Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds.
Composite-likelihood ratio
East Adriatic sheep
Extreme ROH islands
Genomic selection signatures
Integrated haplotype score
Number of segregating sites by length
Journal
Journal of animal science and biotechnology
ISSN: 1674-9782
Titre abrégé: J Anim Sci Biotechnol
Pays: England
ID NLM: 101581293
Informations de publication
Date de publication:
06 Nov 2023
06 Nov 2023
Historique:
received:
15
05
2023
accepted:
04
09
2023
medline:
7
11
2023
pubmed:
7
11
2023
entrez:
7
11
2023
Statut:
epublish
Résumé
The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type. We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis. Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.
Sections du résumé
BACKGROUND
BACKGROUND
The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type.
RESULTS
RESULTS
We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis.
CONCLUSIONS
CONCLUSIONS
Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.
Identifiants
pubmed: 37932811
doi: 10.1186/s40104-023-00936-y
pii: 10.1186/s40104-023-00936-y
pmc: PMC10626677
doi:
Types de publication
Journal Article
Langues
eng
Pagination
142Subventions
Organisme : Hrvatska Zaklada za Znanost
ID : IP-2018-01-8708
Organisme : EU Operational Program Competitiveness and Cohesion 2014-2020
ID : KK.01.1.1.04.0058
Organisme : Ministry of Agriculture, Czech Republic
ID : QK1919156
Informations de copyright
© 2023. The Author(s).
Références
Genes (Basel). 2022 May 31;13(6):
pubmed: 35741748
Am J Pathol. 2013 Jul;183(1):296-303
pubmed: 23665203
PLoS One. 2016 Oct 19;11(10):e0164390
pubmed: 27760167
BMC Genet. 2017 Dec 28;18(Suppl 1):111
pubmed: 29297313
Adv Pharmacol. 2018;81:39-78
pubmed: 29310803
PLoS One. 2012;7(5):e37282
pubmed: 22615965
Genes (Basel). 2022 Oct 15;13(10):
pubmed: 36292755
Genomics. 2021 Sep;113(5):3325-3336
pubmed: 34314829
Anim Genet. 2019 Oct;50(5):512-525
pubmed: 31365135
PLoS Genet. 2013;9(8):e1003681
pubmed: 23966867
Genet Sel Evol. 2022 Jan 24;54(1):5
pubmed: 35073835
Front Genet. 2021 Nov 26;12:752424
pubmed: 34899840
Nucleic Acids Res. 2022 Jul 5;50(W1):W216-W221
pubmed: 35325185
Anim Genet. 2006 Aug;37(4):415-8
pubmed: 16879361
Nucleic Acids Res. 2019 Jan 8;47(D1):D801-D806
pubmed: 30407599
J Biol Chem. 2006 Jul 28;281(30):20749-20760
pubmed: 16714285
ScientificWorldJournal. 2011;11:1641-59
pubmed: 22125424
PLoS One. 2015 May 15;10(5):e0124823
pubmed: 25978040
J Exp Med. 2014 Dec 15;211(13):2519-35
pubmed: 25403443
J Cell Physiol. 2008 Aug;216(2):337-46
pubmed: 18459147
PLoS One. 2014 Apr 14;9(4):e94802
pubmed: 24733441
Animals (Basel). 2022 Apr 29;12(9):
pubmed: 35565582
Genet Sel Evol. 2020 Jan 30;52(1):2
pubmed: 32000665
Sci Rep. 2021 Nov 1;11(1):21363
pubmed: 34725398
PLoS One. 2011 Feb 24;6(2):e14726
pubmed: 21383979
Nat Protoc. 2009;4(1):44-57
pubmed: 19131956
Front Genet. 2022 Sep 14;13:986316
pubmed: 36246651
Mol Hum Reprod. 1997 Feb;3(2):115-31
pubmed: 9239717
PLoS One. 2011;6(7):e21872
pubmed: 21779344
Nat Genet. 2008 May;40(5):575-83
pubmed: 18391952
Mol Biol Evol. 2013 Sep;30(9):2224-34
pubmed: 23777627
Front Genet. 2022 Apr 11;13:887582
pubmed: 35615375
J Infect Dis. 2007 Sep 15;196(6):826-34
pubmed: 17703412
Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11597-604
pubmed: 18697943
Sci Rep. 2016 Feb 17;6:21111
pubmed: 26883901
Anim Biosci. 2022 Sep;35(9):1340-1350
pubmed: 35507856
Anim Genet. 2017 Oct;48(5):560-569
pubmed: 28677334
Mol Biol Evol. 2014 May;31(5):1275-91
pubmed: 24554778
Commun Biol. 2021 Nov 18;4(1):1307
pubmed: 34795381
Front Genet. 2019 Jul 18;10:674
pubmed: 31379930
Zool Res. 2022 Sep 18;43(5):695-705
pubmed: 35843722
Heredity (Edinb). 2015 Nov;115(5):426-36
pubmed: 25990878
Mol Biol Rep. 2023 Apr;50(4):3705-3721
pubmed: 36642776
Genet Sel Evol. 2020 May 14;52(1):25
pubmed: 32408891
BMC Genomics. 2021 Feb 1;22(1):95
pubmed: 33522899
Hum Mol Genet. 2010 Aug 1;19(15):2927-35
pubmed: 20462934
Mol Ecol Resour. 2017 Jan;17(1):78-90
pubmed: 27863062
Appl Anim Behav Sci. 2000 Oct 1;69(3):241-253
pubmed: 10906407
Sci Rep. 2021 Jun 25;11(1):13335
pubmed: 34172761
Neuron. 2014 Jun 4;82(5):1074-87
pubmed: 24908487
Genet Sel Evol. 2018 Mar 22;50(1):9
pubmed: 29566643
J Cell Biol. 1996 Jul;134(2):401-11
pubmed: 8707825
Genet Sel Evol. 2021 Dec 2;53(1):90
pubmed: 34856922
Mol Biol Evol. 2022 Feb 3;39(2):
pubmed: 34893856
PLoS One. 2018 Jul 24;13(7):e0200732
pubmed: 30040835
Genet Epidemiol. 2008 May;32(4):361-9
pubmed: 18271029
Animal. 2021 Feb;15(2):100065
pubmed: 33573944
Animals (Basel). 2020 Apr 15;10(4):
pubmed: 32326606
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
FEBS Lett. 2002 Dec 4;532(1-2):147-52
pubmed: 12459480
Front Genet. 2021 Apr 08;12:639030
pubmed: 33897762
Biochem J. 2008 Feb 15;410(1):101-11
pubmed: 17990982
Mol Biol Evol. 2014 Oct;31(10):2824-7
pubmed: 25015648
Genet Sel Evol. 2013 Oct 29;45:42
pubmed: 24168655
Biochim Biophys Acta. 2005 Jul 25;1730(1):1-9
pubmed: 16005990
J Biol Chem. 2007 Oct 5;282(40):29273-83
pubmed: 17675670
J Proteomics. 2018 Feb 10;172:82-88
pubmed: 29051081
J Cell Physiol. 2012 Dec;227(12):3820-7
pubmed: 22495818
BMC Genomics. 2018 Jan 23;19(1):71
pubmed: 29357834
Genes (Basel). 2022 May 12;13(5):
pubmed: 35627251
Genes (Basel). 2020 Feb 05;11(2):
pubmed: 32033434
Nature. 2002 Oct 24;419(6909):832-7
pubmed: 12397357
Nucleic Acids Res. 2021 Jan 8;49(D1):D884-D891
pubmed: 33137190
Sci Rep. 2016 Jul 26;6:28836
pubmed: 27456605
Biol Res. 2018 Aug 17;51(1):25
pubmed: 30119702
Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27;365(1544):1245-53
pubmed: 20308100
Mol Vis. 2004 Oct 07;10:758-72
pubmed: 15496828
Genet Sel Evol. 2016 Oct 28;48(1):81
pubmed: 27793093
BMC Genomics. 2022 Jul 16;23(1):517
pubmed: 35842584
PLoS One. 2021 Feb 2;16(2):e0246279
pubmed: 33529214
PLoS Genet. 2007 Jun;3(6):e90
pubmed: 17542651
Nature. 2002 Jul 25;418(6896):426-30
pubmed: 12110844
Anim Genet. 2017 Feb;48(1):55-66
pubmed: 27807880
PLoS One. 2014 Aug 15;9(8):e103813
pubmed: 25126940
Genet Sel Evol. 2015 Aug 14;47:66
pubmed: 26272623
J Anim Sci. 2020 May 1;98(5):
pubmed: 32365208
Front Genet. 2022 Jul 15;13:940736
pubmed: 35910220
Genet Sel Evol. 2019 Feb 6;51(1):4
pubmed: 30727969
Mol Biol Evol. 2021 Mar 9;38(3):838-855
pubmed: 32941615
BMC Genomics. 2018 May 8;19(1):338
pubmed: 29739312
Sci Rep. 2015 Sep 11;5:14036
pubmed: 26358086
Front Genet. 2019 Nov 15;10:1174
pubmed: 31803243
J Anim Sci. 2021 Sep 1;99(9):
pubmed: 34255028
Gene. 2014 Oct 10;549(2):252-7
pubmed: 25088569
Sci Rep. 2018 Aug 28;8(1):12984
pubmed: 30154520
Front Genet. 2021 Jul 14;12:699550
pubmed: 34335696
Annu Rev Genet. 2005;39:197-218
pubmed: 16285858
Mol Biol Evol. 2017 Jul 1;34(7):1722-1729
pubmed: 28379502
J Hepatol. 2019 Dec;71(6):1152-1163
pubmed: 31349001
Front Genet. 2019 Apr 02;10:300
pubmed: 31001329
Sci Rep. 2017 Feb 07;7:42048
pubmed: 28169328
Nat Commun. 2016 Feb 02;7:10363
pubmed: 26831939
Front Genet. 2021 Feb 25;12:634986
pubmed: 33719343
BMC Genomics. 2016 Mar 12;17:224
pubmed: 26968377
Mol Ecol. 2011 Aug;20(15):3128-43
pubmed: 21689193
Front Genet. 2019 Nov 29;10:1235
pubmed: 31850078
Front Genet. 2020 Mar 31;11:261
pubmed: 32296459
Gigascience. 2020 Dec 30;9(12):
pubmed: 33377911
Science. 2009 Apr 24;324(5926):532-6
pubmed: 19390051
J Anim Sci Biotechnol. 2021 Aug 5;12(1):95
pubmed: 34348773
Chromosoma. 2016 Jun;125(3):497-521
pubmed: 26464018
Genet Sel Evol. 2016 Feb 08;48:11
pubmed: 26856324
Nature. 2010 Oct 14;467(7317):832-8
pubmed: 20881960
Am J Hum Genet. 2007 Sep;81(3):559-75
pubmed: 17701901
BMC Genomics. 2021 Oct 15;22(1):747
pubmed: 34654366
Genet Mol Res. 2015 Dec 01;14(4):15471-81
pubmed: 26634513
BMC Genomics. 2022 Feb 28;23(1):167
pubmed: 35227193
Front Vet Sci. 2022 Oct 04;9:932034
pubmed: 36268046
Genet Sel Evol. 2020 Sep 4;52(1):52
pubmed: 32887549
Nature. 2002 Feb 21;415(6874):914-7
pubmed: 11859370
Cell Res. 2016 May;26(5):556-73
pubmed: 27033669
Genet Sel Evol. 2015 Aug 14;47:64
pubmed: 26272467
Genet Sel Evol. 2016 Jan 20;48:4
pubmed: 26791855
Front Genet. 2021 Nov 18;12:738879
pubmed: 34868210
Cell Rep. 2019 Mar 5;26(10):2792-2804.e6
pubmed: 30840898
Nat Genet. 2008 May;40(5):609-15
pubmed: 18391951
Am J Respir Crit Care Med. 2019 Jan 1;199(1):52-61
pubmed: 30079747
Anim Genet. 2021 Feb;52(1):99-107
pubmed: 33089531
Nat Commun. 2018 Feb 28;9(1):859
pubmed: 29491421
Anim Genet. 2022 Apr;53(2):237-239
pubmed: 35118693
Genes Dev. 2003 Oct 1;17(19):2436-49
pubmed: 12975321
Front Genet. 2021 Mar 30;12:644091
pubmed: 33859669
BMC Genet. 2015 Sep 15;16:111
pubmed: 26370837
BMC Genomics. 2021 Jan 6;22(1):7
pubmed: 33407115
Anim Genet. 2017 Dec;48(6):698-703
pubmed: 29044715
Genes (Basel). 2021 Jan 30;12(2):
pubmed: 33573244
Am J Hum Genet. 2013 Oct 3;93(4):687-96
pubmed: 24094745
J Comp Neurol. 1992 Oct 22;324(4):603-20
pubmed: 1385496
Leukemia. 2019 May;33(5):1184-1194
pubmed: 30573780
Genet Mol Res. 2014 Jul 25;13(3):5617-25
pubmed: 25117319
Biol Reprod. 2010 May;82(5):876-87
pubmed: 20107206