Estimating of Additive, Dominance, and Epistatic Genetic Variance in Eucalypt Hybrid Population
References
- 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
- 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
- Barton NH (2017) How does epistasis influence the response to selection? Heredity 118: 96–109. https://doi.org/10.1038/hdy.2016.109517611427901509
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Crow JF (2008) Maintaining evolvability. Journal of Genetics 87: 9-353. https://doi.org/10.1007/s12041-008-0057-819147924
- 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
- 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
- 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
- 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
- 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
- Falconer GS, Mackay TFC (1996) Introduction to quantitative genetics. Ed. 4. Longman group Ltd., Edinburgh, United Kingdom. 464p.
- 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
- Gallais A (1990) Théorie de la sélection en amélioration des plantes. Collection Sciences Agronomiques, Masson, Paris, France. 588p.
- 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
- 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
- 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
- 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
- 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
- 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
- Hansen TF (2013) Why epistasis is important for selection and adaptation. Evolution 67-12: 3501–3511. https://doi.org/10.1111/evo.1221424299403
- 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
- 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
- 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
- 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
- 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.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Associates, pp558-563 and 813-816.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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.
- 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
- 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
- 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.
- 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
- 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.
- 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
- 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.
- 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
- 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
- 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
- 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
- Witte J (1998) Gene–environment interaction. In Armitage P. and Colton T. (Eds), Encyclopedia of Biostatistics. Wiley, Chichester, pp1613–1614.
- Wright S (1980) Genic and organismic selection. Evolution 34:825-843. https://doi.org/10.1111/j.1558-5646.1980.tb04022.x28581131
- 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
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