Open Access

Estimating of Additive, Dominance, and Epistatic Genetic Variance in Eucalypt Hybrid Population


Cite

An P, Mukherjee O, Chanda P, Yao L, Engelman CD, Huang CH, Zheng T, Kovac LP, Dubé MP, Liang X, Li J, de Andrade M, Culverhouse R, Malzahn D, Manning AK, Clarke GM, Jung J, Province MA (2009) The Challenge of Detecting Epistasis (G×G Interactions): Genetic Analysis Workshop 16. Genetic Epidemiology 33 (01): 58–67. https://doi.org/10.1002/gepi.20474369228019924703 Search in Google Scholar

Barker SF (1979) Interlocus interactions: a review of experimental evidence. Theoretical Population Biology 16: 323-346. https://doi.org/10.1016/0040-5809(79)90021-2545735 Search in Google Scholar

Barton NH (2017) How does epistasis influence the response to selection? Heredity 118: 96–109. https://doi.org/10.1038/hdy.2016.109517611427901509 Search in Google Scholar

Bernardo R (2020) Reinventing quantitative genetics for plant breeding: something old, something new, something borrowed, something BLUE. Heredity https://doi.org/10.1038/s41437-020-0312-1778468532296132 Search in Google Scholar

Bernardo R, Yu J (2007) Prospects for genome wide selection for quantitative traits in maize. Crop Science 47:1082–1090. https://doi.org/10.2135/cropsci2006.11.0690 Search in Google Scholar

Bouvet J-M, Saya A, Vigneron Ph (2009) Trends in additive, dominance and environmental effects with age for growth traits in Eucalyptus hybrid populations. Euphytica 165: 35-54. https://doi.org/10.1007/s10681-008-9746-x Search in Google Scholar

Bouvet J-M, Makouanzi G, Cros D, Vigneron Ph (2016) Modelling additive and non-additive effects in a hybrid population using genome-wide genotyping: prediction accurary implications. Heredity 116: 146-157. https://doi.org/10.1038/hdy.2015.78480688126328760 Search in Google Scholar

Carlborg Ö, Haley CS (2004) Epistasis; too often neglected in complex trait studies. Nature Reviews Genetics 5: 618-625. https://doi.org/10.1038/nrg140715266344 Search in Google Scholar

Cheverud JM, Routman EJ (1995) Epistasis and its Contribution to Genetic Variance Components. Genetics 139: 1455-1461. https://doi.org/10.1093/genetics/139.3.145512064717768453 Search in Google Scholar

Cheverud JM, Routman EJ (1996) Epistasis as a source of increased additive genetic variance at population bottlenecks. Evolution 50:1042–1051. https://doi.org/10.1111/j.1558-5646.1996.tb02345.x28565298 Search in Google Scholar

Cockerham CC (1954) An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 39: 859-882. https://doi.org/10.1093/genetics/39.6.859120969417247525 Search in Google Scholar

Cordell HJ (2002) Epistasis: what it means, what it doesn’t mean, and statistical methods to detect it in humans. Human Molecular Genetics 11 (20): 2463–2468. https://doi.org/10.1093/hmg/11.20.246312351582 Search in Google Scholar

Costa e Silva J, Borralho NMG, Potts BM (2004) Additive and non-additive genetic parameters from clonally replicated and seedling progenies of Eucalyptus globulus. Theoretical and Applied Genetics 108:1113–1119. https://doi.org/10.1007/s00122-003-1524-515067398 Search in Google Scholar

Crow JF (1987) Population genetics history: a personal view. Annual Review of Genetics 21: 1-22. https://doi.org/10.1146/annurev.ge.21.120187.0002453327458 Search in Google Scholar

Crow JF (2008) Maintaining evolvability. Journal of Genetics 87: 9-353. https://doi.org/10.1007/s12041-008-0057-819147924 Search in Google Scholar

Crow JF (2010) On epistasis: Why it is unimportant in polygenic directional selection. Philosophical Transactions of the Royal Society B 365: 1241-1244. https://doi.org/10.1098/rstb.2009.0275287181420308099 Search in Google Scholar

d’Annunzio R, Conche S, Landais D, Saint-André L, Joffre R, Barthes B (2008) Pairwise comparison of soil organic particle-size distributions in native savannas and Eucalyptus plantations in Congo. Forest Ecology and Management 255: 1050–1056. https://doi.org/10.1016/j.foreco.2007.10.027 Search in Google Scholar

de los Campos G, Hickey JM, Pong-Wong R, Daetwyler HD, Calus MPL (2013) Whole-Genome Regression and Prediction Methods Applied to Plant and Animal Breeding. Genetics 193: 327–345. https://doi.org/10.1534/genetics.112.143313356772722745228 Search in Google Scholar

de Visser JAGM, Cooper TF, Elena SF (2011) The causes of epistasis, rewiew. Proceedings of Royal Society B: Biological Sciences 278 (1725): 3617-3624. https://doi.org/10.1098/rspb.2011.1537320350921976687 Search in Google Scholar

Epron D, Nouvellon Y, Roupsard O, Mouvondy W, Mabiala A, Saint-André L, Joffre R, Jourdan C, Bonnefond J-M, Berbigier P, Hamel O (2004) Spatial and temporal variation of soil respiration in an Eucalyptus plantation in Congo. Forest Ecology and Management 202: 149–160. https://doi.org/10.1016/j.foreco.2004.07.019 Search in Google Scholar

Falconer GS, Mackay TFC (1996) Introduction to quantitative genetics. Ed. 4. Longman group Ltd., Edinburgh, United Kingdom. 464p. Search in Google Scholar

Fisher RA (1918) The correlation between relatives on the supposition of Mendelian inheritance. Transactions of Royal Society of Edinburgh 52 : 399-433. https://doi.org/10.1017/s0080456800012163 Search in Google Scholar

Gallais A (1990) Théorie de la sélection en amélioration des plantes. Collection Sciences Agronomiques, Masson, Paris, France. 588p. Search in Google Scholar

Garcia-Cortes LA, Legarra A, Chevalet C, Toro MA (2013) Variance and Covariance of Actual Relationships between Relatives at One Locus. PLos One 8: 1-5. https://doi.org/10.1371/journal.pone.0057003357984123451134 Search in Google Scholar

Goodnight CJ (1988) Epistasis and the effect of founder events on the additive genetic variance. Evolution 42 (3): 441-454. https://doi.org/10.1111/j.1558-5646.1988.tb04151.x28564006 Search in Google Scholar

Goodnight CJ (2000) Quantitative trait loci and gene interaction: the quantitative genetics of metapopulations. Heredity 84: 587–598. https://doi.org/10.1046/j.1365-2540.2000.00698.x10849084 Search in Google Scholar

Grattapaglia D, Silva-Junior OB, Resende RT, Cappa EP, Müller BSF, Tan B, Isik F, Ratcliffe B, El-Kassaby YA (2018) Quantitative Genetics and Genomics Converge to Accelerate Forest Tree Breeding. Frontiers in Plant Science 9: 1693. https://doi.org/10.3389/fpls.2018.01693626202830524463 Search in Google Scholar

Guo Z, Tucker DM, Lu J, Kishore V, Gay G (2012) Evaluation of genome-wide selection efficiency in maize nested association mapping populations. Theoretical and Applied Genetics 124:261–275. https://doi.org/10.1007/s00122-011-1702-921938474 Search in Google Scholar

Habier D, Fernando RL, Dekkers JCM (2007) The impact of genetic relationship information on genome-assisted breeding values. Genetics 177:2389–2397. https://doi.org/10.1534/genetics.107.081190221948218073436 Search in Google Scholar

Hansen TF (2013) Why epistasis is important for selection and adaptation. Evolution 67-12: 3501–3511. https://doi.org/10.1111/evo.1221424299403 Search in Google Scholar

Heffner EL, Sorrells ME, Jannink JL (2009) Genomic selection for crop improvement. Crop Science 49: 1–12. https://doi.org/10.2135/cropsci2008.08.0512 Search in Google Scholar

Henderson CR (1974) General flexibility of linear model techniques for sire evaluation. Journal of Dairy Science 57:963–972. https://doi.org/10.3168/jds.s0022-0302(74)84993-3 Search in Google Scholar

Hill WG (2010) Understanding and using quantitative genetic variation. Philosophical Transactions of the Royal Society B: Biology Sciences 365: 73-85. https://doi.org/10.1098/rstb.2009.0203284270820008387 Search in Google Scholar

Hill WG, Goddard ME, Visscher PM (2008) Data and theory point to mainly additive genetic variance for complex traits. Plos Genetics 4(2). https://doi.org/10.1371/journal.pgen.1000008.eor Search in Google Scholar

Isik F, Li B, Frampton J (2003) Estimates of additive, dominance and epistatic genetic variances from a clonally replicated test of Loblolly pine. Forest Science 49 (1): 77-88. Search in Google Scholar

Jannink JL (2003) Selection dynamics and limits under additive × additive epistatic gene action. Crop Science 43: 489–497. https://doi.org/10.2135/cropsci2003.0489 Search in Google Scholar

Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct. Genomics 9: 166–177. https://doi.org/10.1093/bfgp/elq00120156985 Search in Google Scholar

Jasnos L, Korona R (2007) Epistatic buffering of fitness loss in yeast double deletion strains. Nature reviews Genetics 39: 550–554. https://doi.org/10.1038/ng198617322879 Search in Google Scholar

Kempthorne O (1954) The correlations between relatives in a random mating population. Proc. Royal Soc. London B 143: 103–113. https://doi.org/10.1098/rspb.1954.0056 Search in Google Scholar

Kerr RJ, Li L, Tier B, Dutkowski GW, McRae TA (2012) Use of the numerator relationship matrix in genetic analysis of autopolyploid species. Theor. Appl. Genet. https://doi.org/10.1007/s00122-012-1785-y22311370 Search in Google Scholar

Lehner B (2011) Molecular mechanisms of epistasis within and between genes. Trends in Genetics 27 (8): 323-331. https://doi.org/10.1016/j.tig.2011.05.00721684621 Search in Google Scholar

Lu PX, Huber DA, White TL (1999) Potential biases of incomplete linear models in heritability estimation and breeding value prediction. Canadian Journal of Forestry Research 29: 724–736. https://doi.org/10.1139/x99-047 Search in Google Scholar

Luan T, Woolliams JA, Ødegård J, Dolezal M, Roman-Ponce SI, Bagnato A, Meuwissen THE (2012) The importance of identity-by-state information for the accuracy of genomic selection. Genetics Selection Evolution 44 (28): 2-7. https://doi.org/10.1186/1297-9686-44-28351733722937985 Search in Google Scholar

Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Associates, pp558-563 and 813-816. Search in Google Scholar

Mackay TFC (2014) Epistasis and quantitative traits: using model organism to study gene-gene interactions. Nature Reviews Genetics 15: 22-23. https://doi.org/10.1038/nrg3627391843124296533 Search in Google Scholar

Mäki-Tanila A, Hill WG (2014) Influence of gene interaction on complex trait variation with multilocus models. Genetics 198: 355–367. https://doi.org/10.1534/genetics.114.165282417494724990992 Search in Google Scholar

Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps. Genetics 157: 1819–1829. https://doi.org/10.1093/genetics/157.4.1819146158911290733 Search in Google Scholar

Moore JH, Williams SM (2005) Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis. Bioessays 27: 637-646. https://doi.org/10.1002/bies.2023615892116 Search in Google Scholar

Nzila JDD, Bouillet J-P, Laclau J-P, Ranger J (2002) The effects of slash management on nutrient cycling and tree growth in Eucalyptus plantations in the Congo. Forest Ecology and Management 171: 209–221. https://doi.org/10.1016/s0378-1127(02)00474-7 Search in Google Scholar

Okada Y, Sim X, Go MJ, Wu JY, Gu D, Takeuchi F, Takahashi A, Maeda S, Tsunoda T, Chen P, Lim S-C, Wong T-Y, Lee J-Y, Han B-G, Chen C-H, Kang D, Tsai F-J, Chang L-C, Fann S-JC, Mei H, Rao DC, Hixson JE, Chen S, Katsuya T, Isono M, Ogihara T, Chambers JC, Zhang W, Kooner JS, The KidneyGen Consortium, The CKDGen Consortium, Albrecht E, The GUGC consortium, Yamamoto K, Kubo M, Nakamura Y, Kamatani N, Kato N, He J, Chen Y-T, Cho Y-S, Tai E-S, Tanaka T (2012) Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations. Nat. Genet. 44(8): 904–909. https://doi.org/10.1038/ng.2352473764522797727 Search in Google Scholar

Paixãoa T, Barton NH (2016) The effect of gene interactions on the long-term response to selection. PNAS 113 (16): 4422-4427. https://doi.org/10.1073/pnas.1518830113484342527044080 Search in Google Scholar

Palucci V, Schaeffer LR, Miglior F, Osborne V (2007) Non-additive genetic effects for fertility traits in Canadian Holstein cattle. Genetics Selection Evolution 39: 181–193. https://doi.org/10.1186/1297-9686-39-2-181268283617306200 Search in Google Scholar

Patterson HD, Thompson R (1971) Recovery of inter-block information when block sizes are equal. Biometrika 58: 545–554. https://doi.org/10.1093/biomet/58.3.545 Search in Google Scholar

Paul AD, Foster GS, Caldwell T, McRae J (1997) Trends in genetic and environmental parameters for height, diameter, and volume in a multilocation clonal study with loblolly pine. Forest Science 43:87–98. Search in Google Scholar

Phillips PC (2008) Epistasis – The essential role of gene interactions in the structure and evolution of genetic systems. Nature Reviews Genetics 9: 855-867. https://doi.org/10.1038/nrg2452268914018852697 Search in Google Scholar

Pichot C, Tessier du Cros E (1989) Estimation of genetic parameters in eastern cottonwood (Populus destoides Bartr.). Consequence for the breeding strategy. Annals of Forest Science 46: 307-324. https://doi.org/10.1051/forest:19890401 Search in Google Scholar

Rosvall O, Lindgren D, Mullin TJ (1998) Sustainability robustness and efficiency of a multi-generation breeding strategy based on within-family clonal selection. Silvae Genetica 47: 307–321. Search in Google Scholar

Shelbourne CJA (1991) Genetic gains from different kinds of breeding population and seed or plant production population. Southern African Forestry Journal 160:49–65. https://doi.org/10.1080/00382167.1992.9630411 Search in Google Scholar

Stonecypher R, Mc Cullough R (1986) Estimates of additive and non-additive genetic variance from a clonal diallel of Douglas-fir Pseudotsuga menziesii (Mirb). Franco. In Proc. Int. Union For. Res. Org. joint Mtg. Working parties Breed. Theor. Prg. Test, Seed, Orch. Villiamsburg/VA. Publ by NCJU Industry Coop. Tree Imp. Prog. pp 211-227. Search in Google Scholar

Su G, Christensen OL, Ostersen T, Henryon M, Mogens S, Lund MS (2012) Estimating Additive and Non-Additive Genetic Variances and Predicting Genetic Merits Using Genome-Wide Dense Single Nucleotide Polymorphism Markers. Plos One 7 (9): 1-7. https://doi.org/10.1371/journal.pone.0045293344170323028912 Search in Google Scholar

Templeton AR (2000) Epistasis and complex traits. In: Epistasis and the Evolutionary Process. Wolf J, Brodie III B, Wade M (Eds). New York, Oxford University Press, pp41-57. Search in Google Scholar

Van Der Werf JHJ, de Boer W (1989) Influence of non-additive effects on estimation of genetic parameters in dairy cattle. Journal of Dairy Science 72: 2606–2614. https://doi.org/10.3168/jds.s0022-0302(89)79401-7 Search in Google Scholar

Verhoeven KJF, Casella G, Mc Intyre LM (2010) Epistasis: Obstacle or Advantage for Mapping Complex Traits? Plos One 5 (8): 1-12. https://doi.org/10.1371/journal.pone.0012264292872520865037 Search in Google Scholar

Wade MJ (2002) A gene’s eye view of epistasis, selection and speciation. J. Evol. Biol. 15: 337–346. https://doi.org/10.1046/j.1420-9101.2002.00413.x Search in Google Scholar

Wan X, Yang C, Yang Q, Zhao H, Yu W (2013) The complete compositional epistasis detection in genome-wide association studies. BMC Genetics 14 (7): http://www.biomedcentral.com/1471-2156/14/7.10.1186/1471-2156-14-7363801323421496 Search in Google Scholar

Witte J (1998) Gene–environment interaction. In Armitage P. and Colton T. (Eds), Encyclopedia of Biostatistics. Wiley, Chichester, pp1613–1614. Search in Google Scholar

Wright S (1980) Genic and organismic selection. Evolution 34:825-843. https://doi.org/10.1111/j.1558-5646.1980.tb04022.x28581131 Search in Google Scholar

Xu S, Jia Z (2007) Genome wide analysis of epistatic effects for quantitative traits in barley. Genetics 175: 1955–1963.10.1534/genetics.106.066571185512317277367 Search in Google Scholar

eISSN:
2509-8934
Language:
English
Publication timeframe:
Volume Open
Journal Subjects:
Life Sciences, Molecular Biology, Genetics, Biotechnology, Plant Science