Genome-wide copy number profiling using high-density SNP array in chickens

Yi, Guoqiang; Qu, Lujiang; Chen, S.; Xu, Guanlong; Yang, Ning

doi:10.1111/age.12267

Cited by 20 publications

(27 citation statements)

References 54 publications

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“…We observed that CNVRs gain were more abundant than losses in the three types of CNVRs in both populations, in agreement with previous studies (JIA et al, 2013;WANG et al, 2012;YI et al, 2015). Conrad et al (2006) reported that duplicated events are more likely to be maintained than deletions, because deletion CNVRs were relatively gene-poor and therefore these genes were subject to purifying selection.…”

Section: Copy Number Variation In the Chicken Genomesupporting

confidence: 92%

“…Most of the previous studies were performed on galGal3.0 (ABERNATHY et al, CROOIJMANS et al, 2013;FAN et al, 2013;LUO et al, 2013;TIAN et al, 2013;WANG et al, 2010WANG et al, , 2012. A few recent studies were performed on galGal4.0 (GORLA et al, 2017;YAN et al, 2015;YI et al, 2014YI et al, , 2015, but to date only our study was performed on the most recent version of the genome (galGal5.0). Therefore, we converted the CNVRs identified in galGal3.0 in some studies to galGal4.0 by CrossMap tool (version 0.2.5) (ZHAO et al, 2014) and we repeated the entire CNV calling analyses performed in our study using the galGal4.0.…”

Section: Qtl Overlap and Gene Enrichmentmentioning

confidence: 99%

“…CNV identification studies from SNP chips in chickens were performed using the Illumina 60K BeadChip developed by Groenen et al (2011) (JIA et al, 2013ZHANG et al, 2014b) and using the high density SNP chip available for the domestic chicken (Affymetrix 600K) developed by Kranis et al (2013) (GORLA et al, 2017YI et al, 2015).…”

Section: Copy Number Variations In the Chicken Genomementioning

confidence: 99%

“…Some studies was performed to identified CNVs on chicken genome using different methodologies and breeds (ABERNATHY et al, 2014;CROOIJMANS et al, 2013;FAN et al, 2013;GORLA et al, 2017;LUO et al, 2013;TIAN et al, 2013;WANG et al, 2010WANG et al, , 2012YAN et al, 2015;YI et al, 2015YI et al, , 2014. However, to the best of our knowledge, the CNV inheritance has not yet clearly elucidated.…”

Section: Introductionmentioning

confidence: 99%

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Inherited copy number variation in the chicken genome and association with breast muscle traits

Godoy¹

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Inherited copy number variation in the chicken genome and association with breast muscle traits Copy number variation (CNV) is an important polymorphism that is associated with a wide range of traits in human, wild and livestock species. In chicken, an important source of animal protein and a developmental model organism, CNV is associated with several phenotypes and evolutionary footprints. However, identification and characterization of CNV inheritance on chicken genome lacks further investigation. We screened CNVs in chicken using two distinct populations with known pedigree. In 826 broilers we identified 25,819 CNVs (4,299 deletions and 21,520 duplications) of which 21,077 were inherited, 201 showed no inheritance and 4,541 were classified as de novo CNVs. In 514 F2 animals (layer and broiler cross) we identified 21,796 CNVs (2,254 deletions and 19,543 duplications) of which 18,230 were inherited, 587 not inherited and 2,979 were classified as de novo CNVs. After a strict filtering step to remove potential false positives and negative CNVs, only 220 (4.84%) and 430 (14.43%) de novo CNVs remained in the broiler and F2 populations, respectively. A total of 33.11% (50 out of 151) of the inherited CNVs identified in ten animals were validated by sequencing data. From the validated CNVs, 64% had more than 80% of their size (bp) validated. A total of 59% and 48.8% were classified as novel CNVs regions (CNVRs) in the broiler and F2, respectively. Considering the Bonferroni-corrected p-values for multiple testing and statistically significant p-values £ 0.01, we found two CNV segments significantly associated with breast weight, one with breast weight yield, six with breast meat weight, 18 CNV segments with breast meat yield, four with breast filet weight and two with breast yield. These CNV segments that were significantly associated overlapped with 181 protein-coding genes. The CNVseg 300, that was associated with all traits and encompass six CNVRs, overlapped a total of 26 protein-coding genes. Among these genes, the gene MYL1 (Myosin Light Chain 1) is expressed in the fast skeletal muscle fibers, and the genes MLPH (Melanophilin), PRLH (Prolactin Releasing Hormone) and RAB17 (Member RAS Oncogene Family), that were associated with the lavender phenotype (feather blue-grey color) and regulation of homeothermy and the metabolism. The present study improves our knowledge about CNV in the chicken genome and provides insight in the distribution and of different classes of CNVs, i.e. inherited and de novo CNVs, in two experimental chicken populations. In addition, the genome-wide association analyses were the first performed on broiler population with breast muscle traits, that are important characteristics for poultry production. The GWAS results allow us to understand the probably relationship between some genes and CNVRs that are significantly associated with breast muscle traits.

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Section: Copy Number Variation In the Chicken Genomesupporting

confidence: 92%

Section: Qtl Overlap and Gene Enrichmentmentioning

confidence: 99%

Section: Copy Number Variations In the Chicken Genomementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Inherited copy number variation in the chicken genome and association with breast muscle traits

Godoy¹

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“…Following the rst two genome-wide scans for CNVs in human genome [7,8], an large number of CNV detection studies have been performed, which revealed that CNVs are ubiquitously distributed in the genome and can in uence the phenotype via regulations of gene expression and gene dosage [9][10][11]. Besides, numerous studies in other species have also shown that CNVs contributed to phenotypic variation of complex diseases and traits [12][13][14][15][16][17][18][19], including MD in chicken [20][21][22]. Two major traditional platforms employed in CNV detection are based on SNP chips, one is known as comparative genomic hybridization (CGH) array, and the other is SNP genotyping array.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing

Bai

Ding

et al. 2020

Preprint

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Background: Marek’s disease (MD) is a highly neoplastic disease primarily affecting chickens, and remains as a chronic infectious disease that threatens the poultry industry. Copy number variation (CNV) has been examined in many species and is recognized as a major source of genetic variation that directly contributes to phenotypic variation such as resistance to infectious diseases. Two highly inbred chicken lines 63 (MD-resistant) and 72 (MD-susceptible), as well as their F1 generation and six recombinant congenic strains (RCSs) with varied susceptibility to MD, are considered as ideal models to identify the complex mechanisms of genetic and molecular resistance to MD.Results: In the present study, to unravel the potential genetic mechanisms underlying resistance to MD, we performed a genome-wide CNV detection using next generation sequencing on the inbred chicken lines with the assistance of CNVnator. As a result, a total of 1,649 CNV regions (CNVRs) were successfully identified after merging all the nine datasets, of which 90 CNVRs were overlapped across all the chicken lines. Within these shared regions, 1,360 harbored genes were identified. In addition, 55 and 44 CNVRs with 62 and 57 harbored genes were specifically identified in line 63 and 72, respectively. Bioinformatics analysis showed that the nearby genes were significantly enriched in 36 GO terms and 6 KEGG pathways including JAK/STAT signaling pathway. Ten CNVRs (nine deletions and one duplication) involved in 10 disease-related genes were selected for validation by using qRT-PCR, all of which were successfully confirmed. Finally, qRT-PCR was also used to validate two deletion events in line 72 that were definitely normal in line 63. One high-confidence gene, IRF2 was identified as the most promising candidate gene underlying resistance and susceptibility to MD in view of its function and overlaps with data from previous study.Conclusions: Our findings provide valuable insights for understanding the genetic mechanism of resistance to MD and the identified gene and pathway could be considered as the subject of further functional characterization.

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Targeted capture enrichment and sequencing identifies extensive nucleotide variation in the turkey MHC-B

2016

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Variation in the major histocompatibility complex (MHC) is increasingly associated with disease susceptibility and resistance in avian species of agricultural importance. This variation includes sequence polymorphisms but also structural differences (gene rearrangement) and copy number variation (CNV). The MHC has now been described for multiple galliform species including the best defined assemblies of the chicken (Gallus gallus) and domestic turkey (Meleagris gallopavo). Using this sequence resource, this study applied high-throughput sequencing to investigate MHC variation in turkeys of North America (NA turkeys). An MHC-specific SureSelect (Agilent) capture array was developed, and libraries were created for 14 turkeys representing domestic (commercial bred), heritage breed, and wild turkeys. In addition, a representative of the Ocellated turkey (M. ocellata) and chicken (G. gallus) was included to test cross-species applicability of the capture array allowing for identification of new species-specific polymorphisms. Libraries were hybridized to ∼12 K cRNA baits and the resulting pools were sequenced. On average, 98% of processed reads mapped to the turkey whole genome sequence and 53% to the MHC target. In addition to the MHC, capture hybridization recovered sequences corresponding to other MHC regions. Sequence alignment and de novo assembly indicated the presence of several additional BG genes in the turkey with evidence for CNV. Variant detection identified an average of 2245 polymorphisms per individual for the NA turkeys, 3012 for the Ocellated turkey, and 462 variants in the chicken (RJF-256). This study provides an extensive sequence resource for examining MHC variation and its relation to health of this agriculturally important group of birds.

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Genome-wide copy number profiling using high-density SNP array in chickens

Cited by 20 publications

References 54 publications

Inherited copy number variation in the chicken genome and association with breast muscle traits

Inherited copy number variation in the chicken genome and association with breast muscle traits

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing

Targeted capture enrichment and sequencing identifies extensive nucleotide variation in the turkey MHC-B

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