A genome-wide analysis of copy number variation in Murciano-Granadina goats.
Journal
Genetics, selection, evolution : GSE
ISSN: 1297-9686
Titre abrégé: Genet Sel Evol
Pays: France
ID NLM: 9114088
Informations de publication
Date de publication:
08 Aug 2020
08 Aug 2020
Historique:
received:
02
03
2020
accepted:
28
07
2020
entrez:
11
8
2020
pubmed:
11
8
2020
medline:
3
2
2021
Statut:
epublish
Résumé
In this work, our aim was to generate a map of the copy number variations (CNV) segregating in a population of Murciano-Granadina goats, the most important dairy breed in Spain, and to ascertain the main biological functions of the genes that map to copy number variable regions. Using a dataset that comprised 1036 Murciano-Granadina goats genotyped with the Goat SNP50 BeadChip, we were able to detect 4617 and 7750 autosomal CNV with the PennCNV and QuantiSNP software, respectively. By applying the EnsembleCNV algorithm, these CNV were assembled into 1461 CNV regions (CNVR), of which 486 (33.3% of the total CNVR count) were consistently called by PennCNV and QuantiSNP and used in subsequent analyses. In this set of 486 CNVR, we identified 78 gain, 353 loss and 55 gain/loss events. The total length of all the CNVR (95.69 Mb) represented 3.9% of the goat autosomal genome (2466.19 Mb), whereas their size ranged from 2.0 kb to 11.1 Mb, with an average size of 196.89 kb. Functional annotation of the genes that overlapped with the CNVR revealed an enrichment of pathways related with olfactory transduction (fold-enrichment = 2.33, q-value = 1.61 × 10 A previous study reported that the average number of CNVR per goat breed was ~ 20 (978 CNVR/50 breeds), which is much smaller than the number we found here (486 CNVR). We attribute this difference to the fact that the previous study included multiple caprine breeds that were represented by small to moderate numbers of individuals. Given the low frequencies of CNV (in our study, the average frequency of CNV is 1.44%), such a design would probably underestimate the levels of the diversity of CNV at the within-breed level. We also observed that functions related with sensory perception, metabolism and embryo development are overrepresented in the set of genes that overlapped with CNV, and that these loci often belong to large multigene families with tens, hundreds or thousands of paralogous members, a feature that could favor the occurrence of duplications or deletions by non-allelic homologous recombination.
Sections du résumé
BACKGROUND
BACKGROUND
In this work, our aim was to generate a map of the copy number variations (CNV) segregating in a population of Murciano-Granadina goats, the most important dairy breed in Spain, and to ascertain the main biological functions of the genes that map to copy number variable regions.
RESULTS
RESULTS
Using a dataset that comprised 1036 Murciano-Granadina goats genotyped with the Goat SNP50 BeadChip, we were able to detect 4617 and 7750 autosomal CNV with the PennCNV and QuantiSNP software, respectively. By applying the EnsembleCNV algorithm, these CNV were assembled into 1461 CNV regions (CNVR), of which 486 (33.3% of the total CNVR count) were consistently called by PennCNV and QuantiSNP and used in subsequent analyses. In this set of 486 CNVR, we identified 78 gain, 353 loss and 55 gain/loss events. The total length of all the CNVR (95.69 Mb) represented 3.9% of the goat autosomal genome (2466.19 Mb), whereas their size ranged from 2.0 kb to 11.1 Mb, with an average size of 196.89 kb. Functional annotation of the genes that overlapped with the CNVR revealed an enrichment of pathways related with olfactory transduction (fold-enrichment = 2.33, q-value = 1.61 × 10
CONCLUSIONS
CONCLUSIONS
A previous study reported that the average number of CNVR per goat breed was ~ 20 (978 CNVR/50 breeds), which is much smaller than the number we found here (486 CNVR). We attribute this difference to the fact that the previous study included multiple caprine breeds that were represented by small to moderate numbers of individuals. Given the low frequencies of CNV (in our study, the average frequency of CNV is 1.44%), such a design would probably underestimate the levels of the diversity of CNV at the within-breed level. We also observed that functions related with sensory perception, metabolism and embryo development are overrepresented in the set of genes that overlapped with CNV, and that these loci often belong to large multigene families with tens, hundreds or thousands of paralogous members, a feature that could favor the occurrence of duplications or deletions by non-allelic homologous recombination.
Identifiants
pubmed: 32770942
doi: 10.1186/s12711-020-00564-4
pii: 10.1186/s12711-020-00564-4
pmc: PMC7414533
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
44Subventions
Organisme : Ministerio de Ciencia, Innovación y Universidades
ID : AGL2016-76108-R
Références
Heredity (Edinb). 2019 May;122(5):636-646
pubmed: 30401973
Hum Genomics. 2009 Apr;3(3):281-90
pubmed: 19403462
Nucleic Acids Res. 2007;35(6):2013-25
pubmed: 17341461
Genome Res. 2008 Aug;18(8):1282-93
pubmed: 18493018
Nat Protoc. 2009;4(1):44-57
pubmed: 19131956
Genome Res. 2009 Feb;19(2):276-83
pubmed: 19141597
BMC Genomics. 2010 Nov 17;11:639
pubmed: 21083884
Photochem Photobiol. 2015 Jan-Feb;91(1):188-200
pubmed: 25155575
Mamm Genome. 2002 Oct;13(10):569-77
pubmed: 12420135
Biotechniques. 2004 Oct;37(4):610-3
pubmed: 15517974
J Lipid Res. 2018 Aug;59(8):1529-1535
pubmed: 29866657
Nat Genet. 2001 Dec;29(4):453-8
pubmed: 11726932
Anim Genet. 2012 Oct;43(5):503-17
pubmed: 22497594
Nucleic Acids Res. 1988 Feb 11;16(3):1215
pubmed: 3344216
BMC Genomics. 2012 Aug 06;13:376
pubmed: 22866901
Genet Sel Evol. 2018 Nov 19;50(1):57
pubmed: 30449276
Front Genet. 2019 May 14;10:412
pubmed: 31139206
Nat Rev Genet. 2015 Mar;16(3):172-83
pubmed: 25645873
Nat Rev Genet. 2019 Mar;20(3):135-156
pubmed: 30514919
Mol Genet Genomic Med. 2015 May;3(3):233-7
pubmed: 26029710
BMC Genomics. 2015 Apr 22;16:330
pubmed: 25896665
Genome Res. 2001 May;11(5):685-702
pubmed: 11337468
J Neurosci. 2003 Sep 10;23(23):8291-301
pubmed: 12967991
PLoS Genet. 2008 Feb 29;4(2):e1000003
pubmed: 18454205
Carcinogenesis. 2014 Sep;35(9):1941-50
pubmed: 24510239
Am J Hum Genet. 2008 Aug;83(2):228-42
pubmed: 18674749
Physiol Rev. 2000 Oct;80(4):1523-631
pubmed: 11015620
Cytogenet Genome Res. 2009;126(4):333-47
pubmed: 20016133
Gigascience. 2018 Dec 1;7(12):
pubmed: 30165633
Am J Physiol Endocrinol Metab. 2006 Oct;291(4):E745-54
pubmed: 16705054
BMC Genomics. 2010 Oct 22;11:593
pubmed: 20969757
J Dairy Sci. 2001 Jan;84(1):241-55
pubmed: 11210039
Genome Res. 2007 Nov;17(11):1665-74
pubmed: 17921354
BMC Genomics. 2015 Jun 05;16:431
pubmed: 26044654
Nat Biotechnol. 2011 May 08;29(6):512-20
pubmed: 21552272
J Dairy Sci. 2017 Jul;100(7):5472-5478
pubmed: 28456410
Genet Sel Evol. 2017 Oct 24;49(1):77
pubmed: 29065859
Methods. 2010 Apr;50(4):262-70
pubmed: 20060046
Sci Rep. 2016 Jun 22;6:28438
pubmed: 27329507
PLoS Genet. 2015 Mar 23;11(3):e1005059
pubmed: 25798845
Nucleic Acids Res. 2009 Jan;37(1):1-13
pubmed: 19033363
Nat Protoc. 2019 Mar;14(3):703-721
pubmed: 30804569
Front Genet. 2016 Nov 22;7:207
pubmed: 27920798
Nucleic Acids Res. 2008 Nov;36(19):e126
pubmed: 18784189
Nucleic Acids Res. 2019 Apr 23;47(7):e39
pubmed: 30722045
PLoS One. 2014 Jan 22;9(1):e86227
pubmed: 24465974
Proc Natl Acad Sci U S A. 2019 Jul 2;116(27):13446-13451
pubmed: 31209046
Front Genet. 2014 Feb 18;5:37
pubmed: 24600474
Front Genet. 2017 Aug 23;8:108
pubmed: 28878807
PLoS Genet. 2019 Dec 16;15(12):e1008536
pubmed: 31841508
Database (Oxford). 2015 Sep 27;2015:
pubmed: 26412852
Brief Funct Genomic Proteomic. 2009 Sep;8(5):353-66
pubmed: 19737800
Nat Rev Genet. 2009 Aug;10(8):551-64
pubmed: 19597530
Genet Sel Evol. 2018 Dec 27;50(1):72
pubmed: 30587124
BMC Genomics. 2013 Sep 02;14:596
pubmed: 24004971
PLoS Genet. 2009 Jun;5(6):e1000512
pubmed: 19521496
BMC Genomics. 2012 Aug 02;13:365
pubmed: 22857264
Nat Genet. 2017 Apr;49(4):643-650
pubmed: 28263316
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Genome Res. 2010 May;20(5):693-703
pubmed: 20212021
BMC Genomics. 2012 Nov 15;13:584
pubmed: 23153364