genome sequence data

Nandolo

Mészáros

Wurzinger

et al. 2020

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Background Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled copy number variation map for African goats. We used sequence data from multiple breeds and from multiple African countries. Results A total of 253,553 CNV (244,876 deletions and 8,677 duplications) were identified, corresponding to an overall average of 1,393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6,231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all 5 geographical areas across Africa, where animals had been sampled. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment. Conclusions This study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats.

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Section: Discussionsupporting

confidence: 60%

Detection of copy number variants in African goats using whole genome sequence data

Nandolo

Mészáros

Wurzinger

et al. 2020

Preprint

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“…The results suggest that there are negligible differences in the sizes of CNV between populations. Some of the CNV displayed large differences between populations, suggestive of population-specific selective pressures.A large proportion of the global CNVR identified in this study (65.1%) are within the CNVR reported by Liu et al[17]. The remaining 34.9% may comprise false positive CNVR and CNVR that were missed by the PennCNV algorithm used in the other study, considering the limitation of CNV detection using SNP data, which include limited coverage for genome, low resolution, and difficulty in detecting novel and rare mutations.…”

supporting

confidence: 59%

“…[68], Cardoso et al [69] and Colli et al [70], and some of them were also used for detection of CNV using 50 K SNP chip data, as reported by Liu et al [17]. A list of the breeds, populations and samples sizes used in the analysis is given in Table 4 while a full list of individual samples can be found in Supplementary Table 7 (Additional file 1).…”

Section: Sample Descriptionmentioning

confidence: 99%

“…Mb (on chromosomes 1, 2, 6, 7, 12, 14 (two regions), 17, 19, 21, 23 (two regions), 27 and 29).Overall, the CNVR covered about 59.2 Mb of the goat genome. Previous work on genome-wide CNV discovery in goats using SNP data done by Liu et al[17] showed that CNVR cover approximately 262 Mb of the goat genome. Of the 978 CNVR reported in that study, 540 CNVR intersected with 819 CNVR identified in our study.…”

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confidence: 99%

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Detection of copy number variants in African goats using whole genome sequence data

Nandolo

Mészáros

Wurzinger

et al. 2020

Preprint

Self Cite

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BackgroundCopy number variations (CNV) are a significant source of variation in the genome, as such they are essential to the genetic characterization of animal breeds. The aim of this study was to develop a fine-scaled copy number variation map for African goats. We used sequence data from multiple breeds and from multiple African countries. ResultsA total of 253,553 CNV (244,876 deletions and 8,677 duplications) were identified, corresponding to an overall average of 1,393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6,231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all 5 geographical areas across Africa, where animals had been sampled. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment. ConclusionsThis study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats.

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“…CNVs do not only extensively exist in the human genome, but have also been detected in various animal genomes. CNV maps of livestock species such as cattle, goats, sheep and pigs have already been published, and studies have shown that these CNVs have some influence on the production performance of livestock [5][6][7][8]. Zhang et al found that a 1 kb sequence deletion in the GBP2 gene of cattle was significantly correlated with growth and development characteristics, indicating that this CNV could serve as a marker for the molecular breeding of cattle [9].…”

Section: Introductionmentioning

confidence: 99%

A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing

Yuan

Guo

et al. 2019

Preprint

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Background Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, important economic traits and the evolution of livestock species. In this study, the genome-wide CNV distribution characteristics of 32 fine-wool sheep from three breeds were analyzed using resequencing.Results A total of 1747604 CNVs were detected in this study, and 7228 CNV regions (CNVR) were obtained after merging overlapping CNVs; these regions accounted for 2.17% of the sheep reference genome. The average length of the CNVRs was 4307.17 bp. “Deletion” events took place more frequently than “duplication” or “both” events. The CNVRs obtained overlapped with previously reported sheep CNVRs to variable extents (4.39%–55.46%). Functional enrichment analysis showed that the CNVR-harboring genes were mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Furthermore, 1855 of the CNVRs were associated with 166 quantitative trait loci (QTL), including milk QTLs, carcass QTLs, and health-related QTLs, among others. In addition, the 32 fine-wool sheep were divided into horned and polled groups to analyze for the selective elimination of CNVRs, and it was found that the RXFP2 gene was strongly influenced by selection.Conclusions In summary, we constructed a genomic CNV map for Chinese indigenous fine-wool sheep using resequencing, thereby providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep.

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Diversity of copy number variation in the worldwide goat population

Cited by 48 publications

References 52 publications

Detection of copy number variants in African goats using whole genome sequence data

Detection of copy number variants in African goats using whole genome sequence data

Detection of copy number variants in African goats using whole genome sequence data

A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing

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