[en] BACKGROUND: Inbreeding coefficients can be estimated either from pedigree data or from genomic data, and with genomic data, they are either global or local (when the linkage map is used). Recently, we developed a new hidden Markov model (HMM) that estimates probabilities of homozygosity-by-descent (HBD) at each marker position and automatically partitions autozygosity in multiple age-related classes (based on the length of HBD segments). Our objectives were to: (1) characterize inbreeding with our model in an intensively selected population such as the Belgian Blue Beef (BBB) cattle breed; (2) compare the properties of the model at different marker densities; and (3) compare our model with other methods. RESULTS: When using 600 K single nucleotide polymorphisms (SNPs), the inbreeding coefficient (probability of sampling an HBD locus in an individual) was on average 0.303 (ranging from 0.258 to 0.375). HBD-classes associated to historical ancestors (with small segments </= 200 kb) accounted for 21.6% of the genome length (71.4% of the total length of the genome in HBD segments), whereas classes associated to more recent ancestors accounted for only 22.6% of the total length of the genome in HBD segments. However, these recent classes presented more individual variation than more ancient classes. Although inbreeding coefficients obtained with low SNP densities (7 and 32 K) were much lower (0.060 and 0.093), they were highly correlated with those obtained at higher density (r = 0.934 and 0.975, respectively), indicating that they captured most of the individual variation. At higher SNP density, smaller HBD segments are identified and, thus, more past generations can be explored. We observed very high correlations between our estimates and those based on homozygosity (r = 0.95) or on runs-of-homozygosity (r = 0.95). As expected, pedigree-based estimates were mainly correlated with recent HBD-classes (r = 0.56). CONCLUSIONS: Although we observed high levels of autozygosity associated with small HBD segments in BBB cattle, recent inbreeding accounted for most of the individual variation. Recent autozygosity can be captured efficiently with low-density SNP arrays and relatively simple models (e.g., two HBD classes). The HMM framework provides local HBD probabilities that are still useful at lower SNP densities.
Disciplines :
Genetics & genetic processes Animal production & animal husbandry
Author, co-author :
Sole Berga, Marina ; Université de Liège - ULiège > Département des productions animales (DPA) > GIGA-R : Génomique animale
Bertrand, Amandine ; Université de Liège - ULiège > Département des sciences de la vie > Génomique fonctionnelle et imagerie moléculaire végétale
Farnir, Frédéric ; Université de Liège - ULiège > Département des productions animales (DPA) > Biostatistiques et bioinformatique appliquées aux sc. vétér.
Gautier, Mathieu
Druet, Tom ; Université de Liège - ULiège > Département des productions animales (DPA) > GIGA-R : Génomique animale
Language :
English
Title :
Age-based partitioning of individual genomic inbreeding levels in Belgian Blue cattle.
Publication date :
2017
Journal title :
Genetics, Selection, Evolution
ISSN :
0999-193X
eISSN :
1297-9686
Publisher :
BioMed Central, United Kingdom
Volume :
49
Issue :
1
Pages :
92
Peer reviewed :
Peer Reviewed verified by ORBi
Tags :
CÉCI : Consortium des Équipements de Calcul Intensif
scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.
Bibliography
Malécot, G., (1948) Les Mathématiques de l'Hérédité, , Masson et Cie Paris
Bjelland, D.W., Weigel, K.A., Vukasinovic, N., Nkrumah, J.D., Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding (2013) J Dairy Sci, 96, pp. 4697-4706. , 1:CAS:528:DC%2BC3sXnslChsbk%3D 23684028
Leroy, G., Inbreeding depression in livestock species: Review and meta-analysis (2014) Anim Genet, 45, pp. 618-628. , 1:STN:280:DC%2BC2cfns1Smuw%3D%3D 24975026
Pryce, J.E., Haile-Mariam, M., Goddard, M.E., Hayes, B.J., Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy (2014) Genet Sel Evol, 46, p. 71. , 25407532 4234836
Charlier, C., Coppieters, W., Rollin, F., Desmecht, D., Agerholm, J.S., Cambisano, N., Highly effective SNP-based association mapping and management of recessive defects in livestock (2008) Nat Genet, 40, pp. 449-454. , 1:CAS:528:DC%2BD1cXjslCgtbY%3D 18344998
Fasquelle, C., Sartelet, A., Li, W., Dive, M., Tamma, N., Michaux, C., Balancing selection of a frame-shift mutation in the MRC2 gene accounts for the outbreak of the crooked tail syndrome in Belgian Blue cattle (2009) PLoS Genet, 5, p. e1000666. , 19779552 2739430
Sartelet, A., Klingbeil, P., Franklin, C.K., Fasquelle, C., Géron, S., Isacke, C.M., Allelic heterogeneity of Crooked Tail Syndrome: Result of balancing selection? (2012) Anim Genet, 43, pp. 604-607. , 1:CAS:528:DC%2BC38Xht1ymsbjI 22497452
Sartelet, A., Druet, T., Michaux, C., Fasquelle, C., Géron, S., Tamma, N., A splice site variant in the bovine RNF11 gene compromises growth and regulation of the inflammatory response (2012) PLoS Genet, 8, p. e1002581. , 1:CAS:528:DC%2BC38XkslagsL8%3D 22438830 3305398
Sartelet, A., Stauber, T., Coppieters, W., Ludwig, C.F., Fasquelle, C., Druet, T., A missense mutation accelerating the gating of the lysosomal Cl-/H+-exchanger ClC-7/Ostm1 causes osteopetrosis with gingival hamartomas in cattle (2014) Dis Model Mech, 7, pp. 119-128. , 1:CAS:528:DC%2BC2cXntVCmsbw%3D 24159188
Sartelet, A., Li, W., Pailhoux, E., Richard, C., Tamma, N., Karim, L., Genome-wide next-generation DNA and RNA sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class H gene (PIGH) and causes arthrogryposis in Belgian Blue cattle (2015) BMC Genomics, 16, p. 316. , 25895751 4404575
Sartelet, A., Harland, C., Tamma, N., Karim, L., Bayrou, C., Li, W., A stop-gain in the laminin, alpha 3 gene causes recessive junctional epidermolysis bullosa in Belgian Blue cattle (2015) Anim Genet, 46, pp. 566-570. , 1:CAS:528:DC%2BC2MXhsF2iu73E 26370913
Ritland, K., Estimators for pairwise relatedness and individual inbreeding coefficients (1996) Genet Res, 67, pp. 175-185
VanRaden, P.M., Efficient methods to compute genomic predictions (2008) J Dairy Sci, 91, pp. 4414-4423. , 1:CAS:528:DC%2BD1cXhtlajtLzO 18946147
McQuillan, R., Leutenegger, A.L., Abdel-Rahman, R., Franklin, C.S., Pericic, M., Barac-Lauc, L., Runs of homozygosity in European populations (2008) Am J Hum Genet, 83, pp. 359-372. , 1:CAS:528:DC%2BD1cXhtFOitr7O 18760389 2556426
Wang, S., Haynes, C., Barany, F., Ott, J., Genome-wide autozygosity mapping in human populations (2009) Genet Epidemiol, 33, pp. 172-180. , 18814273 2802852
Pemberton, T.J., Absher, D., Feldman, M.W., Myers, R.M., Rosenberg, N.A., Li, J.Z., Genomic patterns of homozygosity in worldwide human populations (2012) Am J Hum Genet, 91, pp. 275-292. , 1:CAS:528:DC%2BC38XhtF2nsLjN 22883143 3415543
Broman, K.W., Weber, J.L., Long homozygous chromosomal segments in reference families from the Centre d'Etude du Polymorphisme Humain (1999) Am J Hum Genet, 65, pp. 1493-1500. , 1:STN:280:DC%2BD3c%2Fks1yrsQ%3D%3D 10577902 1288359
Kirin, M., McQuillan, R., Franklin, C.S., Campbell, H., McKeigue, P.M., Wilson, J.F., Genomic runs of homozygosity record population history and consanguinity (2010) PLoS ONE, 5, p. e13996. , 21085596 2981575
Bosse, M., Megens, H.J., Madsen, O., Paudel, Y., Frantz, L., Schook, L., Regions of homozygosity in the porcine genome: Consequence of demography and the recombination landscape (2012) PLoS Genet, 8, p. e1003100. , 1:CAS:528:DC%2BC38XhvVKjtrbJ 23209444 3510040
Ferenčaković, M., Sölkner, J., Curik, I., Estimating autozygosity from high-throughput information: Effects of SNP density and genotyping errors (2013) Genet Sel Evol, 45, p. 42. , 24168655 4176748
Ferenčaković, M., Hamzić, E., Gredler, B., Solberg, T.R., Klemetsdal, G., Curik, I., Estimates of autozygosity derived from runs of homozygosity: Empirical evidence from selected cattle populations (2013) J Anim Breed Genet, 130, pp. 286-293. , 23855630
Purfield, D.C., Berry, D.P., McParland, S., Bradley, D.G., Runs of homozygosity and population history in cattle (2012) BMC Genet, 13, p. 70. , 1:CAS:528:DC%2BC3sXmt1GktL8%3D 22888858 3502433
Leutenegger, A.L., Prum, B., Génin, E., Verny, C., Lemainque, A., Clerget-Darpoux, F., Estimation of the inbreeding coefficient through use of genomic data (2003) Am J Hum Genet, 73, pp. 516-523. , 1:CAS:528:DC%2BD3sXnt1Wqsro%3D 12900793 1180677
Narasimhan, V., Danecek, P., Scally, A., Xue, Y., Tyler-Smith, C., Durbin, R., BCFtools/RoH: A hidden Markov model approach for detecting autozygosity from next-generation sequencing data (2016) Bioinformatics, 32, pp. 1749-1751. , 1:CAS:528:DC%2BC28XhsFWltL%2FL 26826718 4892413
Vieira, F.G., Albrechtsen, A., Nielsen, R., Estimating IBD tracts from low coverage NGS data (2016) Bioinformatics, 32, pp. 2096-2102. , 1:CAS:528:DC%2BC28XhvVekt7fM 27153648
Druet, T., Gautier, M., A model-based approach to characterize individual inbreeding at both global and local genomic scales (2017) Mol Ecol, 26, pp. 5820-5841. , 1:CAS:528:DC%2BC2sXhslGgsL%2FI 28815918
Charlier, C., Li, W., Harland, C., Littlejohn, M., Coppieters, W., Creagh, F., NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock (2016) Genome Res, 26, pp. 1333-1341. , 1:CAS:528:DC%2BC28XhvFyru7jO 27646536 5052051
Sempéré, G., Moazami-Goudarzi, K., Eggen, A., Laloë, D., Gautier, M., Flori, L., WIDDE: A Web-Interfaced next generation database for genetic diversity exploration, with a first application in cattle (2015) BMC Genom, 16, p. 940
Druet, T., Georges, M., LINKPHASE3: An improved pedigree-based phasing algorithm robust to genotyping and map errors (2015) Bioinformatics, 31, pp. 1677-1679. , 1:CAS:528:DC%2BC28Xht1GntLfK 25573918
Utsunomiya, A.T.H., Santos, D.J.A., Boison, S.A., Utsunomiya, Y.T., Milanesi, M., Bickhart, D.M., Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan (2016) BMC Genomics, 17, p. 705. , 27595709 5011828
Faux, P., Druet, T., A strategy to improve phasing of whole-genome sequenced individuals through integration of familial information from dense genotype panels (2017) Genet Sel Evol, 49, p. 46. , 28511677 5434521
Daetwyler, H.D., Capitan, A., Pausch, H., Stothard, P., Van Binsbergen, R., Brøndum, R.F., Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle (2014) Nat Genet, 46, pp. 858-865. , 1:CAS:528:DC%2BC2cXhtFGqsbjI 25017103
Kadri, N.K., Harland, C., Faux, P., Cambisano, N., Karim, L., Coppieters, W., Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle (2016) Genome Res, 26, pp. 1323-1332. , 1:CAS:528:DC%2BC28XhvFyru7jJ 27516620 5052053
Rabiner, L.R., A tutorial on hidden Markov models and selected applications in speech recognition (1989) Proc IEEE, 77, pp. 257-286
Sargolzaei, M., Iwaisaki, H., Colleau, J.J., A fast algorithm for computing inbreeding coefficients in large populations (2005) J Anim Breed Genet, 122, pp. 325-331. , 1:STN:280:DC%2BD2MrhvV2hsQ%3D%3D 16191041
Misztal, I., Tsuruta, S., Strabel, T., Auvray, B., Druet, T., Lee, D.H., BLUPF90 and related programs (BGF90) (2002) Proceedings of 7th World Congress on Genetics Applied to Livestock Production, , 19-23 Aug 2002. Montpellier
VanRaden, P.M., Olson, K.M., Wiggans, G.R., Cole, J.B., Tooker, M.E., Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss (2011) J Dairy Sci, 94, pp. 5673-5682. , 1:CAS:528:DC%2BC3MXhtl2qsLvK 22032391
Yang, J., Benyamin, B., McEvoy, B.P., Gordon, S., Henders, A.K., Nyholt, D.R., Common SNPs explain a large proportion of the heritability for human height (2010) Nat Genet, 42, pp. 565-569. , 1:CAS:528:DC%2BC3cXns1GisL8%3D 20562875 3232052
Yang, J., Lee, S.H., Goddard, M.E., Visscher, P.M., GCTA: A tool for genome-wide complex trait analysis (2011) Am J Hum Genet, 88, pp. 76-82. , 1:CAS:528:DC%2BC3MXktVejtg%3D%3D 21167468 3014363
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A.R., Bender, D., PLINK: A tool set for whole-genome association and population-based linkage analyses (2007) Am J Hum Genet, 81, pp. 559-575. , 1:CAS:528:DC%2BD2sXhtVSqurrL 17701901 1950838
Szmatoła, T., Gurgul, A., Ropka-Molik, K., Jasielczuk, I., Zabek, T., Bugno-Poniewierska, M., Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland (2016) Livest Sci, 188, pp. 72-80
Amin, N., Van Duijn, C.M., Aulchenko, Y.S., A genomic background based method for association analysis in related individuals (2007) PLoS ONE, 2, p. e1274. , 18060068 2093991
Boichard, D., PEDIG: A fortran package for pedigree analysis suited for large populations (2002) Proceedings of 7th World Congress on Genetics Applied to Livestock Production, , INRA, editor 19-23 Aug 2002. Montpellier
Grobet, L., Martin, L.J., Poncelet, D., Pirottin, D., Brouwers, B., Riquet, J., A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle (1997) Nat Genet, 17, pp. 71-74. , 1:CAS:528:DyaK2sXlvVGhtr8%3D 9288100
Druet, T., Pérez-Pardal, L., Charlier, C., Gautier M. Identification of large selective sweeps associated with major genes in cattle (2013) Anim Genet, 44, pp. 758-762. , 1:CAS:528:DC%2BC3sXhs12mtbzO 23859468
Druet, T., Ahariz, N., Cambisano, N., Tamma, N., Michaux, C., Coppieters, W., Selection in action: Dissecting the molecular underpinnings of the increasing muscle mass of Belgian Blue cattle (2014) BMC Genom, 15, p. 796
Peripolli, E., Munari, D.P., Silva, M.V.G.B., Lima, A.L.F., Irgang, R., Baldi, F., Runs of homozygosity: Current knowledge and applications in livestock (2017) Anim Genet, 48, pp. 255-271. , 1:STN:280:DC%2BC2sjislWmsQ%3D%3D 27910110
Hinrichs, D., Meuwissen, T.H.E., Ødegard, J., Holt, M., Vangen, O., Woolliams, J.A., Analysis of inbreeding depression in the first litter size of mice in a long-term selection experiment with respect to the age of the inbreeding (2007) Heredity (Edinburgh), 99, pp. 81-88. , 1:STN:280:DC%2BD2sznslamug%3D%3D
Szpiech, Z.A., Xu, J., Pemberton, T.J., Peng, W., Zöllner, S., Rosenberg, N.A., Long runs of homozygosity are enriched for deleterious variation (2013) Am J Hum Genet, 93, pp. 90-102. , 1:CAS:528:DC%2BC3sXptFKrsLg%3D 23746547 3710769
Cruz, F., Vilà, C., Webster, M.T., The legacy of domestication: Accumulation of deleterious mutations in the dog genome (2008) Mol Biol Evol, 25, pp. 2331-2336. , 1:CAS:528:DC%2BD1cXhtlyqsbrO 18689870
Schubert, M., Jónsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., Prehistoric genomes reveal the genetic foundation and cost of horse domestication (2014) Proc Natl Acad Sci USA, 111, pp. E5661-E5669. , 1:CAS:528:DC%2BC2cXitFCrt7bK 25512547 4284583
Zhang, Z., Guillaume, F., Sartelet, A., Charlier, C., Georges, M., Farnir, F., Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification (2012) Bioinformatics, 28, pp. 2467-2473. , 1:CAS:528:DC%2BC38XhsVehtbbN 22711794
Curik, I., Ferenčaković, M., Sölkner, J., Inbreeding and runs of homozygosity: A possible solution to an old problem (2014) Livest Sci., 166, pp. 26-34
Zhang, Q., Calus, M.P.L., Guldbrandtsen, B., Lund, M.S., Sahana, G., Estimation of inbreeding using pedigree, 50 k SNP chip genotypes and full sequence data in three cattle breeds (2015) BMC Genet, 16, p. 88. , 26195126 4509611
Marras, G., Gaspa, G., Sorbolini, S., Dimauro, C., Ajmone-Marsan, P., Valentini, A., Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy (2015) Anim Genet, 46, pp. 110-121. , 1:CAS:528:DC%2BC2MXjvFynsLc%3D 25530322
Gurgul, A., Szmatoła, T., Topolski, P., Jasielczuk, I., Zukowski, K., Bugno-Poniewierska, M., The use of runs of homozygosity for estimation of recent inbreeding in Holstein cattle (2016) J Appl Genet., 57, pp. 527-530. , 1:STN:280:DC%2BC28njs1eitQ%3D%3D 26803654
Similar publications
Sorry the service is unavailable at the moment. Please try again later.
This website uses cookies to improve user experience. Read more
Save & Close
Accept all
Decline all
Show detailsHide details
Cookie declaration
About cookies
Strictly necessary
Performance
Strictly necessary cookies allow core website functionality such as user login and account management. The website cannot be used properly without strictly necessary cookies.
This cookie is used by Cookie-Script.com service to remember visitor cookie consent preferences. It is necessary for Cookie-Script.com cookie banner to work properly.
Performance cookies are used to see how visitors use the website, eg. analytics cookies. Those cookies cannot be used to directly identify a certain visitor.
Used to store the attribution information, the referrer initially used to visit the website
Cookies are small text files that are placed on your computer by websites that you visit. Websites use cookies to help users navigate efficiently and perform certain functions. Cookies that are required for the website to operate properly are allowed to be set without your permission. All other cookies need to be approved before they can be set in the browser.
You can change your consent to cookie usage at any time on our Privacy Policy page.