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Le QTN, Sugi N, Yamaguchi M, Hirayama T, Kobayashi M, Suzuki Y, Kusano M, Shiba H. Morphological and metabolomics profiling of intraspecific Arabidopsis hybrids in relation to biomass heterosis. Sci Rep 2023; 13:9529. [PMID: 37308530 DOI: 10.1038/s41598-023-36618-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/07/2023] [Indexed: 06/14/2023] Open
Abstract
Heterosis contributes greatly to the worldwide agricultural yield. However, the molecular mechanism underlying heterosis remains unclear. This study took advantage of Arabidopsis intraspecific hybrids to identify heterosis-related metabolites. Forty-six intraspecific hybrids were used to examine parental effects on seed area and germination time. The degree of heterosis was evaluated based on biomass: combinations showing high heterosis of F1 hybrids exhibited a biomass increase from 6.1 to 44% over the better parent value (BPV), whereas that of the low- and no-heterosis hybrids ranged from - 19.8 to 9.8% over the BPV. Metabolomics analyses of F1 hybrids with high heterosis and those with low one suggested that changes in TCA cycle intermediates are key factors that control growth. Notably, higher fumarate/malate ratios were observed in the high heterosis F1 hybrids, suggesting they provide metabolic support associated with the increased biomass. These hybrids may produce more energy-intensive biomass by speeding up the efficiency of TCA fluxes. However, the expression levels of TCA-process-related genes in F1 hybrids were not associated with the intensity of heterosis, suggesting that the post-transcriptional or post-translational regulation of these genes may affect the productivity of the intermediates in the TCA cycle.
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Affiliation(s)
- Quynh Thi Ngoc Le
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
- Thuyloi University, 175 Tay Son, Dong Da, Hanoi, Viet Nam
| | - Naoya Sugi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Masaaki Yamaguchi
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
| | - Touko Hirayama
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Suehiro 1-7-22, Tsurumi, Yokohama, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Japan
| | - Miyako Kusano
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
- RIKEN Center for Sustainable Resource Science, Suehiro 1-7-22, Tsurumi, Yokohama, Japan
| | - Hiroshi Shiba
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan.
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Ten-Nodai 1-1-1, Tsukuba, Ibaraki, Japan.
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Malinowska M, Ruud AK, Jensen J, Svane SF, Smith AG, Bellucci A, Lenk I, Nagy I, Fois M, Didion T, Thorup-Kristensen K, Jensen CS, Asp T. Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass. THE PLANT GENOME 2022; 15:e20253. [PMID: 35975565 DOI: 10.1002/tpg2.20253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
The growing demand for food and feed crops in the world because of growing population and more extreme weather events requires high-yielding and resilient crops. Many agriculturally important traits are polygenic, controlled by multiple regulatory layers, and with a strong interaction with the environment. In this study, 120 F2 families of perennial ryegrass (Lolium perenne L.) were grown across a water gradient in a semifield facility with subsoil irrigation. Genomic (single-nucleotide polymorphism [SNP]), transcriptomic (gene expression [GE]), and DNA methylomic (MET) data were integrated with feed quality trait data collected from control and drought sections in the semifield facility, providing a treatment effect. Deep root length (DRL) below 110 cm was assessed with convolutional neural network image analysis. Bayesian prediction models were used to partition phenotypic variance into its components and evaluated the proportion of phenotypic variance in all traits captured by different regulatory layers (SNP, GE, and MET). The spatial effects and effects of SNP, GE, MET, the interaction between GE and MET (GE × MET) and GE × treatment (GEControl and GEDrought ) interaction were investigated. Gene expression explained a substantial part of the genetic and spatial variance for all the investigated phenotypes, whereas MET explained residual variance not accounted for by SNPs or GE. For DRL, MET also contributed to explaining spatial variance. The study provides a statistically elegant analytical paradigm that integrates genomic, transcriptomic, and MET information to understand the regulatory mechanisms of polygenic effects for complex traits.
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Affiliation(s)
- Marta Malinowska
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Anja Karine Ruud
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Simon Fiil Svane
- Dep. of Plant and Environmental Sciences, Univ. of Copenhagen, Taastrup, Denmark
| | | | - Andrea Bellucci
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Ingo Lenk
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Mattia Fois
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Thomas Didion
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | | | | | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
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Zhang M, Liu YH, Wang Y, Sze SH, Scheuring CF, Qi X, Ekinci O, Pekar J, Murray SC, Zhang HB. Genome-wide identification of genes enabling accurate prediction of hybrid performance from parents across environments and populations for gene-based breeding in maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111424. [PMID: 35995113 DOI: 10.1016/j.plantsci.2022.111424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/07/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Accurate prediction of hybrid offspring complex trait phenotype from parents is paramount to enhanced plant breeding, animal breeding, and human medicine. Here we report genome-wide identification of genes enabling accurate prediction of hybrid offspring complex traits from parents using maize grain yield as the target trait. We identified 181 ZmF1GY genes enabling prediction of maize (Zea mays L.) F1 hybrid grain yield from parents and tested their utility and efficiency for predicting F1 hybrid grain yields from parents using their expressions, genic SNPs, and number of favorable alleles (NFAs), respectively. The ZmF1GY genes predicted hybrid grain yields from parents at an accuracy of 0.86, presented by correlation coefficient between predicted and observed phenotypes, within an environment, 0.74 across environments, and 0.64 across populations, outperforming genomic prediction by 27-406%, 23%, and 40%, respectively. Furthermore, we identified nine of the ZmF1GY genes containing SNPs or InDels in parents that increased or decreased hybrid grain yields by 14-46%. When the NFAs of these nine ZmF1GY genes were used for hybrid grain yield prediction from parents, they predicted hybrid grain yields at an accuracy of 0.79, outperforming genomic prediction by 21% that was based on up to tens of thousands of genome-wide SNPs. These results demonstrate the feasibility of developing a gene toolkit for a species enabling gene-based breeding across environments and populations that is much more powerful and efficient than current breeding, thereby helping secure the world's food production. The methodology is applicable to all crops, livestock, and humans.
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Affiliation(s)
- Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Yun-Hua Liu
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Yinglei Wang
- Department of Computer Science, Cornell University, Ithaca, NY 14853, USA.
| | - Sing-Hoi Sze
- Department of Computer Science and Engineering and Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
| | - Chantel F Scheuring
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Xiaoli Qi
- College of Life Science, Jiamusi University, Jiamusi, Heilongjiang 154007, China.
| | - Ozge Ekinci
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Jacob Pekar
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Seth C Murray
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Hong-Bin Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA.
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Hansen PB, Ruud AK, de los Campos G, Malinowska M, Nagy I, Svane SF, Thorup-Kristensen K, Jensen JD, Krusell L, Asp T. Integration of DNA Methylation and Transcriptome Data Improves Complex Trait Prediction in Hordeum vulgare. PLANTS 2022; 11:plants11172190. [PMID: 36079572 PMCID: PMC9459846 DOI: 10.3390/plants11172190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/30/2022]
Abstract
Whole-genome multi-omics profiles contain valuable information for the characterization and prediction of complex traits in plants. In this study, we evaluate multi-omics models to predict four complex traits in barley (Hordeum vulgare); grain yield, thousand kernel weight, protein content, and nitrogen uptake. Genomic, transcriptomic, and DNA methylation data were obtained from 75 spring barley lines tested in the RadiMax semi-field phenomics facility under control and water-scarce treatment. By integrating multi-omics data at genomic, transcriptomic, and DNA methylation regulatory levels, a higher proportion of phenotypic variance was explained (0.72–0.91) than with genomic models alone (0.55–0.86). The correlation between predictions and phenotypes varied from 0.17–0.28 for control plants and 0.23–0.37 for water-scarce plants, and the increase in accuracy was significant for nitrogen uptake and protein content compared to models using genomic information alone. Adding transcriptomic and DNA methylation information to the prediction models explained more of the phenotypic variance attributed to the environment in grain yield and nitrogen uptake. It furthermore explained more of the non-additive genetic effects for thousand kernel weight and protein content. Our results show the feasibility of multi-omics prediction for complex traits in barley.
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Affiliation(s)
- Pernille Bjarup Hansen
- Center for Quantitative Genetics and Genomics, Aarhus University, 4200 Slagelse, Denmark
- Correspondence: (P.B.H.); (T.A.); Tel.: +45-87158243 (T.A.)
| | - Anja Karine Ruud
- Center for Quantitative Genetics and Genomics, Aarhus University, 4200 Slagelse, Denmark
| | - Gustavo de los Campos
- Departments of Epidemiology & Biostatistics and Statistics & Probability, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Marta Malinowska
- Center for Quantitative Genetics and Genomics, Aarhus University, 4200 Slagelse, Denmark
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus University, 4200 Slagelse, Denmark
| | - Simon Fiil Svane
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Copenhagen University, 2630 Taastrup, Denmark
| | - Kristian Thorup-Kristensen
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Copenhagen University, 2630 Taastrup, Denmark
| | | | - Lene Krusell
- Sejet Plant Breeding, Nørremarksvej 67, 8700 Horsens, Denmark
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, 4200 Slagelse, Denmark
- Correspondence: (P.B.H.); (T.A.); Tel.: +45-87158243 (T.A.)
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Melandri G, Monteverde E, Riewe D, AbdElgawad H, McCouch SR, Bouwmeester H. Can biochemical traits bridge the gap between genomics and plant performance? A study in rice under drought. PLANT PHYSIOLOGY 2022; 189:1139-1152. [PMID: 35166848 PMCID: PMC9157150 DOI: 10.1093/plphys/kiac053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/17/2022] [Indexed: 05/13/2023]
Abstract
The possibility of introducing metabolic/biochemical phenotyping to complement genomics-based predictions in breeding pipelines has been considered for years. Here we examine to what extent and under what environmental conditions metabolic/biochemical traits can effectively contribute to understanding and predicting plant performance. In this study, multivariable statistical models based on flag leaf central metabolism and oxidative stress status were used to predict grain yield (GY) performance for 271 indica rice (Oryza sativa) accessions grown in the field under well-watered and reproductive stage drought conditions. The resulting models displayed significantly higher predictability than multivariable models based on genomic data for the prediction of GY under drought (Q2 = 0.54-0.56 versus 0.35) and for stress-induced GY loss (Q2 = 0.59-0.64 versus 0.03-0.06). Models based on the combined datasets showed predictabilities similar to metabolic/biochemical-based models alone. In contrast to genetic markers, models with enzyme activities and metabolite values also quantitatively integrated the effect of physiological differences such as plant height on GY. The models highlighted antioxidant enzymes of the ascorbate-glutathione cycle and a lipid oxidation stress marker as important predictors of rice GY stability under drought at the reproductive stage, and these stress-related variables were more predictive than leaf central metabolites. These findings provide evidence that metabolic/biochemical traits can integrate dynamic cellular and physiological responses to the environment and can help bridge the gap between the genome and the phenome of crops as predictors of GY performance under drought.
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Affiliation(s)
- Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
| | - Eliana Monteverde
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
- Departamento de Biología Vegetal, Facultad de Agronomía, Laboratorio de Evolución y Domesticación de las Plantas, Universidad de La República, Montevideo, Uruguay
| | - David Riewe
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Hamada AbdElgawad
- Laboratory for Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
- Department of Botany, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Susan R McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
- Plant Hormone Biology group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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Song C, Acuña T, Adler-Agmon M, Rachmilevitch S, Barak S, Fait A. Leveraging a graft collection to develop metabolome-based trait prediction for the selection of tomato rootstocks with enhanced salt tolerance. HORTICULTURE RESEARCH 2022; 9:uhac061. [PMID: 35531316 PMCID: PMC9071376 DOI: 10.1093/hr/uhac061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Grafting has been demonstrated to significantly enhance the salt tolerance of crops. However, breeding efforts to develop enhanced graft combinations are hindered by knowledge-gaps as to how rootstocks mediate scion-response to salt stress. We grafted the scion of cultivated M82 onto rootstocks of 254 tomato accessions and explored the morphological and metabolic responses of grafts under saline conditions (EC = 20 dS m-1) as compared to self-grafted M82 (SG-M82). Correlation analysis and Least Absolute Shrinkage and Selection Operator were performed to address the association between morphological diversification and metabolic perturbation. We demonstrate that grafting the same variety onto different rootstocks resulted in scion phenotypic heterogeneity and emphasized the productivity efficiency of M82 irrespective of the rootstock. Spectrophotometric analysis to test lipid oxidation showed largest variability of malondialdehyde (MDA) equivalents across the population, while the least responsive trait was the ratio of fruit fresh weight to total fresh weight (FFW/TFW). Generally, grafts showed greater values for the traits measured than SG-M82, except for branch number and wild race-originated rootstocks; the latter were associated with smaller scion growth parameters. Highly responsive and correlated metabolites were identified across the graft collection including malate, citrate, and aspartate, and their variance was partly related to rootstock origin. A group of six metabolites that consistently characterized exceptional graft response was observed, consisting of sorbose, galactose, sucrose, fructose, myo-inositol, and proline. The correlation analysis and predictive modelling, integrating phenotype- and leaf metabolite data, suggest a potential predictive relation between a set of leaf metabolites and yield-related traits.
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Affiliation(s)
- Chao Song
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Tania Acuña
- Albert Katz Department of Dryland Biotechnologies, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | | | - Shimon Rachmilevitch
- Albert Katz Department of Dryland Biotechnologies, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Simon Barak
- Albert Katz Department of Dryland Biotechnologies, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Aaron Fait
- Albert Katz Department of Dryland Biotechnologies, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
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Liu YH, Zhang M, Scheuring CF, Cilkiz M, Sze SH, Smith CW, Murray SC, Xu W, Zhang HB. Accurate prediction of complex traits for individuals and offspring from parents using a simple, rapid, and efficient method for gene-based breeding in cotton and maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 316:111153. [PMID: 35151437 DOI: 10.1016/j.plantsci.2021.111153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Accurate, simple, rapid, and inexpensive prediction of complex traits controlled by numerous genes is paramount to enhanced plant breeding, animal breeding, and human medicine. Here we report a novel method that enables accurate, simple, and rapid prediction of complex traits of individuals or offspring from parents based on the number of favorable alleles (NFAs) of the genes controlling the objective traits. The NFAs of 226 cotton fiber length (GFL) genes and nine maize hybrid grain yield related (ZmF1GY) genes were directly used to predict cotton fiber lengths of individual plants and maize grain yields of F1 hybrids from parents, respectively, using prediction model-based methods as controls. The NFAs of the 226 GFL genes predicted cotton fiber lengths at an accuracy of 0.85, as the model methods and outperforming genomic prediction by 82 % - 170 %. The NFAs of the nine ZmF1GY genes predicted grain yields of maize hybrids from parents at an accuracy of 0.80, outperforming genomic prediction by 67 %. Moreover, the prediction accuracies of these traits were consistent across years, environments, and eco-agricultural systems. Importantly, the accurate prediction of these traits directly using the NFAs of the genes allows breeding to be performed in greenhouse, phytotron, or off-season, without the need of the model training and validation steps essential and costly for model-based genomic or genic prediction. Therefore, this new method dramatically outperforms the current model-based genomic methods used for phenotype prediction and streamlines the process of breeding, thus promising to substantially enhance current plant and animal breeding.
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Affiliation(s)
- Yun-Hua Liu
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Chantel F Scheuring
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Mustafa Cilkiz
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Sing-Hoi Sze
- Department of Computer Science and Engineering and Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - C Wayne Smith
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Seth C Murray
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Wenwei Xu
- Texas A&M AgriLife Research, Lubbock, TX 79403, USA
| | - Hong-Bin Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA.
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Dan Z, Chen Y, Li H, Zeng Y, Xu W, Zhao W, He R, Huang W. The metabolomic landscape of rice heterosis highlights pathway biomarkers for predicting complex phenotypes. PLANT PHYSIOLOGY 2021; 187:1011-1025. [PMID: 34608951 PMCID: PMC8491067 DOI: 10.1093/plphys/kiab273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Understanding the molecular mechanisms underlying complex phenotypes requires systematic analyses of complicated metabolic networks and contributes to improvements in the breeding efficiency of staple cereal crops and diagnostic accuracy for human diseases. Here, we selected rice (Oryza sativa) heterosis as a complex phenotype and investigated the mechanisms of both vegetative and reproductive traits using an untargeted metabolomics strategy. Heterosis-associated analytes were identified, and the overlapping analytes were shown to underlie the association patterns for six agronomic traits. The heterosis-associated analytes of four yield components and plant height collectively contributed to yield heterosis, and the degree of contribution differed among the five traits. We performed dysregulated network analyses of the high- and low-better parent heterosis hybrids and found multiple types of metabolic pathways involved in heterosis. The metabolite levels of the significantly enriched pathways (especially those from amino acid and carbohydrate metabolism) were predictive of yield heterosis (area under the curve = 0.907 with 10 features), and the predictability of these pathway biomarkers was validated with hybrids across environments and populations. Our findings elucidate the metabolomic landscape of rice heterosis and highlight the potential application of pathway biomarkers in achieving accurate predictions of complex phenotypes.
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Affiliation(s)
- Zhiwu Dan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yunping Chen
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hui Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yafei Zeng
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wuwu Xu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weibo Zhao
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ruifeng He
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6414, USA
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Gong Y, Yang K, Lin Z, Fang S, Wu X, Zhu R, Peng Y. Remote estimation of leaf area index (LAI) with unmanned aerial vehicle (UAV) imaging for different rice cultivars throughout the entire growing season. PLANT METHODS 2021; 17:88. [PMID: 34376195 PMCID: PMC8353786 DOI: 10.1186/s13007-021-00789-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/01/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Rice is one of the most important grain crops worldwide. The accurate and dynamic monitoring of Leaf Area Index (LAI) provides important information to evaluate rice growth and production. METHODS This study explores a simple method to remotely estimate LAI with Unmanned Aerial Vehicle (UAV) imaging for a variety of rice cultivars throughout the entire growing season. Forty eight different rice cultivars were planted in the study site and field campaigns were conducted once a week. For each campaign, several widely used vegetation indices (VI) were calculated from canopy reflectance obtained by 12-band UAV images, canopy height was derived from UAV RGB images and LAI was destructively measured by plant sampling. RESULTS The results showed the correlation of VI and LAI in rice throughout the entire growing season was weak, and for all tested indices there existed significant hysteresis of VI vs. LAI relationship between rice pre-heading and post-heading stages. The model based on the product of VI and canopy height could reduce such hysteresis and estimate rice LAI of the whole season with estimation errors under 24%, not requiring algorithm re-parameterization for different phenology stages. CONCLUSIONS The progressing phenology can affect VI vs. LAI relationship in crops, especially for rice having quite different canopy spectra and structure after its panicle exsertion. Thus the models solely using VI to estimate rice LAI are phenology-specific and have high uncertainties for post-heading stages. The model developed in this study combines both remotely sensed canopy height and VI information, considerably improving rice LAI estimation at both pre- and post-heading stages. This method can be easily and efficiently implemented in UAV platforms for various rice cultivars during the entire growing season with no rice phenology and cultivar pre-knowledge, which has great potential for assisting rice breeding and field management studies at a large scale.
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Affiliation(s)
- Yan Gong
- School of Remote Sensing and Information Engineering, Wuhan University, Wuhan, China
- Lab for Remote Sensing of Crop Phenotyping, Wuhan University, Wuhan, China
| | - Kaili Yang
- School of Remote Sensing and Information Engineering, Wuhan University, Wuhan, China
| | - Zhiheng Lin
- School of Remote Sensing and Information Engineering, Wuhan University, Wuhan, China
| | - Shenghui Fang
- School of Remote Sensing and Information Engineering, Wuhan University, Wuhan, China
- Lab for Remote Sensing of Crop Phenotyping, Wuhan University, Wuhan, China
| | - Xianting Wu
- College of Life Sciences, Wuhan University, Wuhan, China
- Lab for Remote Sensing of Crop Phenotyping, Wuhan University, Wuhan, China
| | - Renshan Zhu
- College of Life Sciences, Wuhan University, Wuhan, China
- Lab for Remote Sensing of Crop Phenotyping, Wuhan University, Wuhan, China
| | - Yi Peng
- School of Remote Sensing and Information Engineering, Wuhan University, Wuhan, China.
- Lab for Remote Sensing of Crop Phenotyping, Wuhan University, Wuhan, China.
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10
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Knoch D, Werner CR, Meyer RC, Riewe D, Abbadi A, Lücke S, Snowdon RJ, Altmann T. Multi-omics-based prediction of hybrid performance in canola. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1147-1165. [PMID: 33523261 PMCID: PMC7973648 DOI: 10.1007/s00122-020-03759-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/19/2020] [Indexed: 05/05/2023]
Abstract
Complementing or replacing genetic markers with transcriptomic data and use of reproducing kernel Hilbert space regression based on Gaussian kernels increases hybrid prediction accuracies for complex agronomic traits in canola. In plant breeding, hybrids gained particular importance due to heterosis, the superior performance of offspring compared to their inbred parents. Since the development of new top performing hybrids requires labour-intensive and costly breeding programmes, including testing of large numbers of experimental hybrids, the prediction of hybrid performance is of utmost interest to plant breeders. In this study, we tested the effectiveness of hybrid prediction models in spring-type oilseed rape (Brassica napus L./canola) employing different omics profiles, individually and in combination. To this end, a population of 950 F1 hybrids was evaluated for seed yield and six other agronomically relevant traits in commercial field trials at several locations throughout Europe. A subset of these hybrids was also evaluated in a climatized glasshouse regarding early biomass production. For each of the 477 parental rapeseed lines, 13,201 single nucleotide polymorphisms (SNPs), 154 primary metabolites, and 19,479 transcripts were determined and used as predictive variables. Both, SNP markers and transcripts, effectively predict hybrid performance using (genomic) best linear unbiased prediction models (gBLUP). Compared to models using pure genetic markers, models incorporating transcriptome data resulted in significantly higher prediction accuracies for five out of seven agronomic traits, indicating that transcripts carry important information beyond genomic data. Notably, reproducing kernel Hilbert space regression based on Gaussian kernels significantly exceeded the predictive abilities of gBLUP models for six of the seven agronomic traits, demonstrating its potential for implementation in future canola breeding programmes.
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Affiliation(s)
- Dominic Knoch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben Germany
| | - Christian R. Werner
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG Scotland, UK
| | - Rhonda C. Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben Germany
| | - David Riewe
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben Germany
- Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 14195 Berlin, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth, 24363 Holtsee, Germany
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KG, Hohenlieth, 24363 Holtsee, Germany
| | - Sophie Lücke
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KG, Hohenlieth, 24363 Holtsee, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben Germany
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11
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Gemmer MR, Richter C, Schmutzer T, Raorane ML, Junker B, Pillen K, Maurer A. Genome-wide association study on metabolite accumulation in a wild barley NAM population reveals natural variation in sugar metabolism. PLoS One 2021; 16:e0246510. [PMID: 33592061 PMCID: PMC7886226 DOI: 10.1371/journal.pone.0246510] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/20/2021] [Indexed: 12/03/2022] Open
Abstract
Metabolites play a key role in plants as they are routing plant developmental processes and are involved in biotic and abiotic stress responses. Their analysis can offer important information on the underlying processes. Regarding plant breeding, metabolite concentrations can be used as biomarkers instead of or in addition to genetic markers to predict important phenotypic traits (metabolic prediction). In this study, we applied a genome-wide association study (GWAS) in a wild barley nested association mapping (NAM) population to identify metabolic quantitative trait loci (mQTL). A set of approximately 130 metabolites, measured at early and late sampling dates, was analysed. For four metabolites from the early and six metabolites from the late sampling date significant mQTL (grouped as 19 mQTL for the early and 25 mQTL for the late sampling date) were found. Interestingly, all of those metabolites could be classified as sugars. Sugars are known to be involved in signalling, plant growth and plant development. Sugar-related genes, encoding mainly sugar transporters, have been identified as candidate genes for most of the mQTL. Moreover, several of them co-localized with known flowering time genes like Ppd-H1, HvELF3, Vrn-H1, Vrn-H2 and Vrn-H3, hinting on the known role of sugars in flowering. Furthermore, numerous disease resistance-related genes were detected, pointing to the signalling function of sugars in plant resistance. An mQTL on chromosome 1H in the region of 13 Mbp to 20 Mbp stood out, that alone explained up to 65% of the phenotypic variation of a single metabolite. Analysis of family-specific effects within the diverse NAM population showed the available natural genetic variation regarding sugar metabolites due to different wild alleles. The study represents a step towards a better understanding of the genetic components of metabolite accumulation, especially sugars, thereby linking them to biological functions in barley.
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Affiliation(s)
- Mathias Ruben Gemmer
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Richter
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Thomas Schmutzer
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Manish L. Raorane
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Björn Junker
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
- * E-mail:
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12
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Xu Y, Zhao Y, Wang X, Ma Y, Li P, Yang Z, Zhang X, Xu C, Xu S. Incorporation of parental phenotypic data into multi-omic models improves prediction of yield-related traits in hybrid rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:261-272. [PMID: 32738177 PMCID: PMC7868986 DOI: 10.1111/pbi.13458] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 06/14/2020] [Accepted: 07/22/2020] [Indexed: 05/15/2023]
Abstract
Hybrid breeding has been shown to effectively increase rice productivity. However, identifying desirable hybrids out of numerous potential combinations is a daunting challenge. Genomic selection holds great promise for accelerating hybrid breeding by enabling early selection before phenotypes are measured. With the recent advances in multi-omic technologies, hybrid prediction based on transcriptomic and metabolomic data has received increasing attention. However, the current omic-based hybrid prediction has ignored parental phenotypic information, which is of fundamental importance in plant breeding. In this study, we integrated parental phenotypic information into various multi-omic prediction models applied in hybrid breeding of rice and compared the predictabilities of 15 combinations from four sets of predictors from the parents, that is genome, transcriptome, metabolome and phenome. The predictability for each combination was evaluated using the best linear unbiased prediction and a modified fast HAT method. We found significant interactions between predictors and traits in predictability, but joint prediction with various combinations of the predictors significantly improved predictability relative to prediction of any single source omic data for each trait investigated. Incorporation of parental phenotypic data into various omic predictors increased the predictability, averagely by 13.6%, 54.5%, 19.9% and 8.3%, for grain yield, number of tillers per plant, number of grains per panicle and 1000 grain weight, respectively. Among nine models of incorporating parental traits, the AD-All model was the most effective one. This novel strategy of incorporating parental phenotypic data into multi-omic prediction is expected to improve hybrid breeding progress, especially with the development of high-throughput phenotyping technologies.
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Affiliation(s)
- Yang Xu
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyKey Laboratory of Plant Functional Genomics of Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCo‐Innovation Center for Modern Production Technology of Grain CropsAgricultural College of Yangzhou UniversityYangzhouChina
| | - Yue Zhao
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyKey Laboratory of Plant Functional Genomics of Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCo‐Innovation Center for Modern Production Technology of Grain CropsAgricultural College of Yangzhou UniversityYangzhouChina
| | - Xin Wang
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyKey Laboratory of Plant Functional Genomics of Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCo‐Innovation Center for Modern Production Technology of Grain CropsAgricultural College of Yangzhou UniversityYangzhouChina
| | - Ying Ma
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyKey Laboratory of Plant Functional Genomics of Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCo‐Innovation Center for Modern Production Technology of Grain CropsAgricultural College of Yangzhou UniversityYangzhouChina
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyKey Laboratory of Plant Functional Genomics of Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCo‐Innovation Center for Modern Production Technology of Grain CropsAgricultural College of Yangzhou UniversityYangzhouChina
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyKey Laboratory of Plant Functional Genomics of Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCo‐Innovation Center for Modern Production Technology of Grain CropsAgricultural College of Yangzhou UniversityYangzhouChina
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT)MexicoDFMexico
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyKey Laboratory of Plant Functional Genomics of Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCo‐Innovation Center for Modern Production Technology of Grain CropsAgricultural College of Yangzhou UniversityYangzhouChina
| | - Shizhong Xu
- Department of Botany and Plant SciencesUniversity of CaliforniaRiversideCAUSA
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Martins MCM, Mafra V, Monte-Bello CC, Caldana C. The Contribution of Metabolomics to Systems Biology: Current Applications Bridging Genotype and Phenotype in Plant Science. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:91-105. [DOI: 10.1007/978-3-030-80352-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Nam KH, Kim DY, Pack IS, Kim CG. Compositional differences in hybrids between protoporphyrinogen IX oxidase (PPO)-inhibiting herbicide-resistant transgenic rice and weedy rice accessions. Food Chem 2020; 344:128584. [PMID: 33199119 DOI: 10.1016/j.foodchem.2020.128584] [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: 04/09/2020] [Revised: 10/14/2020] [Accepted: 11/04/2020] [Indexed: 10/23/2022]
Abstract
We characterized the metabolites in grains of transgenic protoporphyrinogen IX oxidase-inhibiting herbicide-resistant rice and weedy accessions using GC-MS and examined whether the chemical composition of their hybrids differed from that of the parents. We found that the metabolite profiles of transgenic rice and weedy rice were clearly separated. Although the metabolite profiles of F2 progeny were partially separated from their parents, zygosity did not affect the profiles. The F2 progeny had similar or intermediate levels of most major nutritional components compared with their parents. However, levels of galactopyranose, trehalose, xylofuranose, mannitol, and benzoic acid were higher in the F2 progeny. Some fatty acids and organic acids also showed prominent quantitative differences between the F2 progeny and the parents. Changes in the metabolite levels of transgenic crop-weed hybrids compared to their parents might influence not only the ecological consequences of the hybrids, but also the nutritional quality and food safety.
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Affiliation(s)
- Kyong-Hee Nam
- LMO Research Team, National Institute of Ecology, Seocheon 33657, Republic of Korea.
| | - Do Young Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience & Biotechnology, Cheongju 28116, Republic of Korea
| | - In Soon Pack
- Bio-Evaluation Center, Korea Research Institute of Bioscience & Biotechnology, Cheongju 28116, Republic of Korea
| | - Chang-Gi Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience & Biotechnology, Cheongju 28116, Republic of Korea.
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15
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Gemmer MR, Richter C, Jiang Y, Schmutzer T, Raorane ML, Junker B, Pillen K, Maurer A. Can metabolic prediction be an alternative to genomic prediction in barley? PLoS One 2020; 15:e0234052. [PMID: 32502173 PMCID: PMC7274421 DOI: 10.1371/journal.pone.0234052] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/17/2020] [Indexed: 11/18/2022] Open
Abstract
Like other crop species, barley, the fourth most important crop worldwide, suffers from the genetic bottleneck effect, where further improvements in performance through classical breeding methods become difficult. Therefore, indirect selection methods are of great interest. Here, genomic prediction (GP) based on 33,005 SNP markers and, alternatively, metabolic prediction (MP) based on 128 metabolites with sampling at two different time points in one year, were applied to predict multi-year agronomic traits in the nested association mapping (NAM) population HEB-25. We found prediction abilities of up to 0.93 for plant height with SNP markers and of up to 0.61 for flowering time with metabolites. Interestingly, prediction abilities in GP increased after reducing the number of incorporated SNP markers. The estimated effects of GP and MP were highly concordant, indicating MP as an interesting alternative to GP, being able to reflect a stable genotype-specific metabolite profile. In MP, sampling at an early developmental stage outperformed sampling at a later stage. The results confirm the value of GP for future breeding. With MP, an interesting alternative was also applied successfully. However, based on our results, usage of MP alone cannot be recommended in barley. Nevertheless, MP can assist in unravelling physiological pathways for the expression of agronomically important traits.
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Affiliation(s)
- Mathias Ruben Gemmer
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Richter
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Yong Jiang
- Department of Breeding Research, Quantitative Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Thomas Schmutzer
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Manish L. Raorane
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Björn Junker
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
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16
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Liu YH, Xu Y, Zhang M, Cui Y, Sze SH, Smith CW, Xu S, Zhang HB. Accurate Prediction of a Quantitative Trait Using the Genes Controlling the Trait for Gene-Based Breeding in Cotton. FRONTIERS IN PLANT SCIENCE 2020; 11:583277. [PMID: 33281846 PMCID: PMC7690289 DOI: 10.3389/fpls.2020.583277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/15/2020] [Indexed: 05/03/2023]
Abstract
Accurate phenotype prediction of quantitative traits is paramount to enhanced plant research and breeding. Here, we report the accurate prediction of cotton fiber length, a typical quantitative trait, using 474 cotton (Gossypium ssp.) fiber length (GFL) genes and nine prediction models. When the SNPs/InDels contained in 226 of the GFL genes or the expressions of all 474 GFL genes was used for fiber length prediction, a prediction accuracy of r = 0.83 was obtained, approaching the maximally possible prediction accuracy of a quantitative trait. This has improved by 116%, the prediction accuracies of the fiber length thus far achieved for genomic selection using genome-wide random DNA markers. Moreover, analysis of the GFL genes identified 125 of the GFL genes that are key to accurate prediction of fiber length, with which a prediction accuracy similar to that of all 474 GFL genes was obtained. The fiber lengths of the plants predicted with expressions of the 125 key GFL genes were significantly correlated with those predicted with the SNPs/InDels of the above 226 SNP/InDel-containing GFL genes (r = 0.892, P = 0.000). The prediction accuracies of fiber length using both genic datasets were highly consistent across environments or generations. Finally, we found that a training population consisting of 100-120 plants was sufficient to train a model for accurate prediction of a quantitative trait using the genes controlling the trait. Therefore, the genes controlling a quantitative trait are capable of accurately predicting its phenotype, thereby dramatically improving the ability, accuracy, and efficiency of phenotype prediction and promoting gene-based breeding in cotton and other species.
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Affiliation(s)
- Yun-Hua Liu
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Yang Xu
- Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Yanru Cui
- Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Sing-Hoi Sze
- Department of Computer Science and Engineering and Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - C. Wayne Smith
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Shizhong Xu
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Shizhong Xu,
| | - Hong-Bin Zhang
- Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- Hong-Bin Zhang,
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17
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Dan Z, Chen Y, Zhao W, Wang Q, Huang W. Metabolome-based prediction of yield heterosis contributes to the breeding of elite rice. Life Sci Alliance 2019; 3:3/1/e201900551. [PMID: 31836628 PMCID: PMC6918511 DOI: 10.26508/lsa.201900551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/24/2019] [Accepted: 11/26/2019] [Indexed: 01/15/2023] Open
Abstract
Metabolite profiles obtained from parental seedlings can predict yield heterosis of rice hybrids with correctly dissected population structure across different growth conditions. Improvement of the breeding efficiencies of heterotic crops adaptive to different conditions can mitigate the food shortage crisis due to overpopulation and climate change. To date, diverse molecular markers have been used to guide field phenotypic selection, whereas accurate predictions of complex heterotic traits are rarely reported. Here, we present a practical metabolome-based strategy for predicting yield heterosis in rice. The dissection of population structure based on untargeted metabolite profiles as the initial critical step in multivariate modeling performed better than the screening of predictive variables. Then the assessment of each predictive variable’s contribution to predictive models according to all latent factors was more precise than the conventional first one. Metabolites belonging to specific pathways were closely associated with yield heterosis, and the up-regulation of galactose metabolism promoted robust yield heterosis in hybrids under different growth conditions. Our study demonstrates that metabolome-based predictive models with correctly dissected population structure and screened predictive variables can facilitate accurate predictions of yield heterosis and have great potential for establishing molecular marker–based precision breeding programs.
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Affiliation(s)
- Zhiwu Dan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yunping Chen
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Weibo Zhao
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qiong Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, College of Life Sciences, Wuhan University, Wuhan, China
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18
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Dan Z, Chen Y, Xu Y, Huang J, Huang J, Hu J, Yao G, Zhu Y, Huang W. A metabolome-based core hybridisation strategy for the prediction of rice grain weight across environments. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:906-913. [PMID: 30321482 PMCID: PMC6587747 DOI: 10.1111/pbi.13024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/21/2018] [Accepted: 10/10/2018] [Indexed: 05/05/2023]
Abstract
Marker-based prediction holds great promise for improving current plant and animal breeding efficiencies. However, the predictabilities of complex traits are always severely affected by negative factors, including distant relatedness, environmental discrepancies, unknown population structures, and indeterminate numbers of predictive variables. In this study, we utilised two independent F1 hybrid populations in the years 2012 and 2015 to predict rice thousand grain weight (TGW) using parental untargeted metabolite profiles with a partial least squares regression method. A stable predictive model for TGW was built based on hybrids from the population in 2012 (r = 0.75) but failed to properly predict TGW for hybrids from the population in 2015 (r = 0.27). After integrating hybrids from both populations into the training set, the TGW of hybrids could be predicted but was largely dependent on population structures. Then, core hybrids from each population were determined by principal component analysis and the TGW of hybrids in both environments were successfully predicted (r > 0.60). Moreover, adjusting the population structures and numbers of predictive analytes increased TGW predictability for hybrids in 2015 (r = 0.72). Our study demonstrates that the TGW of F1 hybrids across environments can be accurately predicted based on parental untargeted metabolite profiles with a core hybridisation strategy in rice. Metabolic biomarkers identified from early developmental stage tissues, which are grown under experimental conditions, may represent a workable approach towards the robust prediction of major agronomic traits for climate-adaptive varieties.
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Affiliation(s)
- Zhiwu Dan
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Yunping Chen
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Yanghong Xu
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Junran Huang
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Jishuai Huang
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Jun Hu
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Guoxin Yao
- School of Life and Science TechnologyHubei Engineering UniversityXiaoganChina
| | - Yingguo Zhu
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Wenchao Huang
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
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19
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Westhues M, Heuer C, Thaller G, Fernando R, Melchinger AE. Efficient genetic value prediction using incomplete omics data. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1211-1222. [PMID: 30656353 DOI: 10.1007/s00122-018-03273-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/21/2018] [Indexed: 05/05/2023]
Abstract
Covering a subset of individuals with a quantitative predictor, while imputing records for all others using pedigree or genomic data, could improve the precision of predictions while controlling for costs. Predicting genetic values with high accuracy is pivotal for effective candidate selection in animal and plant breeding. Novel 'omics'-based predictors have been shown to improve upon established genome-based predictions of important complex traits but require laborious and expensive assays. As a consequence, there are various datasets with full genetic marker coverage of all studied individuals but incomplete coverage with other 'omics' data. In animal breeding, single-step prediction was introduced to efficiently combine pedigree information, collected on a large number of animals, with genomic information, collected on a smaller subset of animals, for breeding value estimation without bias. Using two maize datasets of inbred lines and hybrids, we show that the single-step framework facilitates imputing transcriptomic data, boosting forecasts when their predictive ability exceeds that of pedigree or genomic data. Our results suggest that covering only a subset of inbred lines with 'omics' predictors and imputing all others using pedigree or genomic data could enable breeders to improve trait predictions while keeping costs under control. Employing 'omics' predictors could particularly improve candidate selection in hybrid breeding because the success of forecasts is a strongly convex function of predictive ability.
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Affiliation(s)
- Matthias Westhues
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Claas Heuer
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany
- Inguran, LLC dba STGenetics, 22575 SH6 South, Navasota, TX, 77868, USA
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany
| | - Rohan Fernando
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Albrecht E Melchinger
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany.
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Iwanycki Ahlstrand N, Havskov Reghev N, Markussen B, Bruun Hansen HC, Eiriksson FF, Thorsteinsdóttir M, Rønsted N, Barnes CJ. Untargeted metabolic profiling reveals geography as the strongest predictor of metabolic phenotypes of a cosmopolitan weed. Ecol Evol 2018; 8:6812-6826. [PMID: 30038777 PMCID: PMC6053570 DOI: 10.1002/ece3.4195] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/30/2018] [Accepted: 04/22/2018] [Indexed: 12/27/2022] Open
Abstract
Plants produce a multitude of metabolites that contribute to their fitness and survival and play a role in local adaptation to environmental conditions. The effects of environmental variation are particularly well studied within the genus Plantago; however, previous studies have largely focused on targeting specific metabolites. Studies exploring metabolome-wide changes are lacking, and the effects of natural environmental variation and herbivory on the metabolomes of plants growing in situ remain unknown. An untargeted metabolomic approach using ultra-high-performance liquid chromatography-mass spectrometry, coupled with variation partitioning, general linear mixed modeling, and network analysis was used to detect differences in metabolic phenotypes of Plantago major in fifteen natural populations across Denmark. Geographic region, distance, habitat type, phenological stage, soil parameters, light levels, and leaf area were investigated for their relative contributions to explaining differences in foliar metabolomes. Herbivory effects were further investigated by comparing metabolomes from damaged and undamaged leaves from each plant. Geographic region explained the greatest number of significant metabolic differences. Soil pH had the second largest effect, followed by habitat and leaf area, while phenological stage had no effect. No evidence of the induction of metabolic features was found between leaves damaged by herbivores compared to undamaged leaves on the same plant. Differences in metabolic phenotypes explained by geographic factors are attributed to genotypic variation and/or unmeasured environmental factors that differ at the regional level in Denmark. A small number of specialized features in the metabolome may be involved in facilitating the success of a widespread species such as Plantago major into such wide range of environmental conditions, although overall resilience in the metabolome was found in response to environmental parameters tested. Untargeted metabolomic approaches have great potential to improve our understanding of how specialized plant metabolites respond to environmental change and assist in adaptation to local conditions.
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Affiliation(s)
| | | | - Bo Markussen
- Department of Mathematical SciencesUniversity of CopenhagenCopenhagenDenmark
| | | | | | | | - Nina Rønsted
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
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21
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Ferreira DA, Martins MCM, Cheavegatti-Gianotto A, Carneiro MS, Amadeu RR, Aricetti JA, Wolf LD, Hoffmann HP, de Abreu LGF, Caldana C. Metabolite Profiles of Sugarcane Culm Reveal the Relationship Among Metabolism and Axillary Bud Outgrowth in Genetically Related Sugarcane Commercial Cultivars. FRONTIERS IN PLANT SCIENCE 2018; 9:857. [PMID: 29988592 PMCID: PMC6027322 DOI: 10.3389/fpls.2018.00857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 06/01/2018] [Indexed: 05/04/2023]
Abstract
Metabolic composition is known to exert influence on several important agronomic traits, and metabolomics, which represents the chemical composition in a cell, has long been recognized as a powerful tool for bridging phenotype-genotype interactions. In this work, sixteen truly representative sugarcane Brazilian varieties were selected to explore the metabolic networks in buds and culms, the tissues involved in the vegetative propagation of this species. Due to the fact that bud sprouting is a key trait determining crop establishment in the field, the sprouting potential among the genotypes was evaluated. The use of partial least square discriminant analysis indicated only mild differences on bud outgrowth potential under controlled environmental conditions. However, primary metabolite profiling provided information on the variability of metabolic features even under a narrow genetic background, typical for modern sugarcane cultivars. Metabolite-metabolite correlations within and between tissues revealed more complex patterns for culms in relation to buds, and enabled the recognition of key metabolites (e.g., sucrose, putrescine, glutamate, serine, and myo-inositol) affecting sprouting ability. Finally, those results were associated with the genetic background of each cultivar, showing that metabolites can be potentially used as indicators for the genetic background.
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Affiliation(s)
- Danilo A. Ferreira
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
- Genetics and Molecular Biology Graduate Program, University of Campinas, Campinas, Brazil
| | - Marina C. M. Martins
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Adriana Cheavegatti-Gianotto
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Monalisa S. Carneiro
- Department of Biotechnology and Plant and Animal Production, Center for Agricultural Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Rodrigo R. Amadeu
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Juliana A. Aricetti
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Lucia D. Wolf
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Hermann P. Hoffmann
- Department of Biotechnology and Plant and Animal Production, Center for Agricultural Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Luis G. F. de Abreu
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
- Max-Planck Partner Group, Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
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22
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de Abreu e Lima F, Willmitzer L, Nikoloski Z. Classification-driven framework to predict maize hybrid field performance from metabolic profiles of young parental roots. PLoS One 2018; 13:e0196038. [PMID: 29698533 PMCID: PMC5919381 DOI: 10.1371/journal.pone.0196038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/05/2018] [Indexed: 01/10/2023] Open
Abstract
Maize (Zea mays L.) is a staple food whose production relies on seed stocks that largely comprise hybrid varieties. Therefore, knowledge about the molecular determinants of hybrid performance (HP) in the field can be used to devise better performing hybrids to address the demands for sustainable increase in yield. Here, we propose and test a classification-driven framework that uses metabolic profiles from in vitro grown young roots of parental lines from the Dent × Flint maize heterotic pattern to predict field HP. We identify parental analytes that best predict the metabolic inheritance patterns in 328 hybrids. We then demonstrate that these analytes are also predictive of field HP (0.64 ≥ r ≥ 0.79) and discriminate hybrids of good performance (accuracy of 87.50%). Therefore, our approach provides a cost-effective solution for hybrid selection programs.
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Affiliation(s)
| | - Lothar Willmitzer
- Max-Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Zoran Nikoloski
- Max-Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- * E-mail:
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23
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Sprenger H, Erban A, Seddig S, Rudack K, Thalhammer A, Le MQ, Walther D, Zuther E, Köhl KI, Kopka J, Hincha DK. Metabolite and transcript markers for the prediction of potato drought tolerance. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:939-950. [PMID: 28929574 PMCID: PMC5866952 DOI: 10.1111/pbi.12840] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 09/07/2017] [Accepted: 09/12/2017] [Indexed: 05/13/2023]
Abstract
Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. Current potato varieties are highly susceptible to drought stress. In view of global climate change, selection of cultivars with improved drought tolerance and high yield potential is of paramount importance. Drought tolerance breeding of potato is currently based on direct selection according to yield and phenotypic traits and requires multiple trials under drought conditions. Marker-assisted selection (MAS) is cheaper, faster and reduces classification errors caused by noncontrolled environmental effects. We analysed 31 potato cultivars grown under optimal and reduced water supply in six independent field trials. Drought tolerance was determined as tuber starch yield. Leaf samples from young plants were screened for preselected transcript and nontargeted metabolite abundance using qRT-PCR and GC-MS profiling, respectively. Transcript marker candidates were selected from a published RNA-Seq data set. A Random Forest machine learning approach extracted metabolite and transcript markers for drought tolerance prediction with low error rates of 6% and 9%, respectively. Moreover, by combining transcript and metabolite markers, the prediction error was reduced to 4.3%. Feature selection from Random Forest models allowed model minimization, yielding a minimal combination of only 20 metabolite and transcript markers that were successfully tested for their reproducibility in 16 independent agronomic field trials. We demonstrate that a minimum combination of transcript and metabolite markers sampled at early cultivation stages predicts potato yield stability under drought largely independent of seasonal and regional agronomic conditions.
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Affiliation(s)
- Heike Sprenger
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
- Present address:
VIB‐UGent Center for Plant Systems BiologyTechnologiepark 9279052GhentBelgium
| | - Alexander Erban
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Sylvia Seddig
- Federal Research Centre for Cultivated PlantsJulius‐Kühn InstitutInstitute for Resistance Research and Stress ToleranceSanitzGermany
| | - Katharina Rudack
- Federal Research Centre for Cultivated PlantsJulius‐Kühn InstitutInstitute for Resistance Research and Stress ToleranceSanitzGermany
| | - Anja Thalhammer
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
- Present address:
University of PotsdamKarl‐Liebknecht‐Straße 24‐2514476PotsdamGermany
| | - Mai Q. Le
- VNU‐University of SciencesThanh XuanHanoiVietnam
| | - Dirk Walther
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Ellen Zuther
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Karin I. Köhl
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Joachim Kopka
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Dirk K. Hincha
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
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24
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de Abreu E Lima F, Leifels L, Nikoloski Z. Regression-Based Modeling of Complex Plant Traits Based on Metabolomics Data. Methods Mol Biol 2018; 1778:321-327. [PMID: 29761449 DOI: 10.1007/978-1-4939-7819-9_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bridging metabolomics with plant phenotypic responses is challenging. Multivariate analyses account for the existing dependencies among metabolites, and regression models in particular capture such dependencies in search for association with a given trait. However, special care should be undertaken with metabolomics data. Here we propose a modeling workflow that considers all caveats imposed by such large data sets.
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Affiliation(s)
| | - Lydia Leifels
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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25
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Westhues M, Schrag TA, Heuer C, Thaller G, Utz HF, Schipprack W, Thiemann A, Seifert F, Ehret A, Schlereth A, Stitt M, Nikoloski Z, Willmitzer L, Schön CC, Scholten S, Melchinger AE. Omics-based hybrid prediction in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017. [PMID: 28647896 DOI: 10.1007/s00122-017-2934-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Complementing genomic data with other "omics" predictors can increase the probability of success for predicting the best hybrid combinations using complex agronomic traits. Accurate prediction of traits with complex genetic architecture is crucial for selecting superior candidates in animal and plant breeding and for guiding decisions in personalized medicine. Whole-genome prediction has revolutionized these areas but has inherent limitations in incorporating intricate epistatic interactions. Downstream "omics" data are expected to integrate interactions within and between different biological strata and provide the opportunity to improve trait prediction. Yet, predicting traits from parents to progeny has not been addressed by a combination of "omics" data. Here, we evaluate several "omics" predictors-genomic, transcriptomic and metabolic data-measured on parent lines at early developmental stages and demonstrate that the integration of transcriptomic with genomic data leads to higher success rates in the correct prediction of untested hybrid combinations in maize. Despite the high predictive ability of genomic data, transcriptomic data alone outperformed them and other predictors for the most complex heterotic trait, dry matter yield. An eQTL analysis revealed that transcriptomic data integrate genomic information from both, adjacent and distant sites relative to the expressed genes. Together, these findings suggest that downstream predictors capture physiological epistasis that is transmitted from parents to their hybrid offspring. We conclude that the use of downstream "omics" data in prediction can exploit important information beyond structural genomics for leveraging the efficiency of hybrid breeding.
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Affiliation(s)
- Matthias Westhues
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Tobias A Schrag
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Claas Heuer
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany
- Inguran LLC dba STGenetics, 22575 SH6 South, Navasota, TX, 77868, USA
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany
| | - H Friedrich Utz
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Wolfgang Schipprack
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Alexander Thiemann
- Biocenter Klein Flottbek, Developmental Biology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Felix Seifert
- Biocenter Klein Flottbek, Developmental Biology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Anita Ehret
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany
| | - Armin Schlereth
- Max-Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Mark Stitt
- Max-Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Zoran Nikoloski
- Max-Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Lothar Willmitzer
- Max-Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Chris C Schön
- Plant Breeding, Technische Universität München, 85354, Freising, Germany
| | - Stefan Scholten
- Biocenter Klein Flottbek, Developmental Biology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany.
| | - Albrecht E Melchinger
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany.
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26
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de Abreu E Lima F, Westhues M, Cuadros-Inostroza Á, Willmitzer L, Melchinger AE, Nikoloski Z. Metabolic robustness in young roots underpins a predictive model of maize hybrid performance in the field. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:319-329. [PMID: 28122143 DOI: 10.1111/tpj.13495] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/14/2016] [Accepted: 01/23/2017] [Indexed: 05/05/2023]
Abstract
Heterosis has been extensively exploited for yield gain in maize (Zea mays L.). Here we conducted a comparative metabolomics-based analysis of young roots from in vitro germinating seedlings and from leaves of field-grown plants in a panel of inbred lines from the Dent and Flint heterotic patterns as well as selected F1 hybrids. We found that metabolite levels in hybrids were more robust than in inbred lines. Using state-of-the-art modeling techniques, the most robust metabolites from roots and leaves explained up to 37 and 44% of the variance in the biomass from plants grown in two distinct field trials. In addition, a correlation-based analysis highlighted the trade-off between defense-related metabolites and hybrid performance. Therefore, our findings demonstrated the potential of metabolic profiles from young maize roots grown under tightly controlled conditions to predict hybrid performance in multiple field trials, thus bridging the greenhouse-field gap.
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Affiliation(s)
| | - Matthias Westhues
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstr. 21, 70593, Stuttgart, Germany
| | | | - Lothar Willmitzer
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Albrecht E Melchinger
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstr. 21, 70593, Stuttgart, Germany
| | - Zoran Nikoloski
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
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