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Cyplik A, Bocianowski J. A Comparison of Methods to Estimate Additive-by-Additive-by-Additive of QTL×QTL×QTL Interaction Effects by Monte Carlo Simulation Studies. Int J Mol Sci 2023; 24:10043. [PMID: 37373191 DOI: 10.3390/ijms241210043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/05/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
The goal of the breeding process is to obtain new genotypes with traits improved over the parental forms. Parameters related to the additive effect of genes as well as their interactions (such as epistasis of gene-by-gene interaction effect and additive-by-additive-by-additive of gene-by-gene-by-gene interaction effect) can influence decisions on the suitability of breeding material for this purpose. Understanding the genetic architecture of complex traits is a major challenge in the post-genomic era, especially for quantitative trait locus (QTL) effects, QTL-by-QTL interactions and QTL-by-QTL-by-QTL interactions. With regards to the comparing methods for estimating additive-by-additive-by-additive of QTL×QTL×QTL interaction effects by Monte Carlo simulation studies, there are no publications in the open literature. The parameter combinations assumed in the presented simulation studies represented 84 different experimental situations. The use of weighted regression may be the preferred method for estimating additive-by-additive-by-additive of QTL-QTL-QTL triples interaction effects, as it provides results closer to the true values of total additive-by-additive-by-additive interaction effects than using unweighted regression. This is also indicated by the obtained values of the determination coefficients of the proposed models.
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Affiliation(s)
- Adrian Cyplik
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
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Genetic Parameters for Selected Traits of Inbred Lines of Maize (Zea mays L.). APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12146961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This paper presents an estimation of the parameters connected with the additive (a) effect, additive by additive (aa) epistatic effect, and additive by additive by additive (aaa) interaction gene effect for nine quantitative traits of maize (Zea mays L.) inbred lines. To our knowledge, this is the first report about aaa interaction of maize inbred lines. An analysis was performed on 252 lines derived from Plant Breeding Smolice Ltd. (Smolice, Poland)—Plant Breeding and Acclimatization Institute-National Research Institute Group (151 lines) and Małopolska Plant Breeding Ltd. (Kobierzyce, Poland) (101 lines). The total additive effects were significant for all studied cases. Two-way and three-way significant interactions were found in most analyzed cases with a considerable impact on phenotype. Omitting the inclusion of higher-order interactions effect in quantitative genetics may result in a substantial underestimation of additive QTL effects. Expanding models with that information may also be helpful in future homozygous line crossing projects.
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Czyczyło-Mysza IM, Cyganek K, Dziurka K, Quarrie S, Skrzypek E, Marcińska I, Myśków B, Dziurka M, Warchoł M, Kapłoniak K, Bocianowski J. Genetic Parameters and QTLs for Total Phenolic Content and Yield of Wheat Mapping Population of CSDH Lines under Drought Stress. Int J Mol Sci 2019; 20:E6064. [PMID: 31805731 PMCID: PMC6929150 DOI: 10.3390/ijms20236064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 01/29/2023] Open
Abstract
A doubled haploid population of 94 lines from the Chinese Spring × SQ1 wheat cross (CSDH) was used to evaluate additive and epistatic gene action effects on total phenolic content, grain yield of the main stem, grain number per plant, thousand grain weight, and dry weight per plant at harvest based on phenotypic and genotypic observations of CSDH lines. These traits were evaluated under moderate and severe drought stress and compared with well-watered plants. Plants were grown in pots in an open-sided greenhouse. Genetic parameters, such as additive and epistatic effects, affecting total phenolic content, were estimated for eight year-by-drought combinations. Twenty-one markers showed a significant additive effect on total phenolic content in all eight year-by-drought combinations. These markers were located on chromosomes: 1A, 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4A, and 4D. A region on 4AL with a stable QTL controlling the phenolic content, confirmed by various statistical methods is particularly noteworthy. In all years and treatments, three markers significantly linked to QTLs have been identified for both phenols and yield. Thirteen markers were coincident with candidate genes. Our results indicated the importance of both additive and epistatic gene effects on total phenolic content in eight year-by-drought combinations.
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Affiliation(s)
- Ilona Mieczysława Czyczyło-Mysza
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Katarzyna Cyganek
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Kinga Dziurka
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Steve Quarrie
- Faculty of Biology, Belgrade University, Studentski trg 16, 11000 Belgrade, Serbia;
| | - Edyta Skrzypek
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Izabela Marcińska
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Beata Myśków
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin ul. Słowackiego 17, 71-434 Szczecin, Poland;
| | - Michał Dziurka
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Marzena Warchoł
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Kamila Kapłoniak
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland;
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Bocianowski J, Warzecha T, Nowosad K, Bathelt R. Genotype by environment interaction using AMMI model and estimation of additive and epistasis gene effects for 1000-kernel weight in spring barley (Hordeum vulgare L.). J Appl Genet 2019; 60:127-135. [PMID: 30877656 PMCID: PMC6483959 DOI: 10.1007/s13353-019-00490-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/20/2019] [Accepted: 03/05/2019] [Indexed: 12/21/2022]
Abstract
The objective of this study was to assess genotype by environment interaction for 1000-kernel weight in spring barley lines grown in South Poland by the additive main effects and multiplicative interaction model. The study comprised of 32 spring barley (Hordeum vulgare L.) genotypes (two parental genotypes-breeding line 1 N86 and doubled haploid (DH) line RK63/1, and 30 DH lines derived from F1 hybrids), evaluated at six locations in a randomized complete block design, with three replicates. 1000-kernel weight ranged from 24.35 g (for R63N/42 in 2011) to 61.46 g (for R63N/18 in 2008), with an average of 44.80 g. AMMI analyses revealed significant genotype and environmental effects as well as GE interaction with respect to 1000-kernel weight. In the analysis of variance, 16.86% of the total 1000-kernel weight variation was explained by environment, 32.18% by differences between genotypes, and 24.50% by GE interaction. The lines R63N/61, R63N/22, and R63N/1 are recommended for further inclusion in the breeding program because their stability and the highest averages of 1000-kernel weight. The total additive effect of all genes controlling the trait and the total epistasis effect of 1000-kernel weight were estimated. Additive gene action effects based on DH lines were always larger that this parameter estimated on the basis of parental lines. Estimates of additive gene action effects based on the all DH lines were significantly larger than zero in each year of study. Epistasis effects based on all DH lines were statistically significant in 2011 and 2013.
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Affiliation(s)
- Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637, Poznań, Poland.
| | - Tomasz Warzecha
- Department of Plant Breeding and Seed Science, University of Agriculture in Krakow, Łobzowska 24, 31-140, Kraków, Poland
| | - Kamila Nowosad
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Grunwaldzki 24A, 53-363, Wrocław, Poland
| | - Roman Bathelt
- Department of Plant Breeding and Seed Science, University of Agriculture in Krakow, Łobzowska 24, 31-140, Kraków, Poland
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Kumar J, Gupta DS, Gupta S, Dubey S, Gupta P, Kumar S. Quantitative trait loci from identification to exploitation for crop improvement. PLANT CELL REPORTS 2017; 36:1187-1213. [PMID: 28352970 DOI: 10.1007/s00299-017-2127-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/09/2017] [Indexed: 05/24/2023]
Abstract
Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sunanda Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sonali Dubey
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Priyanka Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Institutes, B.P. 6299, Rabat, Morocco
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Bocianowski J. Epistasis interaction of QTL effects as a genetic parameter influencing estimation of the genetic additive effect. Genet Mol Biol 2013; 36:93-100. [PMID: 23569413 PMCID: PMC3615531 DOI: 10.1590/s1415-47572013000100013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 12/12/2012] [Indexed: 11/21/2022] Open
Abstract
Epistasis, an additive-by-additive interaction between quantitative trait loci, has been defined as a deviation from the sum of independent effects of individual genes. Epistasis between QTLs assayed in populations segregating for an entire genome has been found at a frequency close to that expected by chance alone. Recently, epistatic effects have been considered by many researchers as important for complex traits. In order to understand the genetic control of complex traits, it is necessary to clarify additive-by-additive interactions among genes. Herein we compare estimates of a parameter connected with the additive gene action calculated on the basis of two models: a model excluding epistasis and a model with additive-by-additive interaction effects. In this paper two data sets were analysed: 1) 150 barley doubled haploid lines derived from the Steptoe × Morex cross, and 2) 145 DH lines of barley obtained from the Harrington × TR306 cross. The results showed that in cases when the effect of epistasis was different from zero, the coefficient of determination was larger for the model with epistasis than for the one excluding epistasis. These results indicate that epistatic interaction plays an important role in controlling the expression of complex traits.
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Affiliation(s)
- Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Poznan, Poland
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Bocianowski J. The use of weighted multiple linear regression to estimate QTL-by-QTL epistatic effects. Genet Mol Biol 2012; 35:802-9. [PMID: 23271942 PMCID: PMC3526089 DOI: 10.1590/s1415-47572012005000071] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 06/29/2012] [Indexed: 11/22/2022] Open
Abstract
Knowledge of the nature and magnitude of gene effects, as well as their contribution to the control of metric traits, is important in formulating efficient breeding programs for the improvement of plant genetics. Information concerning a genetic parameter such as the additive-by-additive epistatic effect can be useful in traditional breeding. This report describes the results obtained by applying weighted multiple linear regression to estimate the parameter connected with an additive-by-additive epistatic interaction. Three weight variants were used: (1) standard weights based on estimated variances, (2) different weights for minimal, maximal and other lines, and (3) different weights for extreme and other lines. The approach described here combines two methods of estimation, one based on phenotypic observations and the other using molecular marker data. The comparison was done using Monte Carlo simulations. The results show that the application of weighted regression to the marker data yielded estimates similar to those obtained by phenotypic methods.
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Affiliation(s)
- Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznañ University of Life Sciences, Wojska Polskiego, Poznañ, Poland
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