Run of Homozygosity a Procedure to Detecting Inbreeding in Farm Animals
Subject Areas : Camel
م.
نصرتی
1
(Department of Agriculture, Payame Noor University, Tehran, Iran)
Keywords: inbreeding, autozygosity, farm animal, run of homozygosity,
Abstract :
Inbreeding depression is a harmful phenomenon in livestock which is outcome of inbreeding. Inbreeding is consequence mating between two individuals who are more related to each other than average relatedness in population, which results in reducing in fitness of progenies and genetic variability in populations. Development of high-density genome-wide single nucleotide polymorphism (SNP) array facilitated inbreeding measurement as molecular data through calculating autozygosity region in individual genome. Autozygosity refer to chromosomal fragments that are identical-by-descent (IBD) and can be measured using runs of homozygosity (ROH). ROH is therefore defined as contiguous homozygous regions of the genome where two haplotypes inherited from the parents are IBD. The length and frequency of ROH may describe the history and recent bottlenecks in population and also revealed signatures of positive selection in population. Inbreeding coefficient can be derived from ROH (FROH), which is defined as total lengths of all ROH divided by the total autosomal genome length. A lot of studies calculated inbreeding level as FROH in human, cattle, pig, sheep, chicken and other farm animals through SNP array. In most of them, accuracy and preciseness of FROH were confirmed in comparing to FPED, Some of them calculated inbreeding depression by using FROH and some other evaluated the relationship between ROH location with gene and quantitative trait locus (QTL) position on genome. These studies indicated that inbreeding levels in bovine and porcine populations are much higher than those in human populations. Even though most of researches concluded that FROHcan precisely calculated Inbreeding and it can be useful for estimating inbreeding coefficient in absent of pedigree, but some concern were exist in about of panel density, genotyping errors and undetected heterozygosity within continuous ROH which complicated identifying and quantifying ROH. In this review, run of homozygosity is defined and discussed in detail in human and livestock.
Al‑Mamun H.A., Clark S.A., Kwan P. and Gondro C. (2015) Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genet. Sel. Evol. 47, 90.
Alvarez G., Ceballos F.C. and Quinteiro C. (2009). The role of inbreeding in the extinction of a European royal dynasty. PLoSOne. 4, e5174.
Bittles A.H. and Black M.L. (2010). Consanguinity, human evolution, and complex diseases. Proc. Nat. Acad. Sci. 107, 1779-1786.
Bittles A.H. (2003). Consanguineous marriage and childhood health. Dev. Med. Child Neurol. 45, 571-576.
Bjelland D., Weigel K., Vukasinovic N. and Nkrumah J. (2013). Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. J. Dairy Sci. 96, 4697-4706.
Bosse M., Megens H.J., Madsen O., Paudel Y., Frantz L., Schook L., Crooijmans R.P.M.A. and Groenen M.A.M. (2012). Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLoS Genet. 8, e1003100.
Broman K.W. and Weber J.L. (1999). Long homozygous chromosomal segments in reference families from the centre d'etude du polymorphisme humain. Am. J. Hum. Genet. 65, 1493-500.
Campbell H., Carothers A.D., Rudan I., Hayward C., Biloglav Z., Barac L., Pericic M., Janicijevic B., Smolej-Narancic N., Polasek O., Kolcic I., Weber J.L., Hastie N.D., Rudan P. and Wright A.F. (2007). Effects of genome-wide heterozygosity on a range of biomedically relevant human quantitative traits. Hum. Mol. Genet. 16, 233-241.
Carothers A.D., Rudan I., Kolcic I., Polasek O., Hayward C., Wright A.F., Campbell H., Teague P., Hastie N.D. and Weber J.L. (2006). Estimating human inbreeding coefficients: comparison of genealogical and marker heterozygosity approaches. Ann. Hum. Genet. 70, 666-676.
Charlesworth D. and Willis J. (2009). The genetics of inbreeding depression. Nat. Rev. Genet. 10, 783-796.
Crow J.F. (1954). Breeding structure of populations. II. Effective population number. Pp. 543-556 in Statistics and Mathematics in Biology. O. Kempthorne, T.A. Bancroft, J.W. Gowen and J.L. Lush, Eds. Iowa State College Press, Ames, Iowa.
Curik I., Ferenčaković M. and Sölkner S. (2014). Inbreeding and runs of homozygosity: A possible solution to an old problem. Livest. Sci. 166, 26-34.
Curik I., Solkner J. and Stipic N. (2002). Effects of models with finite loci, selection, dominance, epistasis and linkage on inbreeding coefficients based on pedigree and genotypic information. J. Anim. Breed. Genet. 119, 101-115.
Esmailizadeh A.K., Bottema C.D., Sellick G.S., Verbyla A.P., Morris C.A., Cullen N.G. and Pitchford W.S. (2008). Effects of the myostatin F94L substitution on beef traits. J. Anim. Sci. 86, 1038-1046.
Ferenčaković M., Hamzic E., Gredler B., Curik I. and Solkner J. (2011). Runs of homozygosity reveal genome-wideautozygosity in the Austrian fleckvieh cattle. Agric. Conspec. Sci. 76, 325-328.
Ferenčaković M., Sölkner J. and Curik I. (2013a). Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors. Genet. Sel. Evol. 45, 42.
Ferenčaković M., Hamzić E., Gredler B., Solberg T.R., Klemetsdal G., Curik I. and Sölkner J. (2013b). Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations. J. Anim. Breed. Genet. 130, 286-293.
Fernandez A., Toro M.A. and Lopez-Fanjul C. (1995). The effect of inbreeding on the redistribution of genetic variance of fecundity and viability in Tribolium castaneum. Heredity. 75, 376-381.
Fleming D.S., Koltes J.E., Markey A.D., Schmidt C.J., Ashwell C.M., Rothschild M.F., Persia M.E., Reecy J.M. and Lamont S.J. (2016). Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600k genotyping array. BMC Genom. 17, 407.
Ghani M., Reitz C., Cheng R., Vardarajan B.N., Jun G., Sato C., Naj A., Rajbhandary R., Wang L.S., Valladares O., Lin C.F., Larson E.B., Graff-Radford N.R., Evans D., De Jager P.L., Crane P.K., Buxbaum J.D., Murrell J.R., Raj T., Ertekin-Taner N., Logue M., Baldwin C.T., Green R.C., Barnes L.L., Cantwell L.B., Fallin M.D., Go R.C., Griffith P.A., Obisesan T.O., Manly J.J., Lunetta K.L., Kamboh M.I., Lopez O.L., Bennett D.A., Hendrie H., Hall K.S., Goate A.M., Byrd G.S., Kukull W.A., Foroud T.M., Haines J.L., Farrer L.A., Pericak-Vance M.A., Lee J.H., Schellenberg G.D., St George-Hyslop P., Mayeux R. and Rogaeva E. (2015). Association of long runs of homozygosity with alzheimer disease among African American individuals. J. American Med. Assoc. Neurol. 72(11), 1313-1323.
Ghani M., Sato C., Lee J.H., Reitz C., Moreno D., Mayeux R., St George-Hyslop P. and Rogaeva E. (2013). Evidence of recessive Alzheimer disease loci in a Caribbean Hispanic data set: genome-wide survey of runs of homozygosity. J. American Med. Assoc. Neurol. 70(10), 1261-1267.
Gibson J., Morton N.E. and Collins A. (2006). Extended tracts of homozygosity in outbred human populations. Hum. Mol. Genet. 15(5), 789-795.
Gomez‑Raya L., Rodríguez C., Barragán C. and Silió L. (2015). Genomic inbreeding coefficients based on the distribution of the length of runs of homozygosity in a closed line of Iberian pigs. Genet. Sel. Evol. 47, 81.
Gurgul A., Szmatoła T., Topolski P., Jasielczuk I., Żukowski K. and Bugno-Poniewierska M. (2016). The use of runs of homozygosity for estimation of recent inbreeding in Holstein cattle. J. Appl. Genet. 57(4), 1-4.
Gutiérrez-Gi B., Williams J.L., Homer D., Burton D., Haley C.S. and Wiener P. (2008). Search for quantitative trait loci affecting growth and carcass traits in a cross population of beef and dairy cattle. J. Anim. Sci. 87, 24-36.
Hamzić E. (2011). Levels of inbreeding derived from runs of homozygosity: a comparison of Austrian and Norwegian cattle breeds. MS Thesis. University of Natural Resources and Life Science, Vienna, Austria.
Herrero-Medrano J.M., Megens H.J., Groenen M.A., Ramis G., Bosse M.,Pérez-Enciso M. and Crooijmans R.P. (2013). Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula. BMC Genet. 30, 106.
Howard J.T., Maltecca C., Haile-Mariam M., Hayes B.J. and Pryce J.E. (2015). Characterizing homozygosity across United States, New Zealand and Australian Jersey cow and bull populations. BMC Genom. 16, 187.
Howrigan D., Simonson M. and Keller M. (2011). Detecting autozygosity through runs of homozygosity: a comparison of three autozygosity detection algorithms. BMC Genom. 12, 460.
Iacolina L., Scandura M., Goedbloed D.J., Alexandri P., Crooijmans R.P.M.A., Larson G., Archibald A., Apollonio M., Schook L.B., Groenen M.A.M. and Megens H.J. (2016a). Genomic diversity and differentiation of a managed island wild boar population. Heredity. 116, 60-67.
Iacolina L., Stronen A.V., Pertoldi C., Tokarska M., Nørgaard L.S., Muñoz J., Kjærsgaard A., Ruiz-Gonzalez A., Kamiński S. and Purfield D.C. (2016b). Novel graphical analyses of runs of homozygosity among species and livestock breeds. Int. J. Genom. 2016, 1-8.
Kaiser U.B., Katzenellenbogen R.A., Conn P.M. and Chin W.W. (1994). Evidence that signaling pathways by which Thyrotropin-releasing hormone and gonadotropin-releasing hormone act are both common and distinct. Mol. Endocrinol. 8(8), 1038-1048.
Karimi S. (2013). Runs of homozygosity patterns in taurine and indicine cattle breeds. MS Thesis. BOKU University of Natural Resources and Life Science, Vienna, Austria.
Keller M.C., Simonson M.A., Ripke S., Neale B.M., Gejman P.V., Howrigan D.P., Hong Lee S., Lencz T., Levinson D.F. and Sullivan P.F. (2012). Runs of homozygosity implicate autozygosity as a schizophrenia risk factor. PLoSGenet. 8, e1002656.
Keller M., Visscher P. and Goddard M. (2011). Quantification of inbreeding due to distant ancestors and its detection using dense SNP data. Genetics. 189, 237-249.
Khanshour A., Conant E., Juras R. and Cothran E.G. (2013). Microsatellite analysis of genetic diversity and population structure of Arabian horse populations. J. Hered. 104, 386-398.
Kim E.S., Sonstegard T.S., Van Tassell C.P., Wiggans G. and Rothschild M.F. (2015). The relationship between runs of homozygosity and inbreeding in Jersey cattle under selection. PLoSOne. 10(7), e0129967.
Kirin M., McQuillan R., Franklin C.S., Campbell H., McKeigue P.M. and Wilson J.F. (2010). Genomic runs of homozygosity record population history and consanguinity. PLoSOne. 5, e13996.
Lencz T., Lambert C., DeRosse P., Burdick K.E., Morgan T.V., Kane J.M., Kucherlapati R. and Malhotra A.K. (2007). Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc. Natl. Acad. Sci. 104, 19942-19947.
Malécot G. (1984). Les Mathématiques de L'hérédité. Publisher: Masson et Cie, France.
Marras G., Gaspa G., Sorbolini S., Dimauro C.,Ajmone-Marsan P., Valentini A., Williams J.L. and Macciotta N.P. (2015). Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Anim. Genet. 46(2), 110-121.
McQuillan R., Eklund N., Pirastu N., Kuningas M., McEvoy B.P., Esko T., Corre T., Davies G., Kaakinen M., Lyytikäinen L.P., Kristiansson K., Havulinna A.S. and Gögele M. (2012). Evidence of inbreeding depression on human height. PLoSGenet. 8, e1002655.
McQuillan R., Leutenegger A.L., Abdel-Rahman R., Franklin C.S., Pericic M., Barac-Lauc L., Smolej-Narancic N., Janicijevic B., Polasek O., Tenesa A., Macleod A.K., Farrington S.M., Rudan P., Hayward C., Vitart V., Rudan I., Wild S.H., Dunlop M.G., Wright A.F., Campbell H. and Wilson J.F. (2008). Runs of homozygosity in European populations. Am. J. Hum. Genet. 83(3), 359-372.
McWhirter R.E., Thomson R.J., Marthick J.R., Rumbold A.R., Brown M.A., Taylor-Thomson D., Maypilama E.L., Condon J.R. and Dickinson J.L. (2014). Runs of homozygosity and a cluster of vulvar cancer in young Australian Aboriginal women. Gynecol. Oncol. 133(3), 421-426.
Melhem N.M., Lu C., Dresbold C., Middleton F.A., Klei L., Wood S., Faraone S.V., Vinogradov S., Tiobech J., Yano V., Roeder K., Byerley W., Myles-Worsley M. and Devlin B. (2014). Characterizing runs of homozygosity and their impact on risk for psychosis in a population isolate. Am. J. Med. Genet. B Neuropsychiatr Genet. 165(6), 521-530.
Metzger J., Karwath M., Tonda R., Beltran S., Águeda L., Gut M., Gut I.G. and Distl O. (2015). Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses. BMC Genom. 9(16), 764.
Muchadeyi F.C., Malesa M.T., Soma P. and Dzomba E.F. (2015). Runs of homozygosity in Swakara pelt producing sheep: implications on sub-vital performance. Proc. Assoc. Advmt. Anim. Breed. Genet. 21, 310-313.
Nalls M., Guerreiro R., Simon-Sanchez J., Bras J., Traynor B., Gibbs J., Launer L., Hardy J. and Singleton A. (2009). Extended tracts of homozygosity identify novel candidate genes associated with late-onset Alzheimer's disease. Neurogenetics. 10, 183-190.
Nothnagel M., Lu T., Kayser M. and Krawczak M. (2010). Genomic and geographic distribution of SNP-defined runs of homozygosity in Europeans. Hum. Mol. Genet. 19, 2927-2935.
Orazietti J. (2015). Islands AND deserts: patterns of runs of homozygosity in chicken breeds. MS Thesis. University of Natural Resources and Life Science, Vienna, Austria.
Palamara P.F., Lencz T., Darvasi A. and Pe'er I. (2012). Length distributions of identity by descent reveal fine-scale demographic history. Am. J. Hum. Genet. 91, 809-822.
Pemberton T., Absher D., Feldman M., Myers R., Rosenberg N. and Li J. (2012). Genomic patterns of homozygosity in worldwide human populations. Am. J. Hum. Genet. 91, 275-292.
Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A.R., Bender D., Maller J., Sklar P., de Bakker P.I., Daly M.J. and Sham P.C. (2007). Plink: a toolset for whole-genome association and population-based linkage analysis. Am. J. Hum. Genet. 81, 275-291
Purfield D., Berry D., McParland S. and Bradley D. (2012). Runs of homozygosity and population history in cattle. BMC Genet. 13, 70.
SAS Institute. (2012). SAS®/STAT Software, Release 9.1. SAS Institute, Inc., Cary, NC. USA.
Siegenthaler G., Hotz R., Chatellard-Gruaz D., Didierjean L., Hellman U. and Saurat J.H. (1994). Purification and characterization of the human epidermal fatty acid binding protein: localization during epidermal cell differentiation in vivo and in vitro. Biochem. J. 02, 363-371.
Silio L., Rodrıguez M.C., Fernandez A., Barragan C., Ben ıtez R., Ovilo C. and Fernandez A.I. (2013) Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics. J. Anim. Breed. Genet. 130, 349-360.
Simón-Sánchez J., Kilarski L.L., Nalls M.A., Martinez M., Schulte C., Holmans P., Gasser T., Hardy J., Singleton A.B., Wood N.W., Brice A., Heutink P., Williams N. and Morris H.R. (2012). Cooperative genome-wide analysis shows increased homozygosity in early onset Parkinson's disease. PLoSOne. 7(3), e28787.
Sölkner J., Ferencakovic M., Gredler B. and Curik I. (2010). Genomic metrics of individual autozygosity, applied to a cattle population. Pp. 306-307 Proc. 61st Ann. Meet. European Assoc. Anim. Prod. Wageningen, Netherlands.
Stella A., Ajmone-Marsan P., Lazzari B. and Boettcher P. (2010). Identification of selection signatures in cattle breeds selected for dairy production. Genetics. 185, 1451-1461.
Suwanlee S., Baummung R., Solkner J. and Curik I. (2007). Evaluation of ancestral inbreeding coefficients: ballou's formula versus gene dropping. Conserv. Genet. 8, 489-495.
Szmatoła T., Gurgul A., Ropka-Molik K., Jasielczuk I., Ząbek T. and Bugno-Poniewierska M. (2016). Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland. Livest. Sci. 188, 72-80.
Templeton A.R. and Read B. (1994). Inbreeding: one word, several meanings, much confusion. Pp. 91-106 in Conservation Genetics. V. Loeschcke, J. Tomiuk and S.K. Jain, Eds. Birkhäuser–Verlag Publications, Basel, Switzerland.
Thomsen H., Chen B., Figlioli G., Elisei R., Romei C., Cipollini M., Cristaudo A., Bambi F., Hoffmann P., Herms S., Landi S., Hemminki K., Gemignani F. and Försti A. (2016). Runs of homozygosity and inbreeding in thyroid cancer. BMC Cancer. 16, 227.
Thomsen H., Filho M.I., Woltmann A., Johansson R., Eyfjörd J.E., Hamann U., Manjer J., Enquist-Olsson K., Henriksson R., Herms S., Hoffmann P., Chen B., Huhn S., Hemminki K. and Lenner P. (2015). Inbreeding and homozygosity in breast cancer survival. Sci. Rep. 12(5), 16467.
Verweij K.J., Abdellaoui A., Veijola J., Sebert S., Koiranen M., Keller M.C., Järvelin M.R. and Zietsch B.P. (2014). The association of genotype-based inbreeding coefficient with a range of physical and psychological human traits. PLoSOne. 9(7), e103102.
Wang C., Xu Z., Jin G., Hu Z., Dai J., Ma H., Jiang, Y., Hu L., Chu M. and Cao S. (2013). Genome-wide analysis of runs of homozygosity identifies new susceptibility regions of lung cancer in Han Chinese. Int. J. Biomed. Sci. 27, 208.
Wright S. (1922). Coefficients of inbreeding and relationship. Am. Nat. 56, 330-338.
Yang H.C. and Li H.W. (2014). Analysis of homozygosity disequilibrium using whole-genome sequencing data. BMC Proc. 8(1), 17.
Zhang L., Orloff M.S., Reber S., Li S., Zhao Y. and Eng C. (2013). cagTOH: extended approach for identifying tracts of homozygosity. PLoSOne. 8(3), e57772.
Zhang Q., Guldbrandtsen B., Bosse M., Lund M.S. and Sahana G. (2015). Runs of homozygosity and distribution of functional variants in the cattle genome. BMC Genom. 16, 542-545.