Copy number variation in <scp>F</scp>ayoumi and <scp>L</scp>eghorn chickens analyzed using array comparative genomic hybridization

Abernathy, Jason; Li, X.; Jia, Xiaoyun; Chou, Wei-Yuan; Lamont, Susan J.; Crooijmans, R.P.M.A.; Zhou, Huaijun

doi:10.1111/age.12141

Cited by 18 publications

(22 citation statements)

References 65 publications

(185 reference statements)

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“…These unique CNVRs may be recent events in evolution and contribute to breed-specific phenotype and performance [44]. Compared with the eight previous chicken CNV studies [9,[32][33][34]36,[39][40][41], far more CNVRs both on average and in total were found. A total of 6,478 (86.0%) autosomal CNVRs with slightly smaller average size (10.6 kb) were novel, likely due to the higher resolution and sensitivity of NGS method than aCGH and SNP array.…”

Section: Genome-wide Cnv Landscape In the Chicken Genomementioning

confidence: 77%

“…The NGS technology and RD method employed in our work has advantages in both technology platform and genetic diversity compared with the eight previous reports [9,[32][33][34]36,[39][40][41]. Because a significant fraction of CNVs falls into genomic regions not well-covered by microarrays, especially for SD regions lacking sufficient probes [16,23], CNV as a major source of genetic variation is complementary to SNP and could account for a substantial part of missing heritability [14].…”

Section: Discussionmentioning

confidence: 96%

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Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

Liu

et al. 2014

Preprint

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Background: Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we performed a genome-wide CNV analysis in 12 diversified chicken genomes based on whole genome sequencing. Results: A total of 8,840 CNV regions (CNVRs) covering 98.2 Mb and representing 9.4% of the chicken genome were identified, ranging in size from 1.1 to 268.8 kb with an average of 11.1 kb. Sequencing-based predictions were confirmed at a high validation rate by two independent approaches, including array comparative genomic hybridization (aCGH) and quantitative PCR (qPCR). The Pearson's correlation coefficients between sequencing and aCGH results ranged from 0.435 to 0.755, and qPCR experiments revealed a positive validation rate of 91.71% and a false negative rate of 22.43%. In total, 2,214 (25.0%) predicted CNVRs span 2,216 (36.4%) RefSeq genes associated with specific biological functions. Besides two previously reported copy number variable genes EDN3 and PRLR, we also found some promising genes with potential in phenotypic variation. Two genes, FZD6 and LIMS1, related to disease susceptibility/resistance are covered by CNVRs. The highly duplicated SOCS2 may lead to higher bone mineral density. Entire or partial duplication of some genes like POPDC3 may have great economic importance in poultry breeding. Conclusions: Our results based on extensive genetic diversity provide a more refined chicken CNV map and genome-wide gene copy number estimates, and warrant future CNV association studies for important traits in chickens.

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Section: Genome-wide Cnv Landscape In the Chicken Genomementioning

confidence: 77%

Section: Discussionmentioning

confidence: 96%

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

Liu

et al. 2014

Preprint

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“…; Abernathy et al . ). The smaller gap size of the 600 K SNP array could enable more and shorter CNVs to be detected.…”

Section: Discussionmentioning

confidence: 97%

“…; Abernathy et al . ). Specifically, shared CNVRs had more overlapping proportion than did unique CNVRs, suggesting that these CNVRs may have relatively ancient origins or neutral evolutionary histories and seem to be subsequently introgressed in multiple breeds (Clop et al .…”

Section: Discussionmentioning

confidence: 97%

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

Chen

et al. 2015

Anim Genet

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Phenotypic diversity is a direct consequence resulting mainly from the impact of underlying genetic variation, and recent studies have shown that copy number variation (CNV) is emerging as an important contributor to both phenotypic variability and disease susceptibility. Herein, we performed a genome-wide CNV scan in 96 chickens from 12 diversified breeds, benefiting from the high-density Affymetrix 600 K SNP arrays. We identified a total of 231 autosomal CNV regions (CNVRs) encompassing 5.41 Mb of the chicken genome and corresponding to 0.59% of the autosomal sequence. The length of these CNVRs ranged from 2.6 to 586.2 kb with an average of 23.4 kb, including 130 gain, 93 loss and eight both gain and loss events. These CNVRs, especially deletions, had lower GC content and were located particularly in gene deserts. In particular, 102 CNVRs harbored 128 chicken genes, most of which were enriched in immune responses. We obtained 221 autosomal CNVRs after converting probe coordinates to Galgal3, and comparative analysis with previous studies illustrated that 153 of these CNVRs were regarded as novel events. Furthermore, qPCR assays were designed for 11 novel CNVRs, and eight (72.73%) were validated successfully. In this study, we demonstrated that the high-density 600 K SNP array can capture CNVs with higher efficiency and accuracy and highlighted the necessity of integrating multiple technologies and algorithms. Our findings provide a pioneering exploration of chicken CNVs based on a high-density SNP array, which contributes to a more comprehensive understanding of genetic variation in the chicken genome and is beneficial to unearthing potential CNVs underlying important traits of chickens.

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“…CNVs that have potential roles in economically important traits in chickens have been suggested [58]. Other studies also associated CNVs to diseases [59].…”

Section: Copy Number Variationsmentioning

confidence: 99%

Genomics Tools for the Characterization of Genetic Adaptation of Low Input Extensively Raised Chickens

Muchadeyi¹,

Dzomba²

2017

Poultry Science

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Evolutionary change emanating from diferential contribution of genotypes to the next generation can determine success in survival and reproduction in chickens. For extensively raised chickens reared under low-input production systems in smallholder farming areas, conditions of resources deprivation and exposure to diverse and threatening natural selection pressures are common in many countries worldwide. Numerous studies have demonstrated that village chickens and other extensively raised chicken populations represent a valuable source of biodiversity adapted to the local production conditions and selection pressures. Manipulation of their acquired adaptive genetic diversity depends on unravelling the selection footprints in the genomes of these chickens that could point towards candidate genes for traits that enable the animals to survive under the harsh production environments. This chapter summarizes the evidence for chickens adaptation to extreme environments and describes an inventory of modern tools that could be used in characterizing the production systems of chicken genetic resources. The role of natural selection in shaping the biodiversity of chicken genetic resources is discussed. The continued advancement of biotechnological tools to assess chicken populations has been beneicial to research in genetic adaptation. Genomics tools, as evidenced by assays of whole genome and transcriptome sequences, and single nucleotide polymorphism SNP) genotypes of chickens, now allow analyses of functional genomic regions that are linked to adaptation. The use of these methods to characterize and investigate signatures of selection in the chicken genomes is highlighted. This chapter looks at how information on the selection hotspots in the chicken genomes can be manipulated to improve genetic adaptation in indigenous chicken populations with the desire to transfer the beneits to other chicken breeds raised under similar production systems.

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Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization

Cited by 18 publications

References 65 publications

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

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

Genomics Tools for the Characterization of Genetic Adaptation of Low Input Extensively Raised Chickens

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