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Journal articles on the topic 'Genetic Epistasis'

Author: Grafiati

Published: 4 June 2021

Last updated: 28 July 2025

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1

Cheverud, J. M., and E. J. Routman. "Epistasis and its contribution to genetic variance components." Genetics 139, no. 3 (1995): 1455–61. http://dx.doi.org/10.1093/genetics/139.3.1455.

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Abstract We present a new parameterization of physiological epistasis that allows the measurement of epistasis separate from its effects on the interaction (epistatic) genetic variance component. Epistasis is the deviation of two-locus genotypic values from the sum of the contributing single-locus genotypic values. This parameterization leads to statistical tests for epistasis given estimates of two-locus genotypic values such as can be obtained from quantitative trait locus studies. The contributions of epistasis to the additive, dominance and interaction genetic variances are specified. Epis

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Garel, Makouanzi Ekomono Chrissy, and Vigneron Philippe. "Estimating of Additive, Dominance, and Epistatic Genetic Variance in Eucalypt Hybrid Population." Silvae Genetica 71, no. 1 (2022): 39–46. http://dx.doi.org/10.2478/sg-2022-0005.

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Abstract Additive, dominance and epistasis genetic variances were estimated from analysis of a clonally replicated full-sib progeny test grown in the Republic of Congo. Phenotypic variance components were estimated for ages 4 through 25 months for growth and at ages 8 and 18 months for ecophysiological traits. The estimation of genetics effects was derived from the individual mixed model. Genetic structure was incorporated into variances and covariance’s effects based on markers information. The detected genetic effects of epistasis are significant in some traits. This study shows that epistas

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Nodzenski, Michael, Min Shi, Juno M. Krahn, et al. "GADGETS: a genetic algorithm for detecting epistasis using nuclear families." Bioinformatics 38, no. 4 (2021): 1052–58. http://dx.doi.org/10.1093/bioinformatics/btab766.

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Abstract Motivation Epistasis may play an etiologic role in complex diseases, but research has been hindered because identification of interactions among sets of single nucleotide polymorphisms (SNPs) requires exploration of immense search spaces. Current approaches using nuclear families accommodate at most several hundred candidate SNPs. Results GADGETS detects epistatic SNP-sets by applying a genetic algorithm to case-parent or case-sibling data. To allow for multiple epistatic sets, island subpopulations of SNP-sets evolve separately under selection for evident joint relevance to disease r

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YAMAMOTO, AKIHIKO, ROBERT R. H. ANHOLT, and TRUDY F. C. MACKAY. "Epistatic interactions attenuate mutations affecting startle behaviour in Drosophila melanogaster." Genetics Research 91, no. 6 (2009): 373–82. http://dx.doi.org/10.1017/s0016672309990279.

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SummaryEpistasis is an important feature of the genetic architecture of quantitative traits. Previously, we showed that startle-induced locomotor behaviour of Drosophila melanogaster, a critical survival trait, is highly polygenic and exhibits epistasis. Here, we characterize epistatic interactions among homozygous P-element mutations affecting startle-induced locomotion in the Canton-S isogenic background and in 21 wild-derived inbred genetic backgrounds. We find pervasive epistasis for pairwise combinations of homozygous P-element insertional mutations as well as for mutations in wild-derive

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Kao, Chen-Hung, and Zhao-Bang Zeng. "Modeling Epistasis of Quantitative Trait Loci Using Cockerham's Model." Genetics 160, no. 3 (2002): 1243–61. http://dx.doi.org/10.1093/genetics/160.3.1243.

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AbstractWe use the orthogonal contrast scales proposed by Cockerham to construct a genetic model, called Cockerham's model, for studying epistasis between genes. The properties of Cockerham's model in modeling and mapping epistatic genes under linkage equilibrium and disequilibrium are investigated and discussed. Because of its orthogonal property, Cockerham's model has several advantages in partitioning genetic variance into components, interpreting and estimating gene effects, and application to quantitative trait loci (QTL) mapping when compared to other models, and thus it can facilitate t

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Toch, Katarzyna, Mateusz Buczek, and Marta K. Labocha. "Genetic Interactions in Various Environmental Conditions in Caenorhabditis elegans." Genes 14, no. 11 (2023): 2080. http://dx.doi.org/10.3390/genes14112080.

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Although it is well known that epistasis plays an important role in many evolutionary processes (e.g., speciation, evolution of sex), our knowledge on the frequency and prevalent sign of epistatic interactions is mainly limited to unicellular organisms or cell cultures of multicellular organisms. This is even more pronounced in regard to how the environment can influence genetic interactions. To broaden our knowledge in that respect we studied gene–gene interactions in a whole multicellular organism, Caenorhabditis elegans. We screened over one thousand gene interactions, each one in standard

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SWARUP, SHILPA, SUSAN T. HARBISON, LAUREN E. HAHN, et al. "Extensive epistasis for olfactory behaviour, sleep and waking activity in Drosophila melanogaster." Genetics Research 94, no. 1 (2012): 9–20. http://dx.doi.org/10.1017/s001667231200002x.

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SummaryEpistasis is an important feature of the genetic architecture of quantitative traits, but the dynamics of epistatic interactions in natural populations and the relationship between epistasis and pleiotropy remain poorly understood. Here, we studied the effects of epistatic modifiers that segregate in a wild-derived Drosophila melanogaster population on the mutational effects of P-element insertions in Semaphorin-5C (Sema-5c) and Calreticulin (Crc), pleiotropic genes that affect olfactory behaviour and startle behaviour and, in the case of Crc, sleep phenotypes. We introduced Canton-S B

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MALMBERG, RUSSELL L., and RODNEY MAURICIO. "QTL-based evidence for the role of epistasis in evolution." Genetical Research 86, no. 2 (2005): 89–95. http://dx.doi.org/10.1017/s0016672305007780.

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The extent to which epistasis contributes to adaptation and speciation has been a controversial topic in evolutionary genetics. One experimental approach to study epistasis is based on quantitative trait locus (QTL) mapping using molecular markers. Comparisons can be made among all possible pair-wise combinations of the markers, irrespective of whether an additive QTL is associated with a marker; several software packages have been developed that facilitate this. We review several examples of using this approach to identify epistatic QTLs for traits of evolutionary or ecological interest. Whil

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Lair, Kevin P., William E. Bradshaw, and Christina M. Holzapfel. "Evolutionary Divergence of the Genetic Architecture Underlying Photoperiodism in the Pitcher-Plant Mosquito, Wyeomyia smithii." Genetics 147, no. 4 (1997): 1873–83. http://dx.doi.org/10.1093/genetics/147.4.1873.

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Abstract We determine the contribution of composite additive, dominance, and epistatic effects to the genetic divergence of photoperiodic response along latitudinal, altitudinal, and longitudinal gradients in the pitcher-plant mosquito, Wyeomyia smithii. Joint scaling tests of crosses between populations showed wide-spread epistasis as well as additive and dominance differences among populations. There were differences due to epistasis between an alpine population in North Carolina and populations in Florida, lowland North Carolina, and Maine. Longitudinal displacement resulted in differences

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Griswold, Cortland K. "Epistasis can accelerate adaptive diversification in haploid asexual populations." Proceedings of the Royal Society B: Biological Sciences 282, no. 1802 (2015): 20142648. http://dx.doi.org/10.1098/rspb.2014.2648.

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A fundamental goal of the biological sciences is to determine processes that facilitate the evolution of diversity. These processes can be separated into ecological, physiological, developmental and genetic. An ecological process that facilitates diversification is frequency-dependent selection caused by competition. Models of frequency-dependent adaptive diversification have generally assumed a genetic basis of phenotype that is non-epistatic. Here, we present a model that indicates diversification is accelerated by an epistatic basis of phenotype in combination with a competition model that

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Arnqvist, Göran, Nikolas Vellnow, and Locke Rowe. "The effect of epistasis on sexually antagonistic genetic variation." Proceedings of the Royal Society B: Biological Sciences 281, no. 1787 (2014): 20140489. http://dx.doi.org/10.1098/rspb.2014.0489.

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There is increasing evidence of segregating sexually antagonistic (SA) genetic variation for fitness in laboratory and wild populations, yet the conditions for the maintenance of such variation can be restrictive. Epistatic interactions between genes can contribute to the maintenance of genetic variance in fitness and we suggest that epistasis between SA genes should be pervasive. Here, we explore its effect on SA genetic variation in fitness using a two locus model with negative epistasis. Our results demonstrate that epistasis often increases the parameter space showing polymorphism for SA l

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N, RAMAMOORTHI, JEHANGIR K.S, and NADARAJAN N. "GENETIC ARCHITECTURE OF METRIC TRAITS IN PEARL MILLET." Madras Agricultural Journal 83, October (1996): 635–37. http://dx.doi.org/10.29321/maj.10.a01070.

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The P1, P2, F1, F2, BCI and BC2 generations of five pearl millet crosses were studied for six metric traits. The additive dominance model was adequate for plant height, leaf breadth, earhead length and earhead breadth in one cross each. An epistatic digenic model was assumed for other crosses. Heterosis breeding is suggested for improvement of all traits. Duplicate epistasis playes a relatively greater role than complementary epistasis. Among the interactions, dominance X dominance played a major role. Therefore, reciprocal recurrent selection is suggested for development of a superior variety

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Iglesias, M. T., V. S. Peñaranda, C. Vidal, and A. Verschoren. "The 2-epistasis of fitness functions." Bulletin of the Australian Mathematical Society 76, no. 3 (2007): 397–419. http://dx.doi.org/10.1017/s0004972700039769.

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In this note about Genetic Algorithms(GA-), we study the2-epistasisof a fitness function over a search space. This concept is a natural generalisation of that ofepistasis, previously considered by Davidor in 1991 Suys and Verschoren in 1996 and Van Hove and Verschoren in 1994 for example. We completely characterise fitness functions whose 2-epistasis is minimal: these are exactly the second order functions. The validity of 2-epistasis as a measure of hardness with respect to genetic algorithms is checked over some classical laboratory functions. Finally, we obtain an upper bound of the maximal

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Faure, Andre J., Ben Lehner, Verónica Miró Pina, Claudia Serrano Colome, and Donate Weghorn. "An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity." PLOS Computational Biology 20, no. 5 (2024): e1012132. http://dx.doi.org/10.1371/journal.pcbi.1012132.

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Accurate models describing the relationship between genotype and phenotype are necessary in order to understand and predict how mutations to biological sequences affect the fitness and evolution of living organisms. The apparent abundance of epistasis (genetic interactions), both between and within genes, complicates this task and how to build mechanistic models that incorporate epistatic coefficients (genetic interaction terms) is an open question. The Walsh-Hadamard transform represents a rigorous computational framework for calculating and modeling epistatic interactions at the level of ind

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Wen, Jia, Colby T. Ford, Daniel Janies, and Xinghua Shi. "A parallelized strategy for epistasis analysis based on Empirical Bayesian Elastic Net models." Bioinformatics 36, no. 12 (2020): 3803–10. http://dx.doi.org/10.1093/bioinformatics/btaa216.

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Abstract Motivation Epistasis reflects the distortion on a particular trait or phenotype resulting from the combinatorial effect of two or more genes or genetic variants. Epistasis is an important genetic foundation underlying quantitative traits in many organisms as well as in complex human diseases. However, there are two major barriers in identifying epistasis using large genomic datasets. One is that epistasis analysis will induce over-fitting of an over-saturated model with the high-dimensionality of a genomic dataset. Therefore, the problem of identifying epistasis demands efficient stat

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Singh, B. B., U. P. Singh, R. M. Singh, and B. Rai. "Genetic analysis of yield and yield components in field peas." Journal of Agricultural Science 109, no. 1 (1987): 67–71. http://dx.doi.org/10.1017/s0021859600081004.

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SummaryThe genetic parameters controlling the expression of seed yield and the yield components have been studied using both generation mean and triple test cross (TTC) analyses in two crosses of field pea. From generation mean analysis, it is obvious that in addition to significant estimates of additive and dominance components, epistatic components of mean [(i) and (I) types] were also important and duplicate type of epistasis was predominant for all the traits in both sets of crosses. In the TTC analysis, the major genetic component of variance was the additive component, though the dominan

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Eshed, Yuval, and Dani Zamir. "Less-Than-Additive Epistatic Interactions of Quantitative Trait Loci in Tomato." Genetics 143, no. 4 (1996): 1807–17. http://dx.doi.org/10.1093/genetics/143.4.1807.

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Abstract Epistasis plays a role in determining the phenotype, yet quantitative trait loci (QTL) mapping has uncovered little evidence for it. To address this apparent contradiction, we analyzed interactions between individual Lycopersicon pennellii chromosome segments introgressed into an otherwise homogeneous genetic background of L. esculentum (cv. M82). Ten different homozygous introgression lines, each containing from 4 to 58 cM of introgressed DNA, were crossed in a half diallele scheme. The 45 derived double heterozygotes were evaluated in the field for four yield-associated traits, alon

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Hansen, Thomas F., and Günter P. Wagner. "Epistasis and the Mutation Load: A Measurement-Theoretical Approach." Genetics 158, no. 1 (2001): 477–85. http://dx.doi.org/10.1093/genetics/158.1.477.

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Abstract An approximate solution for the mean fitness in mutation-selection balance with arbitrary order of epistatic interaction is derived. The solution is based on the assumptions of coupling equilibrium and that the interaction effects are multilinear. We find that the effect of m-order epistatic interactions (i.e., interactions among groups of m loci) on the load is dependent on the total genomic mutation rate, U, to the mth power. Thus, higher-order gene interactions are potentially important if U is large and the interaction density among loci is not too low. The solution suggests that

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Pillai, Resmi, Harshal Waghulde, Ying Nie, et al. "Isolation and high-throughput sequencing of two closely linked epistatic hypertension susceptibility loci with a panel of bicongenic strains." Physiological Genomics 45, no. 16 (2013): 729–36. http://dx.doi.org/10.1152/physiolgenomics.00077.2013.

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Interactions or epistasis between genetic factors may contribute to “missing heritability.” While linkage analyses detect epistasis, defining the limits of the interacting segments poses a significant challenge especially when the interactions are between loci in close proximity. The goal of the present study was to isolate two such epistatic blood pressure (BP) loci on rat chromosome 5. A panel of S.LEW bicongenic strains along with the corresponding monocongenic strains was constructed. BP of each set comprising of one bicongenic and two corresponding monocongenic strains were determined alo

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Schrauf, Matías F., Johannes W. R. Martini, Henner Simianer, et al. "Phantom Epistasis in Genomic Selection: On the Predictive Ability of Epistatic Models." G3 Genes|Genomes|Genetics 10, no. 9 (2020): 3137–45. http://dx.doi.org/10.1534/g3.120.401300.

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Abstract Genomic selection uses whole-genome marker models to predict phenotypes or genetic values for complex traits. Some of these models fit interaction terms between markers, and are therefore called epistatic. The biological interpretation of the corresponding fitted effects is not straightforward and there is the threat of overinterpreting their functional meaning. Here we show that the predictive ability of epistatic models relative to additive models can change with the density of the marker panel. In more detail, we show that for publicly available Arabidopsis and rice datasets, an in

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Wang, Hui, Yi Zhang, Long Wang, et al. "Heritability Estimates of Growth-Related Traits in Oriental River Prawns, Macrobrachium nipponense." Aquaculture Research 2023 (February 3, 2023): 1–10. http://dx.doi.org/10.1155/2023/8315364.

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Breeding programs in oriental river prawn populations would benefit from a knowledge of heritabilities for growth-related traits to assess their potential for genetic improvement. This study reports the results of heritability estimation and evaluation of epistatic interactions for growth-related traits in oriental river prawn (Macrobrachium nipponense). The results showed that heritability estimates (h2) were low to medium in magnitude, ranging between 0.10 (±0.02) and 0.22 (±0.01) for females and between 0.08 (±0.01) and 0.26 (±0.02) for males. The additive × additive epistasis was direction

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Mullin, T. J., and Y. S. Park. "Estimating genetic gains from alternative breeding strategies for clonal forestry." Canadian Journal of Forest Research 22, no. 1 (1992): 14–23. http://dx.doi.org/10.1139/x92-003.

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Concepts and procedures are presented for the analysis of progeny trials that incorporate clonal replication as a means to resolve variance arising from nonadditive gene effects. Components of variance from the linear model may be expressed in terms of expected covariances among relatives, and these, in turn, may be used to derive approximations of additive, dominance, and epistatic components of genetic variance. In addition to the usual assumptions applied to conventional progeny trials, the use of this expanded genetic model in the analysis of tests with clonal replicates assumes that the g

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Mao, Yongcai, Nicole R. London, Li Ma, Daniel Dvorkin, and Yang Da. "Detection of SNP epistasis effects of quantitative traits using an extended Kempthorne model." Physiological Genomics 28, no. 1 (2006): 46–52. http://dx.doi.org/10.1152/physiolgenomics.00096.2006.

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Epistasis effects (gene interactions) have been increasingly recognized as important genetic factors underlying complex traits. The existence of a large number of single nucleotide polymorphisms (SNPs) provides opportunities and challenges to screen DNA variations affecting complex traits using a candidate gene analysis. In this article, four types of epistasis effects of two candidate gene SNPs with Hardy-Weinberg disequilibrium (HWD) and linkage disequilibrium (LD) are considered: additive × additive, additive × dominance, dominance × additive, and dominance × dominance. The Kempthorne genet

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Sheppard, Brooke, Nadav Rappoport, Po-Ru Loh, Stephan J. Sanders, Noah Zaitlen, and Andy Dahl. "A model and test for coordinated polygenic epistasis in complex traits." Proceedings of the National Academy of Sciences 118, no. 15 (2021): e1922305118. http://dx.doi.org/10.1073/pnas.1922305118.

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Interactions between genetic variants—epistasis—is pervasive in model systems and can profoundly impact evolutionary adaption, population disease dynamics, genetic mapping, and precision medicine efforts. In this work, we develop a model for structured polygenic epistasis, called coordinated epistasis (CE), and prove that several recent theories of genetic architecture fall under the formal umbrella of CE. Unlike standard epistasis models that assume epistasis and main effects are independent, CE captures systematic correlations between epistasis and main effects that result from pathway-level

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IGLESIAS, M. T., V. S. PEÑARANDA, C. VIDAL, and A. VERSCHOREN. "HIGHER EPISTASIS IN GENETIC ALGORITHMS." Bulletin of the Australian Mathematical Society 77, no. 2 (2008): 225–43. http://dx.doi.org/10.1017/s0004972708000233.

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AbstractWe study thek-epistasis of a fitness function over a search space. This concept is a natural generalization of that of epistasis, previously considered by Davidor, Suys and Verschoren and Van Hove and Verschoren [Y. Davidor, in:Foundations of genetic algorithms, Vol. 1, (1991), pp. 23–25; D. Suys and A. Verschoren, ‘Proc Int. Conf. on Intelligent Technologies in Human-Related Sciences (ITHURS’96), Vol. II (1996), pp. 251–258; H. Van Hove and A. Verschoren,Comput. Artificial Intell.14(1994), 271–277], for example. We completely characterize fitness functions whosek-epistasis is minimal:

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Oliveira, Leticia F., Luiz F. F. Brito, Jay S. Johnson, and Renata Veroneze. "PSXII-3 Including Non-Additive Genetic Effects in Genomic Prediction and Estimation of Variance Components for Performance and Heat Stress Traits in Pigs." Journal of Animal Science 101, Supplement_3 (2023): 345–46. http://dx.doi.org/10.1093/jas/skad281.410.

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Abstract Non-additive genetic effects may have important roles in the phenotypic expression of performance and adaptation traits in livestock. Therefore, we aimed to evaluate the inclusion of non-additive genetic effects in genomic prediction models and variance component estimation of performance traits in a purebred pig population and heat tolerance indicators in a crossbred pig population. The first dataset consisted of 3,534 individuals with genotypes for 52,843 SNPs and five pre-adjusted phenotypes from a public database of a purebred pig line. Twelve models fitting or not dominance and/o

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Singh, A. K., A. K. Mall, and P. K. Singh. "Genetic study for epistatic gene effects for major yield contributing traits against drought in rice." Journal of Applied and Natural Science 11, no. 4 (2019): 755–61. http://dx.doi.org/10.31018/jans.v11i4.2173.

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The study subjected to estimate gene effects and inheritance of quantitative traits of rice with Generation Mean Analysis (GMA). Segregation analysis and estimation of genetic parameters under epistatic model indicated partial dominance and importance of additive effects in the inheritance of drought tolerance, respectively. In present study, absence of epistasis by scaling tests was recorded only for plant height in cross NDR-359 x P0 1564, grains per panicle in cross DSL- 63-8 x NDR- 359, test weight in cross Sarjoo-52 x P0 359, harvest-index in cross NDR-359 x P0 1564 and spikelets per pani

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Remold, Susanna. "Understanding specialism when the jack of all trades can be the master of all." Proceedings of the Royal Society B: Biological Sciences 279, no. 1749 (2012): 4861–69. http://dx.doi.org/10.1098/rspb.2012.1990.

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Specialism is widespread in nature, generating and maintaining diversity, but recent work has demonstrated that generalists can be equally fit as specialists in some shared environments. This no-cost generalism challenges the maxim that ‘the jack of all trades is the master of none’, and requires evolutionary genetic mechanisms explaining the existence of specialism and no-cost generalism, and the persistence of specialism in the face of selection for generalism. Examining three well-described mechanisms with respect to epistasis and pleiotropy indicates that sign (or antagonistic) pleiotropy

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Sreelakshmi, Ch, and P. Ramesh Babu. "Genetic analysis of yield and quality traits through generation mean analysis in rice." Oryza-An International Journal on Rice 56, no. 3 (2019): 256–62. http://dx.doi.org/10.35709/ory.2019.56.3.2.

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The present investigation in rice (Oryza sativa L.) was undertaken to study the magnitude of gene action in two cross combinations for eleven yield and twelve quality traits deploying generation mean analysis following six parameter model for parents (P1 and P2), F1, F2, BC1 and BC2 generations during three crop seasons. The results of the scaling tests revealed that the additive-dominance model was inadequate for all of the characters evaluated in both the crosses suggested the existence of epistasis in the inheritance of these characters. Mean values of both the crosses revealed significant

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Priest, Nicholas K., and Michael J. Wade. "Maternal-Zygotic Epistasis and the Evolution of Genetic Diseases." Journal of Biomedicine and Biotechnology 2010 (2010): 1–13. http://dx.doi.org/10.1155/2010/478732.

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Many birth defects and genetic diseases are expressed in individuals that do not carry the disease causing alleles. Genetic diseases observed in offspring can be caused by gene expression in mothers and by interactions between gene expression in mothers and offspring. It is not clear whether the underlying pattern of gene expression (maternal versus offspring) affects the incidence of genetic disease. Here we develop a 2-locus population genetic model with epistatic interactions between a maternal gene and a zygotic gene to address this question. We show that maternal effect genes that affect

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Nanda, Kalpataru, Nihar Ranjan Chakraborty, Debarchana Jena, Diptibala Rout, and Ramlakhan Verma. "Gene action of yield and its contributing traits in wide-compatible elite rice (Oryza sativa L.) restorer lines." Journal of Experimental Biology and Agricultural Sciences 12, no. 6 (2025): 850–59. https://doi.org/10.18006/2024.12(6).850.859.

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Profiling the genetic architecture of quantitative traits, such as yield and its contributing factors, is essential for successful breeding programs. Understanding the genetic components of variation is key to maximizing genetic gains with precision in crop improvement. This study evaluated the genetics of yield and its related traits through generation mean analysis in six generations (P1, P2, F1, F2, B1, and B2) of crosses involving elite restorer lines. Results from the scaling tests indicated that epistatic interactions were present for all traits examined, except for effective tillers per

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Bose, Aritra, Filippo Utro, Daniel E. Platt, and Laxmi Parida. "Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination." Algorithms 14, no. 5 (2021): 136. http://dx.doi.org/10.3390/a14050136.

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As studies move into deeper characterization of the impact of selection through non-neutral mutations in whole genome population genetics, modeling for selection becomes crucial. Moreover, epistasis has long been recognized as a significant component in understanding the evolution of complex genetic systems. We present a backward coalescent model, EpiSimRA, that accommodates multiple loci selection, with multi-way (k-way) epistasis for any arbitrary k. Starting from arbitrary extant populations with epistatic sites, we trace the Ancestral Recombination Graph (ARG), sampling relevant recombinat

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Rau, Christoph D., Natalia M. Gonzales, Joshua S. Bloom, et al. "Modeling epistasis in mice and yeast using the proportion of two or more distinct genetic backgrounds: Evidence for “polygenic epistasis”." PLOS Genetics 16, no. 10 (2020): e1009165. http://dx.doi.org/10.1371/journal.pgen.1009165.

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Background The majority of quantitative genetic models used to map complex traits assume that alleles have similar effects across all individuals. Significant evidence suggests, however, that epistatic interactions modulate the impact of many alleles. Nevertheless, identifying epistatic interactions remains computationally and statistically challenging. In this work, we address some of these challenges by developing a statistical test for polygenic epistasis that determines whether the effect of an allele is altered by the global genetic ancestry proportion from distinct progenitors. Results W

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Chen, Xia, Yexiong Lin, Qiang Qu, Bin Ning, Haowen Chen, and Xiong Li. "An epistasis and heterogeneity analysis method based on maximum correlation and maximum consistence criteria." Mathematical Biosciences and Engineering 18, no. 6 (2021): 7711–26. http://dx.doi.org/10.3934/mbe.2021382.

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<abstract> <p>Tumor heterogeneity significantly increases the difficulty of tumor treatment. The same drugs and treatment methods have different effects on different tumor subtypes. Therefore, tumor heterogeneity is one of the main sources of poor prognosis, recurrence and metastasis. At present, there have been some computational methods to study tumor heterogeneity from the level of genome, transcriptome, and histology, but these methods still have certain limitations. In this study, we proposed an epistasis and heterogeneity analysis method based on genomic single nucleotide pol

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Gallais, A. "Quantitative genetics of doubled haploid populations and application to the theory of line development." Genetics 124, no. 1 (1990): 199–206. http://dx.doi.org/10.1093/genetics/124.1.199.

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Abstract The line value of a genotype is defined as the expected value of all lines that can be derived from this genotype. Specific genetic effects are defined for this value: only additive and additive by additive epistatic effects are necessary. There is no dominance effect for such a value. A general expression for the covariances between related lines is given. From a design with several lines per haplodiploidized plant taken at random from a population it is possible to estimate the additive variance for line value and the variance of additive by additive epistasis for line value. Varian

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Barona, Marco Antonio Acevedo, José Manoel Colombari Filho, Vanderlei da Silva Santos, and Isaias Olívio Geraldi. "Epistatic effects on grain yield of soybean [Glycine max (L.) Merrill]." Crop Breeding and Applied Biotechnology 12, no. 4 (2012): 231–36. http://dx.doi.org/10.1590/s1984-70332012000400001.

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Studies addressing the estimation of genetic parameters in soybean have not emphasized the epistatic effects. The purpose of this study was to estimate the significance of these effects on soybean grain yield, based on the Modified Triple Test Cross design. Thirty-two inbred lines derived from a cross between two contrasting lines were used, which were crossed with two testers (L1 and L2). The experiments were carried out at two locations, in 10 x 10 triple lattice designs with 9 replications, containing 32 lines (Pi ), 64 crosses (32 Pi x L1 and 32 Pi x L2 ) and controls. The variation betwee

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Singh, S., I. S. Pawar, and I. P. Singh. "A study of genotype × environment interaction in three chickpea triple test crosses." Journal of Agricultural Science 107, no. 3 (1986): 549–54. http://dx.doi.org/10.1017/s0021859600069707.

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SUMMARYThe analysis of Perkins & Jinks (1971) was applied to 360 progeny families of three chickpea F2 triple test crosses, namely, F 378 × ICCC 1, P 1198–1 × ICCC 1 and US 613 × BG 203, to detect and measure the interaction of additive, dominance and epistatic gene effects with sowing dates. The families were grown in completely randomized blocks in three replications with two sowing dates, and data were recorded for plant height, number of branches per plant, number of days from sowing to flowering, number of days from sowing to maturity, number of pods per plant, number of grains per pl

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Miller, Anna K., Anlu Chen, Jacquelaine Bartlett, Li Wang, Scott M. Williams, and David A. Buchner. "A Novel Mapping Strategy Utilizing Mouse Chromosome Substitution Strains Identifies Multiple Epistatic Interactions That Regulate Complex Traits." G3: Genes|Genomes|Genetics 10, no. 12 (2020): 4553–63. http://dx.doi.org/10.1534/g3.120.401824.

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The genetic contribution of additive vs. non-additive (epistatic) effects in the regulation of complex traits is unclear. While genome-wide association studies typically ignore gene-gene interactions, in part because of the lack of statistical power for detecting them, mouse chromosome substitution strains (CSSs) represent an alternate approach for detecting epistasis given their limited allelic variation. Therefore, we utilized CSSs to identify and map both additive and epistatic loci that regulate a range of hematologic- and metabolism-related traits, as well as hepatic gene expression. Quan

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Aguirre, Lyndsey, Anat Hendelman, Samuel F. Hutton, David M. McCandlish, and Zachary B. Lippman. "Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size." Science 382, no. 6668 (2023): 315–20. http://dx.doi.org/10.1126/science.adi5222.

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Epistasis between genes is traditionally studied with mutations that eliminate protein activity, but most natural genetic variation is in cis-regulatory DNA and influences gene expression and function quantitatively. In this study, we used natural and engineered cis-regulatory alleles in a plant stem-cell circuit to systematically evaluate epistatic relationships controlling tomato fruit size. Combining a promoter allelic series with two other loci, we collected over 30,000 phenotypic data points from 46 genotypes to quantify how allele strength transforms epistasis. We revealed a saturating d

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Paixão, Tiago, and Nicholas H. Barton. "The effect of gene interactions on the long-term response to selection." Proceedings of the National Academy of Sciences 113, no. 16 (2016): 4422–27. http://dx.doi.org/10.1073/pnas.1518830113.

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The role of gene interactions in the evolutionary process has long been controversial. Although some argue that they are not of importance, because most variation is additive, others claim that their effect in the long term can be substantial. Here, we focus on the long-term effects of genetic interactions under directional selection assuming no mutation or dominance, and that epistasis is symmetrical overall. We ask by how much the mean of a complex trait can be increased by selection and analyze two extreme regimes, in which either drift or selection dominate the dynamics of allele frequenci

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Li, Zhikang, Shannon R. M. Pinson, William D. Park, Andrew H. Paterson, and James W. Stansel. "Epistasis for Three Grain Yield Components in Rice (Oryxa sativa L.)." Genetics 145, no. 2 (1997): 453–65. http://dx.doi.org/10.1093/genetics/145.2.453.

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The genetic basis for three grain yield components of rice, 1000 kernel weight (KW), grain number per panicle (GN), and grain weight per panicle (GWP), was investigated using restriction fragment length polymorphism markers and F4 progeny testing from a cross between rice subspecies japonica (cultivar Lemont from USA) and indica (cv. Teqing from China). Following identification of 19 QTL affecting these traits, we investigated the role of epistasis in genetic control of these phenotypes. Among 63 markers distributed throughout the genome that appeared to be involved in 79 highly significant (P

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Omholt, Stig W., Erik Plahte, Leiv Øyehaug, and Kefang Xiang. "Gene Regulatory Networks Generating the Phenomena of Additivity, Dominance and Epistasis." Genetics 155, no. 2 (2000): 969–80. http://dx.doi.org/10.1093/genetics/155.2.969.

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Abstract We show how the phenomena of genetic dominance, overdominance, additivity, and epistasis are generic features of simple diploid gene regulatory networks. These regulatory network models are together sufficiently complex to catch most of the suggested molecular mechanisms responsible for generating dominant mutations. These include reduced gene dosage, expression or protein activity (haploinsufficiency), increased gene dosage, ectopic or temporarily altered mRNA expression, increased or constitutive protein activity, and dominant negative effects. As classical genetics regards the phen

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Rochet, Sophie. "Epistasis in genetic algorithms revisited." Information Sciences 102, no. 1-4 (1997): 133–55. http://dx.doi.org/10.1016/s0020-0255(97)00017-0.

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Jiang, Yong, and Jochen C. Reif. "Efficient Algorithms for Calculating Epistatic Genomic Relationship Matrices." Genetics 216, no. 3 (2020): 651–69. http://dx.doi.org/10.1534/genetics.120.303459.

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The genomic relationship matrix plays a key role in the analysis of genetic diversity, genomic prediction, and genome-wide association studies. The epistatic genomic relationship matrix is a natural generalization of the classic genomic relationship matrix in the sense that it implicitly models the epistatic effects among all markers. Calculating the exact form of the epistatic relationship matrix requires high computational load, and is hence not feasible when the number of markers is large, or when high-degree of epistasis is in consideration. Currently, many studies use the Hadamard product

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Domingo, Júlia, Pablo Baeza-Centurion, and Ben Lehner. "The Causes and Consequences of Genetic Interactions (Epistasis)." Annual Review of Genomics and Human Genetics 20, no. 1 (2019): 433–60. http://dx.doi.org/10.1146/annurev-genom-083118-014857.

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The same mutation can have different effects in different individuals. One important reason for this is that the outcome of a mutation can depend on the genetic context in which it occurs. This dependency is known as epistasis. In recent years, there has been a concerted effort to quantify the extent of pairwise and higher-order genetic interactions between mutations through deep mutagenesis of proteins and RNAs. This research has revealed two major components of epistasis: nonspecific genetic interactions caused by nonlinearities in genotype-to-phenotype maps, and specific interactions betwee

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Marjanovic-Jeromela, Ana, Radovan Marinkovic, Milan Jockovic, et al. "Evaluation of genetic variance components for some quantitative traits in rapeseed (Brassica napus L.)." Genetika 46, no. 1 (2014): 179–85. http://dx.doi.org/10.2298/gensr1401179m.

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Three hybrid combinations obtained by crossing six winter rapeseed cultivars were analyzed for the impact of genes with additive and dominant effects and their interactions with inheritance of plant height and first lateral branch height. The linkage among the expected progeny means was checked using the scaling test method (Mather, 1949), while the estimates of genetic effects and mode of inheritance was made by the Generation Mean Analysis (Mather and Jinks, 1982). The additive dominant model did not prove adequate for plant height in all three crosses, and for first lateral branch height in

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Wagner, A., G. P. Wagner, and P. Similion. "Epistasis can facilitate the evolution of reproductive isolation by peak shifts: a two-locus two-allele model." Genetics 138, no. 2 (1994): 533–45. http://dx.doi.org/10.1093/genetics/138.2.533.

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Abstract The influence of epistasis on the evolution of reproductive isolation by peak shifts is studied in a two-locus two-allele model of a quantitative genetic character under stabilizing selection. Epistasis is introduced by a simple multiplicative term in the function that maps gene effects onto genotypic values. In the model with only additive effects on the trait, the probability of a peak shift and the amount of reproductive isolation are always inversely related, i.e., the higher the peak shift rate, the lower the amount of reproductive isolation caused by the peak shift. With epistat

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Angeles-Albores, David, Carmie Puckett Robinson, Brian A. Williams, Barbara J. Wold, and Paul W. Sternberg. "Reconstructing a metazoan genetic pathway with transcriptome-wide epistasis measurements." Proceedings of the National Academy of Sciences 115, no. 13 (2018): E2930—E2939. http://dx.doi.org/10.1073/pnas.1712387115.

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RNA-sequencing (RNA-seq) is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Also, quantifying and interpreting epistatic effects using expression profiles remains a challenge. We developed a single coefficient to quantify transcriptome-wide epistasis that reflects the underlying interactions and which can be interpreted intuitively. To demonstrate our approach, we sequenced four single and two double mutants of Caenorhabditis elegans. From thes

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Won, Susan, Alexander V. Michkov, Svetlana Krystofova, Amruta V. Garud та Katherine A. Borkovich. "Genetic and Physical Interactions between Gα Subunits and Components of the Gβγ Dimer of Heterotrimeric G Proteins in Neurospora crassa". Eukaryotic Cell 11, № 10 (2012): 1239–48. http://dx.doi.org/10.1128/ec.00151-12.

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ABSTRACTHeterotrimeric G proteins are critical regulators of growth and asexual and sexual development in the filamentous fungusNeurospora crassa. Three Gα subunits (GNA-1, GNA-2, and GNA-3), one Gβ subunit (GNB-1), and one Gγ subunit (GNG-1) have been functionally characterized, but genetic epistasis relationships between Gβ and Gα subunit genes have not been determined. Physical association between GNB-1 and FLAG-tagged GNG-1 has been previously demonstrated by coimmunoprecipitation, but knowledge of the Gα binding partners for the Gβγ dimer is currently lacking. In this study, the threeN. c

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Hasan, MT, and AC Deb. "Detection of Epistasis and Genetic Parameters of Some Quantitative Traits Through Triple Test Cross Analysis in Chickpea (Cicer Arietinum L.)." Bangladesh Journal of Botany 50, no. 2 (2021): 351–58. http://dx.doi.org/10.3329/bjb.v50i2.54092.

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Triple test cross analysis was carried out to detect the epistasis of thirteen yield and yield components in five chickpea (Cicer arietinum L.) crosses. Total epistatic effect was found to be non-significant for all the studied traits. Partitioning of total epistasis indicated the involvement of ‘i’ type (additive × additive) epistasis for DFF, PHFF, PWH, NPd/P, PdW/P, NS/P and SW/P in cross-1; NPBFF and NSBFF in cross-3 and for PHFF, DMF, PHMF and NSBMF in cross-5. The magnitude of additive component (D) was higher than that of the dominance component (H). Partial degree of dominance (√H/D) w

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