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, FST, and hapFST
|
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 FST 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 FST, 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 FST
|
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 |
FST, 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, FST, 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 FST
|
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) |
FST, 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 FST, LSBL, and di
|
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, di, Rsb, pairwise FST (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 FST, and di
|
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, FST, 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 |
FST-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 |
HP and FST
|
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 |
FST 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, FST, 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 |
FST, 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 |
FST and hapFLK |