Genomic variability in Mexican chicken population using copy number variants

Gorla, Erica; Cozzi, M.C.; Román-Ponce, Sergio Iván; López, F. J. Ruiz; Murillo, Vicente Eliezer Vega; Cerolini, S.; Bagnato, A.; Strillacci, M.G.

doi:10.1186/s12863-017-0524-4

Cited by 39 publications

(71 citation statements)

References 46 publications

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“…This difference was not surprising, as the genomic coverage of SNP chips is poor, which results in the detection of longer CNVRs [17,18]. The CNVRs detected in this study accounted for 2.17% of the sheep reference genome, which falls within the range (0.8%-5.12%) reported for horses, pigs, cattle and chickens [19][20][21][22]. However, the CNVRs identified in individual species accounted for more than 10% of their reference genomes, which may be related to the different genetic backgrounds of the studied animals [23,24].…”

Section: Discussionsupporting

confidence: 55%

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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Section: Discussionsupporting

confidence: 55%

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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“…Elferink [16] found that a segment comprising a chicken prolactin receptor in the Z-chromosome is associated with the growth of the chickenundefineds fast-andslow feather. Gorla [17] provided that a chicken CNV map based on the 600 K SNP chip array jointly with a genome-wide gene copy number estimates in a native chicken population. Other reports have shown two copy number variable genes associated with Marek's disease, namely frizzled family receptor 6 (FZD6) and LIM and senescent cell antigen-like domain 1 (LIMS1) [18,19].…”

Section: Introductionmentioning

confidence: 99%

Detection of CNV in the SH3RF2 gene and its effects on growth and carcass traits in chickens

et al. 2020

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Background: The SH3RF2 gene is a protein-coding gene located in a quantitative trait locus associated with body weight, and its deletion has been shown to be positively associated with body weight in chickens.Results: In the present study, CNV in the SH3RF2 gene was detected in 4079 individuals from 17 populations, including the "Gushi ×Anka" F2 resource population and populations of Chinese native chickens, commercial layers, and commercial broilers. The F2 resource population was then used to investigate the genetic effects of the chicken SH3RF2 gene. The results showed that the local chickens and commercial layers were all homozygous for the wild-type allele. Deletion mutation individuals were detected in all of the commercial broiler breeds except Hubbard broiler. A total of, 798 individuals in the F2 resource group were used to analyze the effects of genotype (DD/ID/II) on chicken production traits. The results showed that CNV was associated with 2-, 6-, 10-, and 12-week body weight (P = 0.026, 0.042, 0.021 and 0.039 respectively) and significantly associated with 8-week breast bone length (P = 0.045). The mutation was significantly associated with 8-week body weight (P = 0.007) and 4-week breast bone length (P = 0.010). CNV was significantly associated with evisceration weight, leg muscle weight, carcass weight, breast muscle weight and gizzard weight (P = 0.032, 0.033, 0.045, 0.004 and 0.000, respectively). Conclusions: CNV of the SH3RF2 gene contributed to variation in the growth and weight gain of chickens.

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“…Noteworthy, different algorithms can display variable sensitivity, consistency and reproducibility (ZHANG et al, 2014b). Nevertheless, PennCNV (WANG et al, 2007) was widely used in previous studies in different species, such as in horse (DUPUIS et al, 2013), pig (CHEN et al, 2012DONG et al, 2015;LONG et al, 2016;SCHIAVO et al, 2014;WANG et al, 2013WANG et al, , 2014, cattle (DA SILVA et al, 2016;DE ALMEIDA SANTANA et al, 2016;DURÁN AGUILAR et al, 2017;MCDANELD et al, 2014;WANG et al, 2015), sheep (LIU et al, 2013, including chicken (GORLA et al, 2017;JIA et al, 2013;RAO et al, 2016;ZHANG et al, 2014a;ZHOU et al, 2014), and display a better consistence in comparison with other algorithms (ZHANG et al, 2014b). Moreover, PennCNV is designed for CNV calling using parentsoffspring trios (WANG et al, 2008), which allows higher confidence for detection of inherited and de novo CNVs in populations with known family structure.…”

Section: Identification Of Cnvmentioning

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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Genomic variability in Mexican chicken population using copy number variants

Cited by 39 publications

References 46 publications

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

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

Detection of CNV in the SH3RF2 gene and its effects on growth and carcass traits in chickens

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

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