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Rio S, Charcosset A, Moreau L, Mary-Huard T. Detecting directional and non-directional epistasis in bi-parental populations using genomic data. Genetics 2023; 224:iyad089. [PMID: 37170627 DOI: 10.1093/genetics/iyad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 01/16/2023] [Accepted: 05/01/2023] [Indexed: 05/13/2023] Open
Abstract
Epistasis, commonly defined as interaction effects between alleles of different loci, is an important genetic component of the variation of phenotypic traits in natural and breeding populations. In addition to its impact on variance, epistasis can also affect the expected performance of a population and is then referred to as directional epistasis. Before the advent of genomic data, the existence of epistasis (both directional and non-directional) was investigated based on complex and expensive mating schemes involving several generations evaluated for a trait of interest. In this study, we propose a methodology to detect the presence of epistasis based on simple inbred biparental populations, both genotyped and phenotyped, ideally along with their parents. Thanks to genomic data, parental proportions as well as shared parental proportions between inbred individuals can be estimated. They allow the evaluation of epistasis through a test of the expected performance for directional epistasis or the variance of genetic values. This methodology was applied to two large multiparental populations, i.e. the American maize and soybean nested association mapping populations, evaluated for different traits. Results showed significant epistasis, especially for the test of directional epistasis, e.g. the increase in anthesis to silking interval observed in most maize inbred progenies or the decrease in grain yield observed in several soybean inbred progenies. In general, the effects detected suggested that shuffling allelic associations of both elite parents had a detrimental effect on the performance of their progeny. This methodology is implemented in the EpiTest R-package and can be applied to any bi/multiparental inbred population evaluated for a trait of interest.
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Affiliation(s)
- Simon Rio
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, 91190 Gif-sur-Yvette, France
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 91120 Palaiseau, France
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Pundir S, Sharma R, Kumar D, Singh VK, Chaturvedi D, Kanwar RS, Röder MS, Börner A, Ganal MW, Gupta PK, Sharma S, Sharma S. QTL mapping for resistance against cereal cyst nematode (Heterodera avenae Woll.) in wheat (Triticum aestivum L.). Sci Rep 2022; 12:9586. [PMID: 35688926 PMCID: PMC9187758 DOI: 10.1038/s41598-022-12988-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/19/2022] [Indexed: 12/02/2022] Open
Abstract
The resistance to cereal cyst nematode (Heterodera avenae Woll.) in wheat (Triticum aestivum L.) was studied using 114 doubled haploid lines from a novel ITMI mapping population. These lines were screened for nematode infestation in a controlled environment for two years. QTL-mapping analyses were performed across two years (Y1 and Y2) as well as combining two years (CY) data. On the 114 lines that were screened, a total of 2,736 data points (genotype, batch or years, and replication combinations) were acquired. For QTL analysis, 12,093 markers (11,678 SNPs and 415 SSRs markers) were used, after filtering the genotypic data, for the QTL mapping. Composite interval mapping, using Haley-Knott regression (hk) method in R/QTL, was used for QTL analysis. In total, 19 QTLs were detected out of which 13 were novel and six were found to be colocalized or nearby to previously reported Cre genes, QTLs or MTAs for H. avenae or H. filipjevi. Nine QTLs were detected across all three groups (Y1, Y2 and CY) including a significant QTL "QCcn.ha-2D" on chromosome 2D that explains 23% of the variance. This QTL colocalized with a previously identified Cre3 locus. Novel QTL, QCcn.ha-2A, detected in the present study could be the possible unreported homeoloci to QCcn.ha-2D, QCcn.ha-2B.1 and QCcn.ha-2B.2. Six significant digenic epistatic interactions were also observed. In addition, 26 candidate genes were also identified including genes known for their involvement in PPNs (plant parasitic nematodes) resistance in different plant species. In-silico expression of putative candidate genes showed differential expression in roots during specific developmental stages. Results obtained in the present study are useful for wheat breeding to generate resistant genetic resources against H. avenae.
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Affiliation(s)
- Saksham Pundir
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
- Department of Botany, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
| | - Rajiv Sharma
- Scotland's Rural College (SRUC), Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Deepak Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
- Department of Botany, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
| | - Vikas Kumar Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
| | - Deepti Chaturvedi
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
| | - Rambir Singh Kanwar
- Department of Nematology, Chaudhary Charan Singh Haryana Agricultural University (CCSHAU), Hisar, Haryana, 125 004, India
| | - Marion S Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland, OT Gatersleben, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland, OT Gatersleben, Germany
| | - Martin W Ganal
- Trait Genetics GmbH, Am Schwabeplan 1b, 06466, Seeland, OT Gatersleben, Germany
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
- Murdoch's Centre for Crop & Food Innovation, Murdoch University, Murdoch, WA 6150, Perth, Australia
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India.
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Ahmadi N. Genetic Bases of Complex Traits: From Quantitative Trait Loci to Prediction. Methods Mol Biol 2022; 2467:1-44. [PMID: 35451771 DOI: 10.1007/978-1-0716-2205-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Conceived as a general introduction to the book, this chapter is a reminder of the core concepts of genetic mapping and molecular marker-based prediction. It provides an overview of the principles and the evolution of methods for mapping the variation of complex traits, and methods for QTL-based prediction of human disease risk and animal and plant breeding value. The principles of linkage-based and linkage disequilibrium-based QTL mapping methods are described in the context of the simplest, single-marker, methods. Methodological evolutions are analysed in relation with their ability to account for the complexity of the genotype-phenotype relations. Main characteristics of the genetic architecture of complex traits, drawn from QTL mapping works using large populations of unrelated individuals, are presented. Methods combining marker-QTL association data into polygenic risk score that captures part of an individual's susceptibility to complex diseases are reviewed. Principles of best linear mixed model-based prediction of breeding value in animal- and plant-breeding programs using phenotypic and pedigree data, are summarized and methods for moving from BLUP to marker-QTL BLUP are presented. Factors influencing the additional genetic progress achieved by using molecular data and rules for their optimization are discussed.
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Affiliation(s)
- Nourollah Ahmadi
- CIRAD, UMR AGAP Institut, Montpellier, France.
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France.
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Elattar MA, Karikari B, Li S, Song S, Cao Y, Aslam M, Hina A, Abou-Elwafa SF, Zhao T. Identification and Validation of Major QTLs, Epistatic Interactions, and Candidate Genes for Soybean Seed Shape and Weight Using Two Related RIL Populations. Front Genet 2021; 12:666440. [PMID: 34122518 PMCID: PMC8195344 DOI: 10.3389/fgene.2021.666440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the genetic mechanism underlying seed size, shape, and weight is essential for enhancing soybean cultivars. High-density genetic maps of two recombinant inbred line (RIL) populations, LM6 and ZM6, were evaluated across multiple environments to identify and validate M-QTLs as well as identify candidate genes behind major and stable quantitative trait loci (QTLs). A total of 239 and 43 M-QTLs were mapped by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM) approaches, from which 180 and 18, respectively, are novel QTLs. Twenty-two QTLs including four novel major QTLs were validated in the two RIL populations across multiple environments. Moreover, 18 QTLs showed significant AE effects, and 40 pairwise of the identified QTLs exhibited digenic epistatic effects. Thirty-four QTLs associated with seed flatness index (FI) were identified and reported here for the first time. Seven QTL clusters comprising several QTLs for seed size, shape, and weight on genomic regions of chromosomes 3, 4, 5, 7, 9, 17, and 19 were identified. Gene annotations, gene ontology (GO) enrichment, and RNA-seq analyses of the genomic regions of those seven QTL clusters identified 47 candidate genes for seed-related traits. These genes are highly expressed in seed-related tissues and nodules, which might be deemed as potential candidate genes regulating the seed size, weight, and shape traits in soybean. This study provides detailed information on the genetic basis of the studied traits and candidate genes that could be efficiently implemented by soybean breeders for fine mapping and gene cloning, and for marker-assisted selection (MAS) targeted at improving these traits individually or concurrently.
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Affiliation(s)
- Mahmoud A Elattar
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.,Agronomy Department, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Benjamin Karikari
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shuguang Li
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shiyu Song
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yongce Cao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Muhammed Aslam
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Aiman Hina
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | | | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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Hu G, Wang B, Gong T, Li R, Guo X, Liu W, Yang Z, Liu C, Li WX, Ning H. Mapping additive and epistatic QTLs for forage quality and yield in soybean [ Glycine max (L.) Merri.] in two environments. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1932593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Guofu Hu
- Department of Pratacultural Science, Institute of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Bo Wang
- Department of Pratacultural Science, Institute of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Ting Gong
- Department of Pratacultural Science, Institute of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Ran Li
- Department of Pratacultural Science, Institute of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Xin Guo
- Department of Pratacultural Science, Institute of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Wei Liu
- Department of Pratacultural Science, Institute of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Zouzhuan Yang
- Department of Pratacultural Science, Institute of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Chunyan Liu
- Heilongjiang Provincial Government Big Data Center, Harbin, PR China
| | - Wen-Xia Li
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Soybean Research Institute, Northeast Agricultural University, Harbin, PR China
| | - Hailong Ning
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Soybean Research Institute, Northeast Agricultural University, Harbin, PR China
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Oyiga BC, Palczak J, Wojciechowski T, Lynch JP, Naz AA, Léon J, Ballvora A. Genetic components of root architecture and anatomy adjustments to water-deficit stress in spring barley. PLANT, CELL & ENVIRONMENT 2020; 43:692-711. [PMID: 31734943 DOI: 10.1111/pce.13683] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 05/26/2023]
Abstract
Roots perform vital roles for adaptation and productivity under water-deficit stress, even though their specific functions are poorly understood. In this study, the genetic control of the nodal-root architectural and anatomical response to water deficit were investigated among diverse spring barley accessions. Water deficit induced substantial variations in the nodal root traits. The cortical, stele, and total root cross-sectional areas of the main-shoot nodal roots decreased under water deficit, but increased in the tiller nodal roots. Root xylem density and arrested nodal roots increased under water deficit, with the formation of root suberization/lignification and large cortical aerenchyma. Genome-wide association study implicated 11 QTL intervals in the architectural and anatomical nodal root response to water deficit. Among them, three and four QTL intervals had strong effects across seasons and on both root architectural and anatomical traits, respectively. Genome-wide epistasis analysis revealed 44 epistatically interacting SNP loci. Further analyses showed that these QTL intervals contain important candidate genes, including ZIFL2, MATE, and PPIB, whose functions are shown to be related to the root adaptive response to water deprivation in plants. These results give novel insight into the genetic architectures of barley nodal root response to soil water deficit stress in the fields, and thus offer useful resources for root-targeted marker-assisted selection.
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Affiliation(s)
| | | | - Tobias Wojciechowski
- Forschungszentrum Jülich, Institute for Bio- and Geosciences (Plant Sciences), Bonn, Germany
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State, State College, Pennsylvania
| | - Ali A Naz
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Jens Léon
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
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Santantonio N, Jannink JL, Sorrells M. Homeologous Epistasis in Wheat: The Search for an Immortal Hybrid. Genetics 2019; 211:1105-1122. [PMID: 30679260 PMCID: PMC6404247 DOI: 10.1534/genetics.118.301851] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/16/2019] [Indexed: 11/18/2022] Open
Abstract
Hybridization between related species results in the formation of an allopolyploid with multiple subgenomes. These subgenomes will each contain complete, yet evolutionarily divergent, sets of genes. Like a diploid hybrid, allopolyploids will have two versions, or homeoalleles, for every gene. Partial functional redundancy between homeologous genes should result in a deviation from additivity. These epistatic interactions between homeoalleles are analogous to dominance effects, but are fixed across subgenomes through self pollination. An allopolyploid can be viewed as an immortalized hybrid, with the opportunity to select and fix favorable homeoallelic interactions within inbred varieties. We present a subfunctionalization epistasis model to estimate the degree of functional redundancy between homeoallelic loci and a statistical framework to determine their importance within a population. We provide an example using the homeologous dwarfing genes of allohexaploid wheat, Rht-1, and search for genome-wide patterns indicative of homeoallelic subfunctionalization in a breeding population. Using the IWGSC RefSeq v1.0 sequence, 23,796 homeoallelic gene sets were identified and anchored to the nearest DNA marker to form 10,172 homeologous marker sets. Interaction predictors constructed from products of marker scores were used to fit the homeologous main and interaction effects, as well as estimate whole genome genetic values. Some traits displayed a pattern indicative of homeoallelic subfunctionalization, while other traits showed a less clear pattern or were not affected. Using genomic prediction accuracy to evaluate importance of marker interactions, we show that homeologous interactions explain a portion of the nonadditive genetic signal, but are less important than other epistatic interactions.
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Affiliation(s)
- Nicholas Santantonio
- Cornell University, Plant Breeding and Genetics Section, School of Integrated Plant Sciences, College of Agriculture and Life Sciences, Ithaca, New York 14853
| | - Jean-Luc Jannink
- Cornell University, Plant Breeding and Genetics Section, School of Integrated Plant Sciences, College of Agriculture and Life Sciences, Ithaca, New York 14853
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853
| | - Mark Sorrells
- Cornell University, Plant Breeding and Genetics Section, School of Integrated Plant Sciences, College of Agriculture and Life Sciences, Ithaca, New York 14853
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Karikari B, Li S, Bhat JA, Cao Y, Kong J, Yang J, Gai J, Zhao T. Genome-Wide Detection of Major and Epistatic Effect QTLs for Seed Protein and Oil Content in Soybean Under Multiple Environments Using High-Density Bin Map. Int J Mol Sci 2019; 20:E979. [PMID: 30813455 PMCID: PMC6412760 DOI: 10.3390/ijms20040979] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/01/2019] [Accepted: 02/19/2019] [Indexed: 01/25/2023] Open
Abstract
Seed protein and oil content are the two important traits determining the quality and value of soybean. Development of improved cultivars requires detailed understanding of the genetic basis underlying the trait of interest. However, it is prerequisite to have a high-density linkage map for precisely mapping genomic regions, and therefore the present study used high-density genetic map containing 2267 recombination bin markers distributed on 20 chromosomes and spanned 2453.79 cM with an average distance of 1.08 cM between markers using restriction-site-associated DNA sequencing (RAD-seq) approach. A recombinant inbred line (RIL) population of 104 lines derived from a cross between Linhefenqingdou and Meng 8206 cultivars was evaluated in six different environments to identify main- and epistatic-effect quantitative trait loci (QTLs)as well as their interaction with environments. A total of 44 main-effect QTLs for protein and oil content were found to be distributed on 17 chromosomes, and 15 novel QTL were identified for the first time. Out of these QTLs, four were major and stable QTLs, viz., qPro-7-1, qOil-8-3, qOil-10-2 and qOil-10-4, detected in at least two environments plus combined environment with R² values >10%. Within the physical intervals of these four QTLs, 111 candidate genes were screened for their direct or indirect involvement in seed protein and oil biosynthesis/metabolism processes based on gene ontology and annotation information. Based on RNA sequencing (RNA-seq) data analysis, 15 of the 111 genes were highly expressed during seed development stage and root nodules that might be considered as the potential candidate genes. Seven QTLs associated with protein and oil content exhibited significant additive and additive × environment interaction effects, and environment-independent QTLs revealed higher additive effects. Moreover, three digenic epistatic QTLs pairs were identified, and no main-effect QTLs showed epistasis. In conclusion, the use of a high-density map identified closely linked flanking markers, provided better understanding of genetic architecture and candidate gene information, and revealed the scope available for improvement of soybean quality through marker assisted selection (MAS).
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Affiliation(s)
- Benjamin Karikari
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shuguang Li
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an 223001, China.
| | - Javaid Akhter Bhat
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yongce Cao
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
- College of Life Science, Yan'an University, Yan'an 716000, China.
| | - Jiejie Kong
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiayin Yang
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an 223001, China.
| | - Junyi Gai
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tuanjie Zhao
- Key Laboratory of Biology and Genetics and Breeding for Soybean, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institution, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
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Teng W, Li W, Zhang Q, Wu D, Zhao X, Li H, Han Y, Li W. Identification of quantitative trait loci underlying seed protein content of soybean including main, epistatic, and QTL × environment effects in different regions of Northeast China. Genome 2017; 60:649-655. [PMID: 28445652 DOI: 10.1139/gen-2016-0189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The objective here was to identify QTL underlying soybean protein content (PC), and to evaluate the additive and epistatic effects of the QTLs. A mapping population, consisting of 129 recombinant inbred lines (RILs), was created by crossing 'Dongnong 46' and 'L-100'. Phenotypic data of the parents and RILs were collected for 4 years in three locations of Heilongjiang Province of China. A total of 213 SSR markers were used to construct a genetic linkage map. Eight QTLs, located on seven chromosomes (Chr), were identified to be associated with PC among the 10 tested environments. Of the seven QTLs, five QTLs, qPR-2 (Satt710, on Chr9), qPR-3 (Sat_122, on Chr12), qPR-5 (Satt543, on Chr17), qPR-7 (Satt163, on Chr18), and qPR-8 (Satt614, on Chr20), were detected in six, seven, seven, six, and seven environments, respectively, implying relatively stable QTLs. qPR-3 could explain 3.33%-11.26% of the phenotypic variation across eight tested environments. qPR-5 and qPR-8 explained 3.64%-10.1% and 11.86%-18.40% of the phenotypic variation, respectively, across seven tested environments. Eight QTLs associated with PC exhibited additive and (or) additive × environment interaction effects. The results showed that environment-independent QTLs often had higher additive effects. Moreover, five epistatic pairwise QTLs were identified in the 10 environments.
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Affiliation(s)
- Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
| | - Wen Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
| | - Qi Zhang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
| | - Depeng Wu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
| | - Haiyan Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China, 150030
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Fu D, Xiao M, Hayward A, Jiang G, Zhu L, Zhou Q, Li J, Zhang M. What is crop heterosis: new insights into an old topic. J Appl Genet 2014; 56:1-13. [PMID: 25027629 DOI: 10.1007/s13353-014-0231-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/28/2014] [Accepted: 07/01/2014] [Indexed: 01/09/2023]
Abstract
Heterosis (or hybrid vigor) refers to a natural phenomenon whereby hybrid offspring of genetically diverse individuals out-perform their parents in multiple traits including yield, adaptability and resistances to biotic and abiotic stressors. Innovations in technology and research continue to clarify the mechanisms underlying crop heterosis, however the intrinsic relationship between the biological basis of heterosis remain unclear. In this review, we aim to provide insight into the molecular genetic basis of heterosis by presenting recent advances in the 'omics' of heterosis and the role of non-coding regions, particularly in relation to energy-use efficiency. We propose that future research should focus on integrating the expanding datasets from different species and hybrid combinations, to mine key heterotic genes and unravel interactive 'omics' networks associated with heterosis. Improved understanding of heterosis and the biological basis for its manipulation in agriculture should help to streamline its use in enhancing crop productivity.
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Affiliation(s)
- Donghui Fu
- The Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China,
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11
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Hansen TF. Why epistasis is important for selection and adaptation. Evolution 2013; 67:3501-11. [PMID: 24299403 DOI: 10.1111/evo.12214] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/04/2013] [Indexed: 12/16/2022]
Abstract
Organisms are built from thousands of genes that interact in complex ways. Still, the mathematical theory of evolution is dominated by a gene-by-gene perspective in which genes are assumed to have the same effects regardless of genetic background. Gene interaction, or epistasis, plays a role in some theoretical developments such as the evolution of recombination, reproductive isolation, and canalization, but is strikingly missing from our standard accounts of phenotypic adaptation. This absence is most puzzling within the field of quantitative genetics, which, despite its polygenic perspective and elaborate statistical representation of epistasis, has not found a single important role for gene interaction in evolution. To the contrary, there is a widespread consensus that epistasis is evolutionary inert, and that all we need to know to predict evolutionary dynamics is the additive component of the genetic variance. This view may have roots in convenience, but also in theoretical results showing that the response to selection derived from epistatic variance components is not permanent and will decay when selection is relaxed. I show that these results are tied to a conceptual confusion, and are misleading as general statements about the significance of epistasis for the selection response and adaptation.
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Affiliation(s)
- Thomas F Hansen
- Department of Biology, University of Oslo, CEES, P.O. Box 1066, Blindern, N-0316 Oslo, Norway.
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12
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Ruan CJ, Teixeira da Silva JA. Metabolomics: creating new potentials for unraveling the mechanisms in response to salt and drought stress and for the biotechnological improvement of xero-halophytes. Crit Rev Biotechnol 2010; 31:153-69. [PMID: 21058928 DOI: 10.3109/07388551.2010.505908] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Breeders have long been interested in understanding the biological function and mechanism of xero-halophytes and their ability for growth in drought-stricken and salinized environments. However, the mechanisms in response to stress have been difficult to unravel because their defenses require regulatory changes to the activation of multiple genes and pathways. Metabolomics is becoming a key tool in comprehensively understanding the cellular response to abiotic stress and represents an important addition to the tools currently employed in genomics-assisted selection for plant improvement. In this review, we highlight the applications of plant metabolomics in characterizing metabolic responses to salt and drought stress, and identifying metabolic quantitative trait loci (QTLs). We also discuss the potential of metabolomics as a tool to unravel stress response mechanisms, and as a viable option for the biotechnological improvement of xero-halophytes when no other genetic information such as linkage maps and QTLs are available, by combining with germplasm-regression-combined marker-trait association identification.
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Affiliation(s)
- Cheng-Jiang Ruan
- Key Laboratory of Biotechnology & Bio-Resources Utilization, Dalian Nationalities University, Dalian City, Liaoning, China.
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13
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Ruan CJ, Xu XX, Shao HB, Jaleel CA. Germplasm-regression-combined (GRC) marker-trait association identification in plant breeding: a challenge for plant biotechnological breeding under soil water deficit conditions. Crit Rev Biotechnol 2010; 30:192-9. [DOI: 10.3109/07388551003649062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Wu X, Blake S, Sleper DA, Shannon JG, Cregan P, Nguyen HT. QTL, additive and epistatic effects for SCN resistance in PI 437654. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:1093-105. [PMID: 19184662 DOI: 10.1007/s00122-009-0965-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 01/06/2009] [Indexed: 05/18/2023]
Abstract
PI 437654 is a unique accession because of its resistance to nearly all HG types (races) of soybean cyst nematode (Heterodera glycines Ichinohe; SCN). Objectives of this study were to confirm and refine the locations and gene action associated with SCN resistance previously discovered in PI 437654, and to identify new QTLs that may have been missed because of low coverage with genetic markers used in previous studies. Using 205 F(7:9) RILs and 276 SSR and AFLP molecular markers covering 2,406.5 cM of 20 linkage groups (LGs), we confirmed and refined the locations of major SCN resistance QTLs on LG-A2, -B1, and -G previously identified in PI 437654 or other resistant sources. We found that these major QTLs have epistatic effects among them or with other loci for SCN resistance. We also detected some new QTLs with additive or epistatic effects for SCN resistance to different HG types (races) on all LGs except LGs-B2 and -D1b. The QTL on LG-G was associated with resistance to HG types 2.5.7, 1.2.5.7, 0, and 2.7 (races 1, 2, 3, and 5), and it contributed a large proportion of the additive effects. The QTL on LG-A2 was associated with resistance to HG types 2.5.7 and 0 (races 1 and 3). The QTL on LG-B1, associated with resistance to HG types 2.5.7, 0, 2.7 (races 1, 3, and 5), was the similar QTL found in PI 90763 and PI 404198B. In addition to QTL on LGs-A2, -B1 and -G, a novel additive QTL associated with SCN resistance to HG types 0, 2.7, and 1.3.5.6.7 (race 3, 5, and 14) was identified on LG-I flanked by Sat_299 and Sat_189. Several minor QTLs on LGs-C1, D1a, H, and K were also found to be associated with SCN resistance. Confirmation of the new resistance QTL is underway by evaluating another RIL population with a different genetic background.
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Affiliation(s)
- Xiaolei Wu
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211, USA.
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