Author |
Year |
SNP panel |
Species |
Objective of using ROHs |
Conclusions |
Gomez-Raya et al.GOMEZ-RAYA, L.; RODRÍGUEZ, C.; BARRAGÁN, C.; SILIÓ, L. Genomic inbreeding coefficients based on the distribution of the length of runs of homozygosity in a closed line of Iberian pigs. Genetics Selection Evolution, v.47, art.81, 2015. DOI: 10.1186/s12711-015-0153-1. https://doi.org/10.1186/s12711-015-0153-...
|
2015 |
35K |
Swine |
Obtain new autozygosity coefficients based on the size and distribution of ROHs and compare them with ROH frequency (FROH) and pedigree information (FPED) |
New coefficients of autozygosity provided additional information on recent consanguinity |
Howard et al. HOWARD, J.T.; HAILE-MARIAM, M.; PRYCE, J.E.; MALTECCA, C. Investigation of regions impacting inbreeding depression and their association with the additive genetic effect for United States and Australia Jersey dairy cattle. BMC Genomics, v.16, art.813, 2015. DOI: 10.1186/s12864-015-2001-7. https://doi.org/10.1186/s12864-015-2001-...
|
2015 |
54K |
Bovine |
Identify regions of the genome that suffered diversity losses due to consanguinity and determine the relationship between additive effects and ROHs |
Several regions are associated with ROH < 4 Mb in the studied population and there is correlation between genetic additive effect and ROH < 4 Mb, which is an indicative of the influence of geographical location on homozygosity |
Kim et al. KIM, E.-S.; SONSTEGARD, T.S.; VAN TASSELL, C.P.; WIGGANS, G.; ROTHSCHILD, M.F. The relationship between runs of homozygosity and inbreeding in Jersey cattle under selection. PLoS ONE, v.10, e0129967, 2015b. DOI: 10.1371/journal.pone.0129967. https://doi.org/10.1371/journal.pone.012...
|
2015b |
54K |
Bovine |
Identify the association between ROHs and consanguinity coefficients (F), as well as analyze ROHs identified in populations of dairy cattle |
ROHs reflect homozygosis strongly affected by recent artificial selection |
Kim et al. KIM, E.-S.; SONSTEGARD, T.S.; ROTHSCHILD, M.F. Recent artificial selection in U.S. Jersey cattle impacts autozygosity levels of specific genomic regions. BMC Genomics, v.16, art.302, 2015a. DOI: 10.1186/s12864-015-1500-x. https://doi.org/10.1186/s12864-015-1500-...
|
2015a |
54K |
Bovine |
Identify selection signatures in Jersey cattle under selection since 1960 and compare them by the method for the identification of selection signatures via extended haplotypes |
The analysis of the estimated ROHs allows to efficiently identify selection signatures |
Marras et al. MARRAS, G.; GASPA, G.; SORBOLINI, S.; DIMAURO, C.; AJMONE-MARSAN, P.; VALENTINI, A.; WILLIAMS, J.L.; MACCIOTTA, N.P.P. Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Animal Genetics, v.46, p.110-121, 2015. DOI: 10.1111/age.12259. https://doi.org/10.1111/age.12259...
|
2015 |
54K |
Bovine |
Compare FROH with the coefficient of genomic inbreeding matrices (FGRM) and FPED, in five different bovine breeds |
ROH is a powerful tool to estimate the coefficient of consanguinity |
Metzger et al. METZGER, J.; KARWATH, M.; TONDA, R.; BELTRAN, S.; ÁGUEDA, L.; GUT, M.; GUT, I.G.; DISTL, O. Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses. BMC Genomics, v.16, art.764, 2015. DOI: 10.1186/s12864-015-1977-3. https://doi.org/10.1186/s12864-015-1977-...
|
2015 |
50K |
Equine |
Identify selection signatures in improved and non-improved horses |
The size and frequency of ROHs vary according to population diversity and selection pressure |
Saura et al. SAURA, M.; FERNÁNDEZ, A.; VARONA, L.; FERNÁNDEZ, A.I.; CARA, M.Á.R. de; BARRAGÁN, C.; VILLANUEVA, B. Detecting inbreeding depression for reproductive traits in Iberian pigs using genome-wide data. Genetics Selection Evolution, v.47, art.1, 2015. DOI: 10.1186/s12711-014-0081-5. https://doi.org/10.1186/s12711-014-0081-...
|
2015 |
60K |
Swine |
Detect genomic regions responsible for the loss of genetic variability in reproductive characteristics of improved swine |
Genomic estimates based on the presence or absence of ROHs are a viable alternative for the detection of variability losses due to consanguinity |
Zavarez et al. ZAVAREZ, L.B.; UTSUNOMIYA, Y.T.; CARMO, A.S.; NEVES, H.H.R.; CARVALHEIRO, R.; FERENČAKOVIĆ, M.; PÉREZ O’BRIEN, A.M.; CURIK, I.; COLE, J.B.; VAN TASSELL, C.P.; SILVA, M.V.G.B. da; SONSTEGARD, T.S.; SÖLKNER, J.; GARCIA, J.F. Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes. Frontiers in Genetics, v.6, p.1-8, 2015. DOI: 10.3389/fgene.2015.00005. https://doi.org/10.3389/fgene.2015.00005...
|
2015 |
777K |
Bovine |
Characterize levels of autozygosity, based on ROHs, in a population of Nellore cattle |
The analysis of ROHs allows characterizing herds according to their endogamy levels, besides identifying genomic regions with possible selection signatures for the breed |
Zhang et al.ZHANG, Q.; CALUS, M.P.L.; GULDBRANDTSEN, B.; LUND, M.S.; SAHANA, G. Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds. BMC Genetics, v.16, art.88, 2015a. DOI: 10.1186/s12863-015-0227-7. https://doi.org/10.1186/s12863-015-0227-...
|
2015a |
54K |
Bovine |
Compare different estimators of coefficient of consanguinity, calculated from pedigree information, with data from 50K SNP chip and from complete sequencing and estimate based on ROH |
FROH reflects direct homozygosity levels because it is not affected by allele frequencies, whereas FPED is limited due to its dependence on correct pedigree information |
Zhang et al. ZHANG, Q.; GULDBRANDTSEN, B.; BOSSE, M.; LUND, M.S.; SAHANA, G. Runs of homozygosity and distribution of functional variants in the cattle genome. BMC Genomics, v.16, art.542, 2015b. DOI: 10.1186/s12864-015-1715-x https://doi.org/10.1186/s12864-015-1715-...
|
2015b |
Complete genome |
Bovine |
Study ROH patterns to verify the effect of selection pressure and demography in the increase in the frequency of deleterious and non-deleterious sequences within ROHs |
ROH is efficient to detect functional variants in bovine populations and contributes for a better understanding of endogamy and selection effects in these populations |
Mastrangelo et al. MASTRANGELO, S.; TOLONE, M.; DI GERLANDO, R.; FONTANESI, L.; SARDINA, M.T.; PORTOLANO, B. Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds. Animal, v.10, p.746-754, 2016. DOI: 10.1017/S1751731115002943. https://doi.org/10.1017/S175173111500294...
|
2016 |
54K |
Bovine |
Quantify consanguinity from information on ROHs estimated in three different bovine breeds of economic importance |
Consanguinity values in three bovine breeds, obtained via the detection and distribution of ROHs, evidenced the need of implementing conservation programs aiming to control consanguinity levels |
Gurgul et al. GURGUL, A.; SZMATOLA, T.; TOPOLSKI, P.; JASIELCZUK, I.; ŻUKOWSKI, K.; BUGNO-PONIEWIERSKA, M. The use of runs of homozygosity for estimation of recent inbreeding in Holstein cattle. Journal of Applied Genetics, v.57, p.527-530, 2016. DOI: 10.1007/s13353-016-0337-6. https://doi.org/10.1007/s13353-016-0337-...
|
2016 |
54K |
Bovine |
Compare FROH, FGRM, and FPED, test the correlation between these coefficients, and analyze if ROH or GRM may be interesting to estimate recent consanguinity in Holstein cattle |
Correlations between FROH and FPED tend to increase with the increase of pedigree information and indicate that FROH is the most recommended to estimate recent consanguinity |
Szmatoła et al. SZMATOŁA, T.; GURGUL, A.; ROPKA-MOLIK, K.; JASIELCZUK, I.; ZĄBEK, T.; BUGNO-PONIEWIERSKA, M. Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland. Livestock Science, v.188, p.72-80, 2016. DOI: 10.1016/j.livsci.2016.04.006. https://doi.org/10.1016/j.livsci.2016.04...
|
2016 |
54K |
Bovine |
Characterize ROHs in four different bovine breeds and identify genomic regions with a high frequency of ROHs and that have been subjected to directional selection |
The size and distribution of ROHs vary according to the studied breed, with different ROH patterns for native, conserved or commercial breeds, and to possible selection signatures |
Reverter et al. REVERTER, A.; PORTO-NETO, L.R.; FORTES, M.R.S.; KASARAPU, P.; CARA, M.A.R. de; BURROW, H.M.; LEHNERT, S.A. Genomic inbreeding depression for climatic adaptation of tropical beef cattle. Journal of Animal Science, v.95, p.3809-3821, 2017. DOI: 10.2527/jas2017.1643. https://doi.org/10.2527/jas2017.1643...
|
2017 |
729K 71K 19K |
Bovine |
Compare FGRM, the coefficient of homozygosity (FHOM), and FROH as estimators of consanguinity using data from three different panel densities in zebu cattle |
In heterogeneous populations (crossed animals), endogamy measures that do not depend on allele frequency, such as FHOM and FROH, are better recommended to estimate endogamy |