Detection and evaluation of selection signatures in sheep

Paim, Tiago do Prado; Ianella, Patrícia; Paiva, Samuel Rezende; Caetano, Alexandre Rodrigues; Pimentel, Concepta Margaret McManus

doi:10.1590/S0100-204X2018000500001

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Pesquisa Agropecuária Brasileira

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REVIEW • Pesq. agropec. bras. 53 (05) • May 2018 • https://doi.org/10.1590/S0100-204X2018000500001 copy

Detection and evaluation of selection signatures in sheep

Detecção e avaliação de assinaturas de seleção em ovinos

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract:

The recent development of genome-wide single nucleotide polymorphism (SNP) arrays made it possible to carry out several studies with different species. The selection process can increase or reduce allelic (or genic) frequencies at specific loci in the genome, besides dragging neighboring alleles in the chromosome. This way, genomic regions with increased frequencies of specific alleles are formed, caracterizing selection signatures or selective sweeps. The detection of these signatures is important to characterize genetic resources, as well as to identify genes or regions involved in the control and expression of important production and economic traits. Sheep are an important species for theses studies as they are dispersed worldwide and have great phenotypic diversity. Due to the large amounts of genomic data generated, specific statistical methods and softwares are necessary for the detection of selection signatures. Therefore, the objectives of this review are to address the main statistical methods and softwares currently used for the analysis of genomic data and the identification of selection signatures; to describe the results of recent works published on selection signatures in sheep; and to discuss some challenges and opportunities in this research field.

Index terms:
Ovis aries; analysis software; animal genetic resources; genetic improvement; genomics; molecular genetics; SNP markers

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[TFN1] ⁽¹⁾
OS, operational system: W, Windows; L, Linux, and M, MacOS. ⁽²⁾License: OS, open source; F, free for all users; and L, licensed, requiring payment by all users. ⁽³⁾Several softwares of data management can be used in multiple categories, such as, for example, PLINK, JMP Genomics, Golden Helix SNP & Variation Suite. ⁽⁴⁾Package of the R software. Source: adapted from Nicolazzi (2015)NICOLAZZI, E.L.; BIFFANI, S.; BISCARINI, F.; OROZCO-TERWENGEL, P.; CAPRERA, A.; NAZZICARI, N.; STELLA, A. Software solutions for the livestock genomics SNP array revolution. Animal Genetics, v.46, p.343-353, 2015. DOI: 10.1111/age.12295.
https://doi.org/10.1111/age.12295... and Cadzow et al. (2014)CADZOW, M.; BOOCOCK, J.; NGUYEN, H.T.; WILCOX, P.; MERRIMAN, T.R.; BLACK, M.A. A bioinformatics workflow for detecting signatures of selection in genomic data. Frontiers in Genetics, v.5, art.293, 2014. DOI: 10.3389/fgene.2014.00293.
https://doi.org/10.3389/fgene.2014.00293... .

Function	Name	OS⁽¹⁾	License⁽²⁾	Link or source
SNP data management⁽³⁾	PLINK 1.07	W/L/M	F	http://zzz.bwh.harvard.edu/plink/download.shtml
	PLINK 1.90	W/L/M	F	https://www.cog-genomics.org/plink2
	snpQC	W/L/M	OS	http://www-personal.une.edu.au/~cgondro2/snpQC.htm
	JMP Genomics	W/L/M	L	http://www.jmp.com/software/genomics/
	Golden Helix SNP & Variation Suite	W/L/M	L	http://www.goldenhelix.com/SNP_Variation/index.html
	Progeny	W/L	L	http://www.progenygenetics.com/clinical/trial
	BC/GENOME	L	L	http://www.bcplatforms.com/news/product-category/academia/#bcgenome-2
	SNPpy	L	OS	https://bitbucket.org/faheem/snppy
	GBrowse	L/M	OS	http://gmod.org/wiki/GBrowse
	IGV	W/L/M	OS	http://www.broadinstitute.org/igv/
	PGDSpider	W/L/M	OS	http://www.cmpg.unibe.ch/software/PGDSpider/
	fcGENE	W/L	OS	http://sourceforge.net/projects/fcgene/
	Python	W/L/M	F	https://www.python.org/
	Multicore⁽⁴⁾	W/L/M	F	https://cran.r-project.org/src/contrib/Archive/multicore/
Imputation	FImpute	L/M	F	http://www.aps.uoguelph.ca/~msargol/fimpute/
	Beagle	L/W/M	F	http://faculty.washington.edu/browning/beagle/beagle.html
	IMPUTE2	L/W/M	F	https://mathgen.stats.ox.ac.uk/impute/impute_v2.html
	MACH	L/W/M	F	http://www.sph.umich.edu/csg/abecasis/MACH/tour/imputation.html
	PedImpute	L/M	OS	http://dekoppel.eu/pedimpute/
	ALPHAPHASE	W/L/M	F	https://sites.google.com/site/hickeyjohn/alphaphase
	FINDHAP	L	OS	http://aipl.arsusda.gov/software/findhap/
Population genomics and selective sweeps	Sweed	L	OS	http://sco.h-its.org/exelixis/web/software/sweed/index.html
	Arlequin	W/L/M	F	http://cmpg.unibe.ch/software/arlequin35/
	Selscan	W/L/M	F	https://github.com/szpiech/selscan
	VCFtools	L/M	F	http://vcftools.sourceforge.net/
	BayeScan	L/M	F	http://cmpg.unibe.ch/software/BayeScan/index.html
	ADMIXTURE	L/M	F	https://www.genetics.ucla.edu/software/admixture/
	fastStructure	W/L/M	F	http://rajanil.github.io/fastStructure/
	LFMM	W/L/M	F	http://membres-timc.imag.fr/Olivier.Francois/lfmm/index.htm
	MatSAM	W	F	http://www.econogene.eu/software/sam/
	DIYABC	W/L/M	F	http://www1.montpellier.inra.fr/CBGP/diyabc/
	popABC	W/M/L	F	https://code.google.com/p/popabc/
	OmegaPlus	W/L	F	http://www.exelixis-lab.org/software.html
	Pool-HMM	W/L	F	https://qgp.jouy.inra.fr
	XP-CLR	W/L	F	https://reich.hms.harvard.edu/software
	hapFLK	W/L	F	https://forge-dga.jouy.inra.fr/projects/hapflk/files
	Sweep	W/L	F	http://www.broadinstitute.org/mpg/sweep/
	REHH⁽⁴⁾	W/L	F	http://cran.r-project.org/
	SweepFinder	W/L	F	Huber et al. (2016)HUBER, C.D.; DEGIORGIO, M.; HELLMANN, I.; NIELSEN, R. Detecting recent selective sweeps while controlling for mutation rate and background selection. Molecular Ecology, v.25, p.142-155, 2016. DOI: 10.1111/mec.13351. https://doi.org/10.1111/mec.13351...
	VariScan	W/L/M	F	http://www.ub.edu/softevol/variscan/

Reference	Population or breed (number of individuals)	Objectives	Methods and softwares applied⁽¹⁾
Fariello et al. (2013)FARIELLO, M.I.; BOITARD, S.; NAYA, H.; SANCRISTOBAL, M.; SERVIN, B. Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics, v.193, p.929-941, 2013. DOI: 10.1534/genetics.112.147231. https://doi.org/10.1534/genetics.112.147...	Sheep HapMap	To validate the hapFLK method to detect selective sweeps	hapFLK, FLK, F_ST, and hapF_ST
Fariello et al. (2014)FARIELLO, M.-I.; SERVIN, B.; TOSSER-KLOPP, G.; RUPP, R.; MORENO, C.; CRISTOBAL, M.S.; BOITARD, S. Selection signatures in worldwide sheep populations. PLoS ONE, v.9, e103813, 2014. DOI: 10.1371/journal.pone.0103813. https://doi.org/10.1371/journal.pone.010...	Sheep HapMap	To confirm the selective sweeps found by F_ST and identify new ones	hapFLK and FLK
Gutiérrez-Gil et al. (2014)GUTIÉRREZ-GIL, B.; JOSE ARRANZ, J.; PONG-WONG, R.; GARCIA-GÁMEZ, E.; KIJAS, J.; WIENER, P. Application of selection mapping to identify genomic regions associated with dairy production in sheep. PLoS ONE, v.9, e94623, 2014. DOI: 10.1371/journal.pone.0094623. https://doi.org/10.1371/journal.pone.009...	Sheep HapMap (5 milk breeds and 5 non-milk breeds)	To identify selective sweeps related to milk production	Pairwise F_ST, observed heterozygosity, and regression analysis to detect asymptotic patterns of heterozygosity
Grasso et al. (2014)GRASSO, A.N.; GOLDBERG, V.; NAVAJAS, E.A.; IRIARTE, W.; GIMENO, D.; AGUILAR, I.; MEDRANO, J.F.; RINCÓN, G.; CIAPPESONI, G. Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep. Genetics and Molecular Biology, v.37, p.389-395, 2014. DOI: 10.1590/S1415-47572014000300011. https://doi.org/10.1590/S1415-4757201400...	Merino (110), Corriedale (108), and Creola (10)	To identify genetic diversity within and between three sheep breeds	fastStructure, PCA, and F_ST
Lv et al. (2014)LV, F.-H.; AGHA, S.; KANTANEN, J.; COLLI, L.; STUCKI, S.; KIJAS, J.W.; JOOST, S.; LI, M.-H.; MARSAN, P.A. Adaptations to climate-mediated selective pressures in sheep. Molecular Biology and Evolution, v.31, p.3324-3343, 2014. DOI: 10.1093/molbev/msu264. https://doi.org/10.1093/molbev/msu264...	32 autochthonous breeds (1.224)	To characterize genetic effects of climatic adaptation, identifying related selective sweeps	Arlequin, PLINK, MatSAM, LFMM, SmartPCA, fastStructure, and Sweep
McRae et al. (2014)MCRAE, K.M.; MCEWAN, J.C.; DODDS, K.G.; GEMMELL, N.J. Signatures of selection in sheep bred for resistance or susceptibility to gastrointestinal nematodes. BMC Genomics, v.15, art.637, 2014. DOI: 10.1186/1471-2164-15-637. https://doi.org/10.1186/1471-2164-15-637...	Romney (180) and Perendale (149)	To identify selective sweeps, within and between two breeds, related to resistance or susceptibility to gastrointestinal nematodes	F_ST, Peddrift, fastPHASE, EHH (Sweep v1.1), XP-EHH, and iHS (Pritchard)
Moioli et al. (2013)MOIOLI, B.; SCATÀ, M.C.; STERI, R.; NAPOLITANO, F.; CATILO, G. Signatures of selection identify loci associated with milk yield in sheep. BMC Genetics, v.14, art.76, 2013. DOI: 10.1186/1471-2156-14-76. https://doi.org/10.1186/1471-2156-14-76...	Altamurana (100)	To identify regions that affect milk production	Random animal effect and Fisher’s exact test (SAS, (SAS Institute, Inc., Cary, NC, USA)
Moioli et al. (2016)MOIOLI, B.; D’ANDREA, S.; DE GROSSI, L.; SEZZI, E.; DE SANCTIS, B.; CATILLO, G.; STERI, R.; VALENTINI, A.; PILLA, F. Genomic scan for identifying candidate genes for paratuberculosis resistance in sheep. Animal Production Science, v.56, p.1046-1055, 2016. DOI: 10.1071/AN14826. https://doi.org/10.1071/AN14826...	Sarda breed (100)	To identify candidate genes for immune response and relationship with paratuberculosis resistance	Effect of allelic substitution (SAS Institute, Inc., Cary, NC, USA)
Moradi et al. (2012)MORADI, M.H.; NEJATI-JAVAREMI, A.; MORADI-SHAHRBABAK, M.; DODDS, K.G.; MCEWAN, J.C. Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genetics, v.13, art.10, 2012. DOI: 10.1186/1471-2156-13-10. https://doi.org/10.1186/1471-2156-13-10...	Zel (47) and Lori-Bakhtiari (47) breeds, as well as Sheep HapMap (7 breeds)	To perform selective sweeps between fat and thin-tail Iranian breeds and to compare divergent breeds for this trait in Sheep HapMap	PCA using the R software, F_ST, homozygosity, and fastPHASE
Zhu et al. (2015)ZHU, C.; FAN, H.; YUAN, Z.; HU, S.; ZHANG, L.; WEI, C.; ZHANG, Q.; ZHAO, F.; DU, L. Detection of selection signatures on the X chromosome in three sheep breeds. International Journal of Molecular Sciences, v.16, p.20360-20374, 2015. DOI: 10.3390/ijms160920360. https://doi.org/10.3390/ijms160920360...	German Mutton (89), Dorper (47), and Sunit (12)	To identify selective sweeps in chromosome X in three sheep breeds	PLINK, Beagle, iHS, and F_ST
Randhawa et al. (2014)RANDHAWA, I.A.S.; KHATKAR, M.S.; THOMSON, P.C.; RAADSMA, H.W. Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep. BMC Genetics, v.15, art.34, 2014. DOI: 10.1186/1471-2156-15-34. https://doi.org/10.1186/1471-2156-15-34...	37 pooled breeds (1,489) and 36 horned breeds (1,290); 3 double-muscle breeds (149) and 71 normal muscle breeds (2,654)	37 pooled breeds (1,489) and 36 horned breeds (1,290); 3 double-muscle breeds (149) and 71 normal muscle breeds (2,654)	F_ST, XP-EHH, DAF, and CSS
Wang et al. (2015)WANG, H.; ZHANG, L.; CAO, J.; WU, M.; MA, X.; LIU, Z.; LIU, R.; ZHAO, F.; WEI, C.; DU, L. Genome-wide specific selection in three domestic sheep breeds. PLoS ONE, v.10, p. e0128688, 2015. DOI: 10.1371/journal.pone.0128688. https://doi.org/10.1371/journal.pone.012...	White Dorper (100), fat-tailed Chinese Mongolian (61), and German Mutton Merino (161)	White Dorper (100), fat-tailed Chinese Mongolian (61), and German Mutton Merino (161)	PCA, pairwise F_ST, LSBL, and d_i
Wei et al. (2015)WEI, C.; WANG, H.; LIU, G.; WU, M.; CAO, J.; LIU, Z.; LIU, R.; ZHAO, F.; ZHANG, L.; LU, J.; LIU, C.; DU, L. Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds. BMC Genomics, v.16, art.194, 2015. DOI: 10.1186/s12864-015-1384-9. https://doi.org/10.1186/s12864-015-1384-...	10 Chinese breeds (140)	10 Chinese breeds (140)	PCA, fastStructure, neighbor-joining-tree, d_i, Rsb, pairwise F_ST (Genepop), and fastPHASE
Gorkhali et al. (2016)GORKHALI, N.A.; DONG, K.; YANG, M.; SONG, S.; KADER, A.; SHRESTHA, B.S.; HE, X.; ZHAO, Q.; PU, Y.; LI, X.; KIJAS, J.; GUAN, W.; HAN, J.; JIANG, L.; MA, Y. Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas. Scientific Reports, v.6, art.29963, 2016. DOI: 10.1038/srep29963. https://doi.org/10.1038/srep29963...	24 sheep from each of the following 4 Nepalese breeds: Bhyanglung, Baruwal, Kage, and Lampuchhre	24 sheep from each of the following four Nepalese breeds: Bhyanglung, Baruwal, Kage, and Lampuchhre	PCA, pairwise F_ST, and d_i
Yang et al. (2016YANG, J.; LI, W.-R.; LV, F.-H.; HE, S.-G.; TIAN, S.-L.; PENG, W.-F.; SUN, Y.-W.; ZHAO, Y.-X.; TU., X.-L., ZHANG, M.; XIE, X.-L.; WANG, Y.-T.; LI, J.-Q.; LIU, Y.-G.; SHEN, Z.-Q.; WANG, F.; LIU, G.-J.; LU, H.-F.; KANTANEN, J.; HAN, J.-L.; LI, M.-H.; LIU, M.-J. Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments. Molecular Biology and Evolution, v.33, p.2576-2592, 2016. DOI: 10.1093/molbev/msw129. https://doi.org/10.1093/molbev/msw129... )	77 Chinese native sheep from 21 representative breeds	77 Chinese native sheep from 21 representative breeds	Runs of homozygosity, F_ST, XP-EHH, and LFMM
Manunza et al. (2016)MANUNZA, A.; CARDOSO, T.F.; NOCE, A.; MARTÍNEZ, A.; PONS, A.; BERMEJO, L.A.; LANDI, V.; SÀNCHEZ, A.; JORDANA, J.; DELGADO, J.V.; ADÁN, S.; CAPOTE, J.; VIDAL, O.; UGARTE, E.; ARRANZ, J.J.; CALVO, J.H.; CASELLAS, J. AMILLS, M. Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK. Scientific Reports, v.6, art.27296, 2016. DOI: 10.1038/srep27296. https://doi.org/10.1038/srep27296...	370 animals from 11 Spanish breeds	370 animals from 11 Spanish breeds	F_ST-outlier approach in the BayeScan software, hapFLK, and FLK
Liu et al. (2016)LIU, Z.; JI, Z.; WANG, G.; CHAO, T.; HOU, L.; WANG, J. Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions. BMC Genomics, v.17, art.863, 2016. DOI: 10.1186/s12864-016-3212-2. https://doi.org/10.1186/s12864-016-3212-...	8 sheep populations with 20 individuals from each one	8 sheep populations with 20 individuals from each one	H_P and F_ST
Zhao et al. (2016)ZHAO, F.; WEI, C.; ZHANG, L.; LIU, J.; WANG, G.; ZENG, T.; DU, L. A genome scan of recent positive selection signatures in three sheep populations. Journal of Integrative Agriculture, v.15, p.162-174, 2016. DOI: 10.1016/S2095-3119(15)61080-2. https://doi.org/10.1016/S2095-3119(15)61...	Sunite (66), German Mutton (159), and Dorper (93)	Sunite (66), German Mutton (159), and Dorper (93)	REHH and XP-EHH
Wei et al. (2016)WEI, C.; WANG, H.; LIU, G.; ZHAO, F.; KIJAS, J.W.; MA, Y.; LU, J.; ZHANG, L.; CAO, J.; WU, M.; WANG, G.; LIU, R.; LIU, Z.; ZHANG, S.; LIU, C.; DU, L. Genome-wide analysis reveals adaptation to high altitudes in Tibetan sheep. Scientific Reports, v.6, art.26770, 2016. DOI: 10.1038/srep26770. https://doi.org/10.1038/srep26770...	Hu (12), Tong (15), large-tailed Han (15), Lop (15), Tibetan (14), Sichuan (14), and Nagqu (37)	To study the adaptive evolution of high-altitude sheep by analyzing seven breeds	F_ST and XP-EHH
Purfield et al. (2017)PURFIELD, D.C.; MCPARLAND, S.; WALL, E.; BERRY, D.P. The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PLoS ONE, v.12, e0176780, 2017. DOI: 10.1371/journal.pone.0176780. https://doi.org/10.1371/journal.pone.017...	Belclare (658), Beltex (64), Charollais (665), Suffolk (784), Texel (489), and Vendeen (629)	To quantify the genetic diversity in six commercial sheep breeds with the aim of identifying genomic regions that have been subjected to selection	Runs of homozygosity, F_ST, and hapFLK
Gouveia et al. (2017)GOUVEIA, J.J. de S.; PAIVA, S.R.; MCMANUS, C.M.; CAETANO, A.R.; KIJAS, J.W.; FACÓ, O.; AZEVEDO, H.C.; ARAUJO, A.M. de; SOUZA, C.J.H. de; YAMAGISHI, M.E.B.; CARNEIRO, P.L.S.; LÔBO, R.N.B.; OLIVEIRA, S.M.P. de; SILVA, M.V.G.B. da. Genome-wide search for signatures of selection in three major Brazilian locally adapted sheep breeds. Livestock Science, v.197, p.36-45, 2017. DOI: 10.1016/j.livsci.2017.01.006. https://doi.org/10.1016/j.livsci.2017.01...	Brazilian Creole (22), Morada Nova (22), and Santa Inês (45)	To identify genomic regions that may have been under selection and, therefore, may explain ecological and production differences among three Brazilian locally adapted sheep breeds	F_ST, Rsb, and iHS
Yuan et al. (2017)YUAN, Z.; LIU, E.; LIU, Z.; KIJAS, J.W.; ZHU, C.; HU, S.; MA, X.; ZHANG, L.; DU, L.; WANG, H.; WEI, C. Selection signature analysis reveals genes associated with tail type in Chinese indigenous sheep. Animal Genetics, v.48, p.55-66, 2017. DOI: 10.1111/age.12477. https://doi.org/10.1111/age.12477...	Hu (12), Tong (15), large-tailed Han (15), Lop (15), Tibetan (14), Sichuan (14), and Nagqu (37)	To identify genes associated with tail fat deposition in Chinese populations	F_ST and hapFLK