Genome-wide detection of CNVs and their association with performance traits in broilers

Copy number variations (CNV) are an important source of genetic variation. CNV has been increasingly studied and frequently associated with diseases and productive traits in livestock animals. However, CNV‐based genome‐wide association studies (GWAS) in Santa Inês sheep, one of the principal sheep breeds in Brazil, have not yet been reported. Thus, the aim of this study was to investigate the association between CNV and growth, efficiency and carcass traits in sheep. The Illumina OvineSNP50 BeadChip array was used to detect CNV in 491 Santa Inês individuals. Then, CNV‐based GWAS was performed with a linear mixed model approach considering a genomic relationship matrix, for ten traits: (1) growth: body weight at three (W3) and six (W6) months of age; (2) efficiency: residual feed intake (RFI) and feed efficiency (FE) and (3) carcass: external carcass length (ECL), leg length (LL), carcass yield (CY), commercial cuts weight (CCW), loin eye area (LEA) and subcutaneous fat thickness (SFT). We identified 1,167 autosomal CNV in 438 sheep, with 294 non‐redundant CNV, ranging from 21.8 to 861.9 kb, merged into 216 distinct copy number variation regions (CNVRs). One significant CNV segment (pFDR‐value<0.05) in OAR3 was associated with CY, while another significant CNV in OAR6 was associated with RFI. Additionally, another 5 CNV segments were considered relevant for investigation in the future studies. The significant segments overlapped 4 QTLs and spanned 8 genes, including the SPAST,TGFA and ADGRL3 genes, involved in cell differentiation and energy metabolism. Therefore, the results of the present study increase knowledge about CNV in sheep, their possible impacts on productive traits, and provide information for future investigations, being especially useful for those interested in structural variations in the sheep genome.

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“…CNV has been identified in different livestock populations (Fernandes et al, 2021; Y. L. Lee et al, 2020;Z. Wang et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…CNV has been identified in different livestock populations (Fernandes et al., 2021; Y. L. Lee et al., 2020; Z. Wang et al., 2020). In sheep, CNV regions (CNVR) were significantly associated with milk production (Di Gerlando et al., 2019) and growth traits (Jiang et al., 2019; Z. Wang et al., 2020).…”

Section: Introductionmentioning

confidence: 99%

CNV detection and their association with growth, efficiency and carcass traits in Santa Inês sheep

Ladeira

Pilonetto

Fernandes

et al. 2022

J Animal Breeding Genetics

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“…Numerous studies have been performed to identify CNVR in other species e.g., cattle [ 20 ], pig [ 43 ], goat [ 26 ], sheep [ 23 ], chicken [ 17 ], and buffalo [ 37 ]. Several studies indicated that CNVs could be highly associated with economically important traits in these species [ 29 , 67 – 69 ]. To our knowledge, the current study provides the first genome-wide CNV detection in American mink.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide detection of copy number variation in American mink using whole-genome sequencing

et al. 2022

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Background Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. Results A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). Conclusions This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.

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“…Since 2006, several studies in humans and animals have identified the association between CNV polymorphisms and different complex phenotypic traits 7 . Several studies have shown the usefulness of CNVs data for describing the genetic basis of phenotypic variations in a variety of species like cattle 11 , 12 , dog 13 , chicken 14 , 15 , pig 16 , 17 , goat 18 , 19 , and rabbit 20 . As for sheep, Fontanesi et al 21 provided the first comparative map of CNVs in the sheep genome using a cross-species array comparative genome hybridization (aCGH).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds

Moradi

Mahmodi

Farahani

et al. 2022

Sci Rep

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Copy number variation (CNV) is one of the main sources of variation between different individuals that has recently attracted much researcher interest as a major source for heritable variation in complex traits. The aim of this study was to identify CNVs in Afghan indigenous sheep consisting of three Arab, Baluchi, and Gadik breeds using genomic arrays containing 53,862 single nucleotide polymorphism (SNP) markers. Data were analyzed using the Hidden Markov Model (HMM) of PennCNV software. In this study, out of 45 sheep studied, 97.8% (44 animals) have shown CNVs. In total, 411 CNVs were observed for autosomal chromosomes and the entire sequence length of around 144 Mb was identified across the genome. The average number of CNVs per each sheep was 9.13. The identified CNVs for Arab, Baluchi, and Gadik breeds were 306, 62, and 43, respectively. After merging overlapped regions, a total of 376 copy number variation regions (CNVR) were identified, which are 286, 50, and 40 for Arab, Baluchi, and Gadik breeds, respectively. Bioinformatics analysis was performed to identify the genes and QTLs reported in these regions and the biochemical pathways involved by these genes. The results showed that many of these CNVRs overlapped with the genes or QTLs that are associated with various pathways such as immune system development, growth, reproduction, and environmental adaptions. Furthermore, to determine a genome-wide pattern of selection signatures in Afghan sheep breeds, the unbiased estimates of FST was calculated and the results indicated that 37 of the 376 CNVRs (~ 10%) have been also under selection signature, most of those overlapped with the genes influencing production, reproduction and immune system. Finally, the statistical methods used in this study was applied in an external dataset including 96 individuals of the Iranian sheep breed. The results indicated that 20 of the 114 CNVRs (18%) identified in Iranian sheep breed were also identified in our study, most of those overlapped with the genes influencing production, reproduction and immune system. Overall, this is the first attempts to develop the genomic map of loss and gain variation in the genome of Afghan indigenous sheep breeds, and may be important to shed some light on the genomic regions associated with some economically important traits in these breeds.

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Genome-wide detection of CNVs and their association with performance traits in broilers

Cited by 34 publications

References 92 publications

CNV detection and their association with growth, efficiency and carcass traits in Santa Inês sheep

CNV detection and their association with growth, efficiency and carcass traits in Santa Inês sheep

Genome-wide detection of copy number variation in American mink using whole-genome sequencing

Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds

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