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Li W, Boer MP, van Rossum BJ, Zheng C, Joosen RVL, van Eeuwijk FA. statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations. Bioinformatics 2022; 38:5134-5136. [PMID: 36193999 PMCID: PMC9665859 DOI: 10.1093/bioinformatics/btac662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/23/2022] [Accepted: 10/03/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Multi-parent populations (MPPs) are popular for QTL mapping because they combine wide genetic diversity in parents with easy control of population structure, but a limited number of software tools for QTL mapping are specifically developed for general MPP designs. RESULTS We developed an R package called statgenMPP, adopting a unified identity-by-descent (IBD)-based mixed model approach for QTL analysis in MPPs. The package offers easy-to-use functionalities of IBD calculations, mixed model solutions and visualizations for QTL mapping in a wide range of MPP designs, including diallele, nested-association mapping populations, multi-parent advanced genetic inter-cross populations and other complicated MPPs with known crossing schemes. AVAILABILITY AND IMPLEMENTATION The R package statgenMPP is open-source and freely available on CRAN at https://CRAN.R-project.org/package=statgenMPP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wenhao Li
- Biometris, Wageningen University and Research Center, Wageningen, 6700 AC, The Netherlands
| | | | - Bart-Jan van Rossum
- Biometris, Wageningen University and Research Center, Wageningen, 6700 AC, The Netherlands
| | - Chaozhi Zheng
- Biometris, Wageningen University and Research Center, Wageningen, 6700 AC, The Netherlands
| | | | - Fred A van Eeuwijk
- Biometris, Wageningen University and Research Center, Wageningen, 6700 AC, The Netherlands
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Li W, Boer MP, Zheng C, Joosen RVL, van Eeuwijk FA. An IBD-based mixed model approach for QTL mapping in multiparental populations. Theor Appl Genet 2021; 134:3643-3660. [PMID: 34342658 PMCID: PMC8519866 DOI: 10.1007/s00122-021-03919-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/16/2021] [Indexed: 05/16/2023]
Abstract
The identity-by-descent (IBD)-based mixed model approach introduced in this study can detect quantitative trait loci (QTLs) referring to the parental origin and simultaneously account for multilevel relatedness of individuals within and across families. This unified approach is proved to be a powerful approach for all kinds of multiparental population (MPP) designs. Multiparental populations (MPPs) have become popular for quantitative trait loci (QTL) detection. Tools for QTL mapping in MPPs are mostly developed for specific MPPs and do not generalize well to other MPPs. We present an IBD-based mixed model approach for QTL mapping in all kinds of MPP designs, e.g., diallel, Nested Association Mapping (NAM), and Multiparental Advanced Generation Intercross (MAGIC) designs. The first step is to compute identity-by-descent (IBD) probabilities using a general Hidden Markov model framework, called reconstructing ancestry blocks bit by bit (RABBIT). Next, functions of IBD information are used as design matrices, or genetic predictors, in a mixed model approach to estimate variance components for multiallelic genetic effects associated with parents. Family-specific residual genetic effects are added, and a polygenic effect is structured by kinship relations between individuals. Case studies of simulated diallel, NAM, and MAGIC designs proved that the advanced IBD-based multi-QTL mixed model approach incorporating both kinship relations and family-specific residual variances (IBD.MQMkin_F) is robust across a variety of MPP designs and allele segregation patterns in comparison to a widely used benchmark association mapping method, and in most cases, outperformed or behaved at least as well as other tools developed for specific MPP designs in terms of mapping power and resolution. Successful analyses of real data cases confirmed the wide applicability of our IBD-based mixed model methodology.
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Affiliation(s)
- Wenhao Li
- Biometris, Wageningen University and Research Center, P.O Box 100, 6700 AC, Wageningen, The Netherlands
| | - Martin P Boer
- Biometris, Wageningen University and Research Center, P.O Box 100, 6700 AC, Wageningen, The Netherlands
| | - Chaozhi Zheng
- Biometris, Wageningen University and Research Center, P.O Box 100, 6700 AC, Wageningen, The Netherlands
| | - Ronny V L Joosen
- Rijk Zwaan Breeding B.V., P.O Box 40, 2678 ZG, De Lier, The Netherlands
| | - Fred A van Eeuwijk
- Biometris, Wageningen University and Research Center, P.O Box 100, 6700 AC, Wageningen, The Netherlands.
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Abstract
INTRODUCTION Seed germination is inherently related to seed metabolism, which changes throughout its maturation, desiccation and germination processes. The metabolite content of a seed and its ability to germinate are determined by underlying genetic architecture and environmental effects during development. OBJECTIVE This study aimed to assess an integrative approach to explore genetics modulating seed metabolism in different developmental stages and the link between seed metabolic- and germination traits. METHODS We have utilized gas chromatography-time-of-flight/mass spectrometry (GC-TOF/MS) metabolite profiling to characterize tomato seeds during dry and imbibed stages. We describe, for the first time in tomato, the use of a so-called generalized genetical genomics (GGG) model to study the interaction between genetics, environment and seed metabolism using 100 tomato recombinant inbred lines (RILs) derived from a cross between Solanum lycopersicum and Solanum pimpinellifolium. RESULTS QTLs were found for over two-thirds of the metabolites within several QTL hotspots. The transition from dry to 6 h imbibed seeds was associated with programmed metabolic switches. Significant correlations varied among individual metabolites and the obtained clusters were significantly enriched for metabolites involved in specific biochemical pathways. CONCLUSIONS Extensive genetic variation in metabolite abundance was uncovered. Numerous identified genetic regions that coordinate groups of metabolites were detected and these will contain plausible candidate genes. The combined analysis of germination phenotypes and metabolite profiles provides a strong indication for the hypothesis that metabolic composition is related to germination phenotypes and thus to seed performance.
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Affiliation(s)
- Rashid H. Kazmi
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Leo A. J. Willems
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ronny V. L. Joosen
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Noorullah Khan
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Wilco Ligterink
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Henk W. M. Hilhorst
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Huo H, Henry IM, Coppoolse ER, Verhoef-Post M, Schut JW, de Rooij H, Vogelaar A, Joosen RVL, Woudenberg L, Comai L, Bradford KJ. Rapid identification of lettuce seed germination mutants by bulked segregant analysis and whole genome sequencing. Plant J 2016; 88:345-360. [PMID: 27406937 DOI: 10.1111/tpj.13267] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 05/07/2023]
Abstract
Lettuce (Lactuca sativa) seeds exhibit thermoinhibition, or failure to complete germination when imbibed at warm temperatures. Chemical mutagenesis was employed to develop lettuce lines that exhibit germination thermotolerance. Two independent thermotolerant lettuce seed mutant lines, TG01 and TG10, were generated through ethyl methanesulfonate mutagenesis. Genetic and physiological analyses indicated that these two mutations were allelic and recessive. To identify the causal gene(s), we applied bulked segregant analysis by whole genome sequencing. For each mutant, bulked DNA samples of segregating thermotolerant (mutant) seeds were sequenced and analyzed for homozygous single-nucleotide polymorphisms. Two independent candidate mutations were identified at different physical positions in the zeaxanthin epoxidase gene (ABSCISIC ACID DEFICIENT 1/ZEAXANTHIN EPOXIDASE, or ABA1/ZEP) in TG01 and TG10. The mutation in TG01 caused an amino acid replacement, whereas the mutation in TG10 resulted in alternative mRNA splicing. Endogenous abscisic acid contents were reduced in both mutants, and expression of the ABA1 gene from wild-type lettuce under its own promoter fully complemented the TG01 mutant. Conventional genetic mapping confirmed that the causal mutations were located near the ZEP/ABA1 gene, but the bulked segregant whole genome sequencing approach more efficiently identified the specific gene responsible for the phenotype.
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Affiliation(s)
- Heqiang Huo
- Seed Biotechnology Center, Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California, Davis, CA, 95616, USA
| | | | | | - Johan W Schut
- Rijk Zwaan Breeding B.V., 2678, ZG De Lier, The Netherlands
| | - Han de Rooij
- Rijk Zwaan Breeding B.V., 2678, ZG De Lier, The Netherlands
| | - Aat Vogelaar
- Rijk Zwaan Breeding B.V., 2678, ZG De Lier, The Netherlands
| | | | - Leo Woudenberg
- Rijk Zwaan Breeding B.V., 2678, ZG De Lier, The Netherlands
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California, Davis, CA, 95616, USA
| | - Kent J Bradford
- Seed Biotechnology Center, Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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Zych K, Li Y, van der Velde JK, Joosen RVL, Ligterink W, Jansen RC, Arends D. Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains. BMC Bioinformatics 2015; 16:51. [PMID: 25886992 PMCID: PMC4339742 DOI: 10.1186/s12859-015-0475-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/26/2015] [Indexed: 11/11/2022] Open
Abstract
Background Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers. Results The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping. We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population. Conclusion The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R package for QTL studies. Pheno2Geno is freely available on CRAN under “GNU GPL v3”. The Pheno2Geno package as well as the tutorial can also be found at: http://pheno2geno.nl. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0475-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Konrad Zych
- University of Groningen, Groningen Bioinformatics Centre, Nijenborgh 7, Groningen, 9747, AG, The Netherlands. .,Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa Street 7, Krakow, 30-387, Poland.
| | - Yang Li
- University of Groningen, Groningen Bioinformatics Centre, Nijenborgh 7, Groningen, 9747, AG, The Netherlands. .,University of Groningen, University Medical Center Groningen, Department of Genetics, PO Box 30001, Groningen, 9700, RB, The Netherlands.
| | - Joeri K van der Velde
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, PO Box 30001, Groningen, 9700, RB, The Netherlands.
| | - Ronny V L Joosen
- Wageningen University, Wageningen Seed Lab, Droevendaalsesteeg 1, Wageningen, The Netherlands.
| | - Wilco Ligterink
- Wageningen University, Wageningen Seed Lab, Droevendaalsesteeg 1, Wageningen, The Netherlands.
| | - Ritsert C Jansen
- University of Groningen, Groningen Bioinformatics Centre, Nijenborgh 7, Groningen, 9747, AG, The Netherlands.
| | - Danny Arends
- University of Groningen, Groningen Bioinformatics Centre, Nijenborgh 7, Groningen, 9747, AG, The Netherlands.
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Joosen RVL, Ligterink W, Hilhorst HWM, Keurentjes JJB. Advances in genetical genomics of plants. Curr Genomics 2011; 10:540-9. [PMID: 20514216 PMCID: PMC2817885 DOI: 10.2174/138920209789503914] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2009] [Revised: 07/24/2009] [Accepted: 07/29/2009] [Indexed: 11/25/2022] Open
Abstract
Natural variation provides a valuable resource to study the genetic regulation of quantitative traits. In quantitative trait locus (QTL) analyses this variation, captured in segregating mapping populations, is used to identify the genomic regions affecting these traits. The identification of the causal genes underlying QTLs is a major challenge for which the detection of gene expression differences is of major importance. By combining genetics with large scale expression profiling (i.e. genetical genomics), resulting in expression QTLs (eQTLs), great progress can be made in connecting phenotypic variation to genotypic diversity. In this review we discuss examples from human, mouse, Drosophila, yeast and plant research to illustrate the advances in genetical genomics, with a focus on understanding the regulatory mechanisms underlying natural variation. With their tolerance to inbreeding, short generation time and ease to generate large families, plants are ideal subjects to test new concepts in genetics. The comprehensive resources which are available for Arabidopsis make it a favorite model plant but genetical genomics also found its way to important crop species like rice, barley and wheat. We discuss eQTL profiling with respect to cis and trans regulation and show how combined studies with other ‘omics’ technologies, such as metabolomics and proteomics may further augment current information on transcriptional, translational and metabolomic signaling pathways and enable reconstruction of detailed regulatory networks. The fast developments in the ‘omics’ area will offer great potential for genetical genomics to elucidate the genotype-phenotype relationships for both fundamental and applied research.
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Affiliation(s)
- R V L Joosen
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
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Joosen RVL, Kodde J, Willems LAJ, Ligterink W, van der Plas LHW, Hilhorst HWM. GERMINATOR: a software package for high-throughput scoring and curve fitting of Arabidopsis seed germination. Plant J 2010; 62:148-59. [PMID: 20042024 DOI: 10.1111/j.1365-313x.2009.04116.x] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Over the past few decades seed physiology research has contributed to many important scientific discoveries and has provided valuable tools for the production of high quality seeds. An important instrument for this type of research is the accurate quantification of germination; however gathering cumulative germination data is a very laborious task that is often prohibitive to the execution of large experiments. In this paper we present the germinator package: a simple, highly cost-efficient and flexible procedure for high-throughput automatic scoring and evaluation of germination that can be implemented without the use of complex robotics. The germinator package contains three modules: (i) design of experimental setup with various options to replicate and randomize samples; (ii) automatic scoring of germination based on the color contrast between the protruding radicle and seed coat on a single image; and (iii) curve fitting of cumulative germination data and the extraction, recap and visualization of the various germination parameters. The curve-fitting module enables analysis of general cumulative germination data and can be used for all plant species. We show that the automatic scoring system works for Arabidopsis thaliana and Brassica spp. seeds, but is likely to be applicable to other species, as well. In this paper we show the accuracy, reproducibility and flexibility of the germinator package. We have successfully applied it to evaluate natural variation for salt tolerance in a large population of recombinant inbred lines and were able to identify several quantitative trait loci for salt tolerance. Germinator is a low-cost package that allows the monitoring of several thousands of germination tests, several times a day by a single person.
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Affiliation(s)
- Ronny V L Joosen
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands.
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Joosen RVL, Lammers M, Balk PA, Brønnum P, Konings MCJM, Perks M, Stattin E, van Wordragen MF, van der Geest ALHM. Correlating gene expression to physiological parameters and environmental conditions during cold acclimation of Pinus sylvestris, identification of molecular markers using cDNA microarrays. Tree Physiol 2006; 26:1297-313. [PMID: 16815832 DOI: 10.1093/treephys/26.10.1297] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Scots pine (Pinus sylvestris L.) seedlings were grown under different conditions (three field locations, two seasons and two climate room regimes), and then analyzed for freezing tolerance of shoots and roots and for transcript abundance in apical buds based on a cDNA microarray containing about 1500 expressed sequence tags (ESTs) from buds of cold-treated Scots pine seedlings. In a climate room providing long daily photoperiods and high temperatures, seedlings did not develop freezing tolerance, whereas seedlings in a climate room set to provide declining temperatures and day lengths developed moderate freezing tolerance. Control seedlings grown outside under field conditions developed full freezing tolerance. Differences in physiological behavior of the different seedling groups, combined with molecular analysis, allowed identification of a large group of genes, expression of which changed during the development of freezing tolerance. Transcript abundance of several of these genes was highly correlated with freezing tolerance in seedlings differing in provenance, field location or age, making them excellent candidate marker genes for molecular tests for freezing tolerance.
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Affiliation(s)
- Ronny V L Joosen
- Plant Research International B.V., 6700 AA Wageningen, The Netherlands
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