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Kirchgessner N, Hodel M, Studer B, Patocchi A, Broggini GAL. FruitPhenoBox - a device for rapid and automated fruit phenotyping of small sample sizes. Plant Methods 2024; 20:74. [PMID: 38783345 DOI: 10.1186/s13007-024-01206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Fruit appearance of apple (Malus domestica Borkh.) is accession-specific and one of the main criteria for consumer choice. Consequently, fruit appearance is an important selection criterion in the breeding of new cultivars. It is also used for the description of older varieties or landraces. In commercial apple production, sorting devices are used to classify large numbers of fruit from a few cultivars. In contrast, the description of fruit from germplasm collections or breeding programs is based on only a few fruit from many accessions and is mostly performed visually by pomology experts. Such visual ratings are laborious, often difficult to compare and remain subjective. RESULTS Here we report on a morphometric device, the FruitPhenoBox, for automated fruit weighing and appearance description using computer-based analysis of five images per fruit. Recording of approximately 100 fruit from each of 15 apple cultivars using the FruitPhenoBox was rapid, with an average handling and recording time of less than eleven seconds per fruit. Comparison of fruit images from the 15 apple cultivars identified significant differences in shape index, fruit width, height and weight. Fruit shape was characteristic for each cultivar, while fruit color showed larger variation within sample sets. Assessing a subset of 20 randomly selected fruit per cultivar, fruit height, width and weight were described with a relative margin of error of 2.6%, 2.2%, and 6.2%, respectively, calculated from the mean value of all available fruit. CONCLUSIONS The FruitPhenoBox allows for the rapid and consistent description of fruit appearance from individual apple accessions. By relating the relative margin of error for fruit width, height and weight description with different sample sizes, it was possible to determine an appropriate fruit sample size to efficiently and accurately describe the recorded traits. Therefore, the FruitPhenoBox is a useful tool for breeding and the description of apple germplasm collections.
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Affiliation(s)
- Norbert Kirchgessner
- Crop Science, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich, 8092, Switzerland
| | - Marius Hodel
- Fruit Breeding, Research Division Plant Breeding, Mueller-Thurgau-Strasse 29, Agroscope, Waedenswil, 8820, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich, 8092, Switzerland
| | - Andrea Patocchi
- Fruit Breeding, Research Division Plant Breeding, Mueller-Thurgau-Strasse 29, Agroscope, Waedenswil, 8820, Switzerland
| | - Giovanni A L Broggini
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich, 8092, Switzerland.
- ETH Zurich c/o Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil, 8820, Switzerland.
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Keller B, Jung M, Bühlmann-Schütz S, Hodel M, Studer B, Broggini GAL, Patocchi A. The genetic basis of apple shape and size unraveled by digital phenotyping. G3 (Bethesda) 2024; 14:jkae045. [PMID: 38441135 PMCID: PMC11075547 DOI: 10.1093/g3journal/jkae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/23/2024] [Accepted: 02/22/2024] [Indexed: 05/08/2024]
Abstract
Great diversity of shape, size, and skin color is observed among the fruits of different apple genotypes. These traits are critical for consumers and therefore interesting targets for breeding new apple varieties. However, they are difficult to phenotype and their genetic basis, especially for fruit shape and ground color, is largely unknown. We used the FruitPhenoBox to digitally phenotype 525 genotypes of the apple reference population (apple REFPOP) genotyped for 303,148 single nucleotide polymorphism (SNP) markers. From the apple images, 573 highly heritable features describing fruit shape and size as well as 17 highly heritable features for fruit skin color were extracted to explore genotype-phenotype relationships. Out of these features, seven principal components (PCs) and 16 features with the Pearson's correlation r < 0.75 (selected features) were chosen to carry out genome-wide association studies (GWAS) for fruit shape and size. Four PCs and eight selected features were used in GWAS for fruit skin color. In total, 69 SNPs scattered over all 17 apple chromosomes were significantly associated with round, conical, cylindrical, or symmetric fruit shapes and fruit size. Novel associations with major effect on round or conical fruit shapes and fruit size were identified on chromosomes 1 and 2. Additionally, 16 SNPs associated with PCs and selected features related to red overcolor as well as green and yellow ground color were found on eight chromosomes. The identified associations can be used to advance marker-assisted selection in apple fruit breeding to systematically select for desired fruit appearance.
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Affiliation(s)
- Beat Keller
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Michaela Jung
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Simone Bühlmann-Schütz
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Marius Hodel
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Giovanni A L Broggini
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Andrea Patocchi
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
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3
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Chen Y, Kölliker R, Mascher M, Copetti D, Himmelbach A, Stein N, Studer B. An improved chromosome-level genome assembly of perennial ryegrass ( Lolium perenne L.). GigaByte 2024; 2024:gigabyte112. [PMID: 38496214 PMCID: PMC10940895 DOI: 10.46471/gigabyte.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/27/2024] [Indexed: 03/19/2024] Open
Abstract
This work is an update and extension of the previously published article "Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly" by Frei et al. The published genome assembly of the doubled haploid perennial ryegrass (Lolium perenne L.) genotype Kyuss (Kyuss v1.0) marked a milestone for forage grass research and breeding. However, order and orientation errors may exist in the pseudo-chromosomes of Kyuss, since barley (Hordeum vulgare L.), which diverged 30 million years ago from perennial ryegrass, was used as the reference to scaffold Kyuss. To correct for structural errors possibly present in the published Kyuss assembly, we de novo assembled the genome again and generated 50-fold coverage high-throughput chromosome conformation capture (Hi-C) data to assist pseudo-chromosome construction. The resulting new chromosome-level assembly Kyuss v2.0 showed improved quality with high contiguity (contig N50 = 120 Mb), high completeness (total BUSCO score = 99%), high base-level accuracy (QV = 50), and correct pseudo-chromosome structure (validated by Hi-C contact map). This new assembly will serve as a better reference genome for Lolium spp. and greatly benefit the forage and turf grass research community.
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Affiliation(s)
- Yutang Chen
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland, Germany
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland, Germany
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
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Keller B, Soto J, Steier A, Portilla-Benavides AE, Raatz B, Studer B, Walter A, Muller O, Urban MO. Linking photosynthesis and yield reveals a strategy to improve light use efficiency in a climbing bean breeding population. J Exp Bot 2024; 75:901-916. [PMID: 37878015 PMCID: PMC10837016 DOI: 10.1093/jxb/erad416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/21/2023] [Indexed: 10/26/2023]
Abstract
Photosynthesis drives plant physiology, biomass accumulation, and yield. Photosynthetic efficiency, specifically the operating efficiency of PSII (Fq'/Fm'), is highly responsive to actual growth conditions, especially to fluctuating photosynthetic photon fluence rate (PPFR). Under field conditions, plants constantly balance energy uptake to optimize growth. The dynamic regulation complicates the quantification of cumulative photochemical energy uptake based on the intercepted solar energy, its transduction into biomass, and the identification of efficient breeding lines. Here, we show significant effects on biomass related to genetic variation in photosynthetic efficiency of 178 climbing bean (Phaseolus vulgaris L.) lines. Under fluctuating conditions, the Fq'/Fm' was monitored throughout the growing period using hand-held and automated chlorophyll fluorescence phenotyping. The seasonal response of Fq'/Fm' to PPFR (ResponseG:PPFR) achieved significant correlations with biomass and yield, ranging from 0.33 to 0.35 and from 0.22 to 0.31 in two glasshouse and three field trials, respectively. Phenomic yield prediction outperformed genomic predictions for new environments in four trials under different growing conditions. Investigating genetic control over photosynthesis, one single nucleotide polymorphism (Chr09_37766289_13052) on chromosome 9 was significantly associated with ResponseG:PPFR in proximity to a candidate gene controlling chloroplast thylakoid formation. In conclusion, photosynthetic screening facilitates and accelerates selection for high yield potential.
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Affiliation(s)
- Beat Keller
- Crop Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Jonatan Soto
- Bean Program, Crops for nutrition and health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Angelina Steier
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - Bodo Raatz
- Bean Program, Crops for nutrition and health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Achim Walter
- Crop Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Onno Muller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Milan O Urban
- Bean Program, Crops for nutrition and health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Goettelmann F, Koebnik R, Roman-Reyna V, Studer B, Kölliker R. High genomic plasticity and unique features of Xanthomonas translucens pv. graminis revealed through comparative analysis of complete genome sequences. BMC Genomics 2023; 24:741. [PMID: 38053038 DOI: 10.1186/s12864-023-09855-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Xanthomonas translucens pv. graminis (Xtg) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly of draft genome sequences, and only one complete genome sequence was available, preventing comprehensive comparative genomic analyses. Such comparative analyses are essential in understanding the mechanisms involved in the virulence of pathogens and to identify virulence factors involved in pathogenicity. RESULTS In this study, we produced high-quality, complete genome sequences of four strains of Xtg, complementing the recently obtained complete genome sequence of the Xtg pathotype strain. These genomic resources allowed for a comprehensive comparative analysis, which revealed a high genomic plasticity with many chromosomal rearrangements, although the strains were highly related. A high number of transposases were exclusively found in Xtg and corresponded to 413 to 457 insertion/excision transposable elements per strain. These mobile genetic elements are likely to be involved in the observed genomic plasticity and may play an important role in the adaptation of Xtg. The pathovar was found to lack a type IV secretion system, and it possessed the smallest set of type III effectors in the species. However, three XopE and XopX family effectors were found, while in the other pathovars of the species two or less were present. Additional genes that were specific to the pathovar were identified, including a unique set of minor pilins of the type IV pilus, 17 TonB-dependent receptors (TBDRs), and 11 plant cell wall degradative enzymes. CONCLUSION These results suggest a high adaptability of Xtg, conferred by the abundance of mobile genetic elements, which could play a crucial role in pathogen adaptation. The large amount of such elements in Xtg compared to other pathovars of the species could, at least partially, explain its high virulence and broad host range. Conserved features that were specific to Xtg were identified, and further investigation will help to determine genes that are essential to pathogenicity and host adaptation of Xtg.
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Affiliation(s)
- Florian Goettelmann
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Veronica Roman-Reyna
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.
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6
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Younis OG, Turchetta M, Ariza Suarez D, Yates S, Studer B, Athanasiadis IN, Krause A, Buhmann JM, Corinzia L. ChromaX: a fast and scalable breeding program simulator. Bioinformatics 2023; 39:btad691. [PMID: 37991849 PMCID: PMC10709540 DOI: 10.1093/bioinformatics/btad691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/08/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023] Open
Abstract
SUMMARY ChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two orders of magnitude faster than existing tools with standard hardware. This offers breeders and scientists new opportunities to simulate genetic gain and optimize breeding schemes. AVAILABILITY AND IMPLEMENTATION The documentation is available at https://chromax.readthedocs.io. The code is available at https://github.com/kora-labs/chromax.
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Affiliation(s)
- Omar G Younis
- Department of Computer Science, ETH Zurich, Zürich, 8092, Switzerland
| | - Matteo Turchetta
- Department of Computer Science, ETH Zurich, Zürich, 8092, Switzerland
| | - Daniel Ariza Suarez
- Department of Environmental Systems Science, Molecular Plant Breeding, ETH Zurich, Switzerland
| | - Steven Yates
- Department of Environmental Systems Science, Molecular Plant Breeding, ETH Zurich, Switzerland
| | - Bruno Studer
- Department of Environmental Systems Science, Molecular Plant Breeding, ETH Zurich, Switzerland
| | - Ioannis N Athanasiadis
- Department of Social Sciences, Wageningen University & Research, Wageningen, 6708, The Netherlands
| | - Andreas Krause
- Department of Computer Science, ETH Zurich, Zürich, 8092, Switzerland
| | - Joachim M Buhmann
- Department of Computer Science, ETH Zurich, Zürich, 8092, Switzerland
| | - Luca Corinzia
- Department of Computer Science, ETH Zurich, Zürich, 8092, Switzerland
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7
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Zhang K, He Y, Lu X, Shi Y, Zhao H, Li X, Li J, Liu Y, Ouyang Y, Tang Y, Ren X, Zhang X, Yang W, Sun Z, Zhang C, Quinet M, Luthar Z, Germ M, Kreft I, Janovská D, Meglič V, Pipan B, Georgiev MI, Studer B, Chapman MA, Zhou M. Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility. Mol Plant 2023; 16:1427-1444. [PMID: 37649255 PMCID: PMC10512774 DOI: 10.1016/j.molp.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/24/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/01/2023]
Abstract
Common buckwheat (Fagopyrum esculentum) is an ancient crop with a world-wide distribution. Due to its excellent nutritional quality and high economic and ecological value, common buckwheat is becoming increasingly important throughout the world. The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat, but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly. Here we report the assembly of a chromosome-scale high-quality reference genome of F. esculentum var. homotropicum, a homozygous self-pollinating variant of common buckwheat. Comparative genomics revealed that two cultivated buckwheat species, common buckwheat (F. esculentum) and Tartary buckwheat (F. tataricum), underwent metabolomic divergence and ecotype differentiation. The expansion of several gene families in common buckwheat, including FhFAR genes, is associated with its wider distribution than Tartary buckwheat. Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat. Furthermore, we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat. Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups. Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period, a key agronomic trait controlling the yield of outcrossing crops, and that Fh06G015130 is a crucial gene underlying flavor-associated flavonoids. Intriguingly, we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common buckwheat. Collectively, our results elucidate the genetic basis of speciation, ecological adaptation, fertility, and unique flavor of common buckwheat, and provide new resources for future genomics-assisted breeding of this economically important crop.
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Affiliation(s)
- Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Yuqi He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Xiang Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Yaliang Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Hui Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaobo Li
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China
| | - Jinlong Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Yang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Yinan Ouyang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Yu Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Xue Ren
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China
| | - Weifei Yang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China
| | - Zhaoxia Sun
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China; Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Taiyuan 030031, Shanxi, China
| | - Chunhua Zhang
- Tongliao Institute Agricultural and Animal Husbandry Sciences, Tongliao 028015, Inner Mongolia, China
| | - Muriel Quinet
- Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute-Agronomy (ELI-A), Université Catholique de Louvain, Croix du Sud 4-5, boîte L7.07.13, B-1348, Louvain-la-Neuve, Belgium
| | - Zlata Luthar
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Mateja Germ
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Ivan Kreft
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; Nutrition Institute, Tržaška 40, 1000 Ljubljana, Slovenia
| | - Dagmar Janovská
- Gene Bank, Crop Research Institute, Drnovská 507, Prague 6, Czech Republic
| | - Vladimir Meglič
- Agricultural Institute of Slovenia, Hacquetova ulica, Ljubljana, Slovenia
| | - Barbara Pipan
- Agricultural Institute of Slovenia, Hacquetova ulica, Ljubljana, Slovenia
| | - Milen I Georgiev
- Laboratory of Metabolomics, Institute of Microbiology, Bulgarian Academy of Sciences, Plovdiv, Bulgaria; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China.
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Van Wijk N, Studer B, van den Berg C, Lansink M, Siebler M, Schmidt-Wilcke T. Highly Prevalent Malnutrition, Lower Nutritional Intake, And Lower Blood Levels Of Nutritional Compounds In Sub-Acute Stroke Patients With Or Without Dysphagia. Clin Nutr ESPEN 2023. [DOI: 10.1016/j.clnesp.2022.09.137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Majka J, Glombik M, Doležalová A, Kneřová J, Ferreira MTM, Zwierzykowski Z, Duchoslav M, Studer B, Doležel J, Bartoš J, Kopecký D. Both male and female meiosis contribute to non-Mendelian inheritance of parental chromosomes in interspecific plant hybrids (Lolium × Festuca). New Phytol 2023; 238:624-636. [PMID: 36658468 DOI: 10.1111/nph.18753] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 11/20/2022] [Accepted: 01/14/2023] [Indexed: 06/17/2023]
Abstract
Some interspecific plant hybrids show unequal transmission of chromosomes from parental genomes to the successive generations. It has been suggested that this is due to a differential behavior of parental chromosomes during meiosis. However, underlying mechanism is unknown. We analyzed chromosome composition of the F2 generation of Festuca × Lolium hybrids and reciprocal backcrosses to elucidate effects of male and female meiosis on the shift in parental genome composition. We studied male meiosis, including the attachment of chromosomes to the karyokinetic spindle and gene expression profiling of the kinetochore genes. We found that Lolium and Festuca homoeologues were transmitted differently to the F2 generation. Female meiosis led to the replacement of Festuca chromosomes by their Lolium counterparts. In male meiosis, Festuca univalents were attached less frequently to microtubules than Lolium univalents, lagged in divisions and formed micronuclei, which were subsequently eliminated. Genome sequence analysis revealed a number of non-synonymous mutations between copies of the kinetochore genes from Festuca and Lolium genomes. Furthermore, we found that outer kinetochore proteins NDC80 and NNF1 were exclusively expressed from the Lolium allele. We hypothesize that silencing of Festuca alleles results in improper attachment of Festuca chromosomes to karyokinetic spindle and subsequently their gradual elimination.
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Affiliation(s)
- Joanna Majka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 77900, Olomouc, Czech Republic
- Institute of Plant Genetics, Polish Academy of Sciences, 60479, Poznan, Poland
| | - Marek Glombik
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 77900, Olomouc, Czech Republic
- Department of Crop Genetics, John Innes Centre, Norwich. NR4 7UH, UK
| | - Alžběta Doležalová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 77900, Olomouc, Czech Republic
| | - Jana Kneřová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 77900, Olomouc, Czech Republic
| | - Marco Tulio Mendes Ferreira
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 77900, Olomouc, Czech Republic
- Department of Biology, Federal University of Lavras, 37200-000, Lavras, MG, Brazil
| | | | - Martin Duchoslav
- Department of Botany, Palacký University, 77900, Olomouc, Czech Republic
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 77900, Olomouc, Czech Republic
| | - Jan Bartoš
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 77900, Olomouc, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 77900, Olomouc, Czech Republic
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10
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Ariza-Suarez D, Keller B, Spescha A, Aparicio JS, Mayor V, Portilla-Benavides AE, Buendia HF, Bueno JM, Studer B, Raatz B. Genetic analysis of resistance to bean leaf crumple virus identifies a candidate LRR-RLK gene. Plant J 2023; 114:23-38. [PMID: 35574650 DOI: 10.1111/tpj.15810] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Bean leaf crumple virus (BLCrV) is a novel begomovirus (family Geminiviridae, genus Begomovirus) infecting common bean (Phaseolus vulgaris L.), threatening bean production in Latin America. Genetic resistance is required to ensure yield stability and reduce the use of insecticides, yet the available resistance sources are limited. In this study, three common bean populations containing a total of 558 genotypes were evaluated in different yield and BLCrV resistance trials under natural infection in the field. A genome-wide association study identified the locus BLC7.1 on chromosome Pv07 at 3.31 Mbp, explaining 8 to 16% of the phenotypic variation for BLCrV resistance. In comparison, whole-genome regression models explained 51 to 78% of the variation and identified the same region on Pv07 to confer resistance. The most significantly associated markers were located within the gene model Phvul.007G040400, which encodes a leucine-rich repeat receptor-like kinase subfamily III member and is likely to be involved in the innate immune response against the virus. The allelic diversity within this gene revealed five different haplotype groups, one of which was significantly associated with BLCrV resistance. As the same genome region was previously reported to be associated with resistance against other geminiviruses affecting common bean, our study highlights the role of previous breeding efforts for virus resistance in the accumulation of positive alleles against newly emerging viruses. In addition, we provide novel diagnostic single-nucleotide polymorphism markers for marker-assisted selection to exploit BLC7.1 for breeding against geminivirus diseases in one of the most important food crops worldwide.
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Affiliation(s)
- Daniel Ariza-Suarez
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Beat Keller
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
- Crop Science, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Anna Spescha
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Johan Steven Aparicio
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Victor Mayor
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Hector Fabio Buendia
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Juan Miguel Bueno
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Bodo Raatz
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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11
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Schlathölter I, Broggini GAL, Streb S, Studer B, Patocchi A. Field study of the fire-blight-resistant cisgenic apple line C44.4.146. Plant J 2023; 113:1160-1175. [PMID: 36609772 DOI: 10.1111/tpj.16083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Cisgenesis, the genetic modification of a plant with genes from a sexually compatible plant, was used to confer fire blight resistance to the cultivar 'Gala Galaxy' by amendment of the resistance gene FB_MR5, resulting in the line C44.4.146. To verify whether cisgenesis changed other tree-, flower- or fruit-related traits, a 5-year field trial was conducted with trees of C44.4.146 and multiple control genotypes, including members of the 'Gala' sports group. None of the 44 investigated tree-, flower- or fruit-related traits significantly differed between C44.4.146 and at least one of the control genotypes in all observation years. However, fruits of C44.4.146 and its wild-type 'Gala Galaxy' from tissue culture were paler in color than fruits of 'Gala Galaxy' that had not undergone tissue culture. There was no significant and consistently detected difference in the fruit flesh and peel metabolome of C44.4.146 compared with the control genotypes. Finally, the disease resistance of C44.4.146 was confirmed also when the fire blight pathogen was inoculated through the flowers. We conclude that the use of cisgenesis to confer fire blight resistance to 'Gala Galaxy' in C44.4.146 did not have unintended effects, and that the in vitro establishment of 'Gala Galaxy' had a greater effect on C44.4.146 properties than its generation applying cisgenesis.
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Affiliation(s)
- Ina Schlathölter
- Breeding Research, Research Division Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, 8820, Waedenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Giovanni A L Broggini
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Sebastian Streb
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Andrea Patocchi
- Breeding Research, Research Division Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, 8820, Waedenswil, Switzerland
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12
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Rohner M, Manzanares C, Yates S, Thorogood D, Copetti D, Lübberstedt T, Asp T, Studer B. Fine-Mapping and Comparative Genomic Analysis Reveal the Gene Composition at the S and Z Self-incompatibility Loci in Grasses. Mol Biol Evol 2022; 40:6882748. [PMID: 36477354 PMCID: PMC9825253 DOI: 10.1093/molbev/msac259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/12/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Self-incompatibility (SI) is a genetic mechanism of hermaphroditic plants to prevent inbreeding after self-pollination. Allogamous Poaceae species exhibit a unique gametophytic SI system controlled by two multi-allelic and independent loci, S and Z. Despite intense research efforts in the last decades, the genes that determine the initial recognition mechanism are yet to be identified. Here, we report the fine-mapping of the Z-locus in perennial ryegrass (Lolium perenne L.) and provide evidence that the pollen and stigma components are determined by two genes encoding DUF247 domain proteins (ZDUF247-I and ZDUF247-II) and the gene sZ, respectively. The pollen and stigma determinants are located side-by-side and were genetically linked in 10,245 individuals of two independent mapping populations segregating for Z. Moreover, they exhibited high allelic diversity as well as tissue-specific gene expression, matching the expected characteristics of SI determinants known from other systems. Revisiting the S-locus using the latest high-quality whole-genome assemblies revealed a similar gene composition and structure as found for Z, supporting the hypothesis of a duplicated origin of the two-locus SI system of grasses. Ultimately, comparative genomic analyses across a wide range of self-compatible and self-incompatible Poaceae species revealed that the absence of a functional copy of at least one of the six putative SI determinants is accompanied by a self-compatible phenotype. Our study provides new insights into the origin and evolution of the unique gametophytic SI system in one of the largest and economically most important plant families.
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Affiliation(s)
- Marius Rohner
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Chloé Manzanares
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Daniel Thorogood
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Dario Copetti
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland,Arizona Genomics Institute, School of Plant Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Torben Asp
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
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13
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Frey LA, Vleugels T, Ruttink T, Schubiger FX, Pégard M, Skøt L, Grieder C, Studer B, Roldán-Ruiz I, Kölliker R. Phenotypic variation and quantitative trait loci for resistance to southern anthracnose and clover rot in red clover. Theor Appl Genet 2022; 135:4337-4349. [PMID: 36153770 PMCID: PMC9734235 DOI: 10.1007/s00122-022-04223-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/14/2022] [Indexed: 06/02/2023]
Abstract
High variability for and candidate loci associated with resistance to southern anthracnose and clover rot in a worldwide collection of red clover provide a first basis for genomics-assisted breeding. Red clover (Trifolium pratense L.) is an important forage legume of temperate regions, particularly valued for its high yield potential and its high forage quality. Despite substantial breeding progress during the last decades, continuous improvement of cultivars is crucial to ensure yield stability in view of newly emerging diseases or changing climatic conditions. The high amount of genetic diversity present in red clover ecotypes, landraces, and cultivars provides an invaluable, but often unexploited resource for the improvement of key traits such as yield, quality, and resistance to biotic and abiotic stresses. A collection of 397 red clover accessions was genotyped using a pooled genotyping-by-sequencing approach with 200 plants per accession. Resistance to the two most pertinent diseases in red clover production, southern anthracnose caused by Colletotrichum trifolii, and clover rot caused by Sclerotinia trifoliorum, was assessed using spray inoculation. The mean survival rate for southern anthracnose was 22.9% and the mean resistance index for clover rot was 34.0%. Genome-wide association analysis revealed several loci significantly associated with resistance to southern anthracnose and clover rot. Most of these loci are in coding regions. One quantitative trait locus (QTL) on chromosome 1 explained 16.8% of the variation in resistance to southern anthracnose. For clover rot resistance we found eight QTL, explaining together 80.2% of the total phenotypic variation. The SNPs associated with these QTL provide a promising resource for marker-assisted selection in existing breeding programs, facilitating the development of novel cultivars with increased resistance against two devastating fungal diseases of red clover.
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Affiliation(s)
- Lea A Frey
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Tim Vleugels
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
| | - Franz X Schubiger
- Agroscope, Plant Breeding, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Marie Pégard
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, UR4 (UR P3F), 86600, Lusignan, France
| | - Leif Skøt
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Christoph Grieder
- Agroscope, Plant Breeding, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland.
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14
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Schlathölter I, Meissle M, Boeriis T, Heimo D, Studer B, Broggini GAL, Romeis J, Patocchi A. No adverse dietary effect of a cisgenic fire blight resistant apple line on the non-target arthropods Drosophila melanogaster and Folsomia candida. Ecotoxicol Environ Saf 2022; 241:113749. [PMID: 35696966 DOI: 10.1016/j.ecoenv.2022.113749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/28/2022] [Revised: 06/04/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
Genetic modification of apple cultivars through cisgenesis can introduce traits, such as disease resistance from wild relatives, quickly and without crossing. This approach was used to generate the cisgenic apple line C44.4.146, a 'Gala Galaxy' carrying the fire blight resistance gene FB_MR5. In contrast to traditionally bred apple cultivars, genetically modified (GM) plants need to undergo a regulatory risk assessment considering unintended effects before approval for commercial release. To determine potential unintended effects of C44.4.146, we assessed major leaf components and effects on the fitness of the decomposers Drosophila melanogaster (fruit fly) and Folsomia candida (collembolan), which were fed a diet amended with powdered apple leaf material. Leaf material of 'Gala Galaxy', several natural 'Gala' mutants, and the unrelated apple cultivar 'Ladina' were used for comparison. The genetic modification did not alter major leaf components and did not adversely affect survival, growth, or fecundity of the two decomposers. Consistent with previous studies with other GM crops, the differences between conventionally bred cultivars were greater than between the GM line and its non-GM wild type. These data provide a baseline for future risk assessments.
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Affiliation(s)
- Ina Schlathölter
- Agroscope, Research Division Plant Breeding, Breeding Research Group, Mueller-Thurgau-Strasse 29, 8820 Waedenswil, Switzerland; Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Michael Meissle
- Agroscope, Research Division Agroecology and Environment, Biosafety Research Group, Reckenholzstrasse 191, 8046 Zurich, Switzerland
| | - Timea Boeriis
- Agroscope, Research Division Plant Breeding, Breeding Research Group, Mueller-Thurgau-Strasse 29, 8820 Waedenswil, Switzerland
| | - Dominique Heimo
- Agroscope, Research Division Methods Development and Analytics, Feed Chemistry Group, Route de la Tioleyre 4, 1725 Posieux, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Giovanni A L Broggini
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Jörg Romeis
- Agroscope, Research Division Agroecology and Environment, Biosafety Research Group, Reckenholzstrasse 191, 8046 Zurich, Switzerland
| | - Andrea Patocchi
- Agroscope, Research Division Plant Breeding, Breeding Research Group, Mueller-Thurgau-Strasse 29, 8820 Waedenswil, Switzerland.
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15
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Keller B, Ariza-Suarez D, Portilla-Benavides AE, Buendia HF, Aparicio JS, Amongi W, Mbiu J, Msolla SN, Miklas P, Porch TG, Burridge J, Mukankusi C, Studer B, Raatz B. Improving Association Studies and Genomic Predictions for Climbing Beans With Data From Bush Bean Populations. Front Plant Sci 2022; 13:830896. [PMID: 35557726 PMCID: PMC9085748 DOI: 10.3389/fpls.2022.830896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/25/2022] [Indexed: 05/29/2023]
Abstract
Common bean (Phaseolus vulgaris L.) has two major origins of domestication, Andean and Mesoamerican, which contribute to the high diversity of growth type, pod and seed characteristics. The climbing growth habit is associated with increased days to flowering (DF), seed iron concentration (SdFe), nitrogen fixation, and yield. However, breeding efforts in climbing beans have been limited and independent from bush type beans. To advance climbing bean breeding, we carried out genome-wide association studies and genomic predictions using 1,869 common bean lines belonging to five breeding panels representing both gene pools and all growth types. The phenotypic data were collected from 17 field trials and were complemented with 16 previously published trials. Overall, 38 significant marker-trait associations were identified for growth habit, 14 for DF, 13 for 100 seed weight, three for SdFe, and one for yield. Except for DF, the results suggest a common genetic basis for traits across all panels and growth types. Seven QTL associated with growth habits were confirmed from earlier studies and four plausible candidate genes for SdFe and 100 seed weight were newly identified. Furthermore, the genomic prediction accuracy for SdFe and yield in climbing beans improved up to 8.8% when bush-type bean lines were included in the training population. In conclusion, a large population from different gene pools and growth types across multiple breeding panels increased the power of genomic analyses and provides a solid and diverse germplasm base for genetic improvement of common bean.
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Affiliation(s)
- Beat Keller
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Daniel Ariza-Suarez
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Bean Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Hector Fabio Buendia
- Bean Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Winnyfred Amongi
- Bean Program, International Center for Tropical Agriculture (CIAT), Kampala, Uganda
| | - Julius Mbiu
- Tanzania Agricultural Research Institute (TARI), Dodoma, Tanzania
| | - Susan Nchimbi Msolla
- Department of Crop Science and Horticulture, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Phillip Miklas
- Department of Agriculture, Agriculture Research Service (USDA-ARS), Prosser, WA, United States
| | - Timothy G. Porch
- Department of Agriculture, Agriculture Research Service (USDA-ARS), Tropical Agriculture Research Station, Mayaguez, PR, United States
| | - James Burridge
- Department of Plant Science, The Pennsylvania State University, University Park, PA, United States
| | - Clare Mukankusi
- Bean Program, International Center for Tropical Agriculture (CIAT), Kampala, Uganda
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Bodo Raatz
- Bean Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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16
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Goettelmann F, Roman-Reyna V, Cunnac S, Jacobs JM, Bragard C, Studer B, Koebnik R, Kölliker R. Complete Genome Assemblies of All Xanthomonas translucens Pathotype Strains Reveal Three Genetically Distinct Clades. Front Microbiol 2022; 12:817815. [PMID: 35310401 PMCID: PMC8924669 DOI: 10.3389/fmicb.2021.817815] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 11/18/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
The Xanthomonas translucens species comprises phytopathogenic bacteria that can cause serious damage to cereals and to forage grasses. So far, the genomic resources for X. translucens were limited, which hindered further understanding of the host–pathogen interactions at the molecular level and the development of disease-resistant cultivars. To this end, we complemented the available complete genome sequence of the X. translucens pv. translucens pathotype strain DSM 18974 by sequencing the genomes of all the other 10 X. translucens pathotype strains using PacBio long-read technology and assembled complete genome sequences. Phylogeny based on average nucleotide identity (ANI) revealed three distinct clades within the species, which we propose to classify as clades Xt-I, Xt-II, and Xt-III. In addition to 2,181 core X. translucens genes, a total of 190, 588, and 168 genes were found to be exclusive to each clade, respectively. Moreover, 29 non-transcription activator-like effector (TALE) and 21 TALE type III effector classes were found, and clade- or strain-specific effectors were identified. Further investigation of these genes could help to identify genes that are critically involved in pathogenicity and/or host adaptation, setting the grounds for the development of new resistant cultivars.
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Affiliation(s)
- Florian Goettelmann
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Sébastien Cunnac
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Claude Bragard
- Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
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17
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Jung M, Keller B, Roth M, Aranzana MJ, Auwerkerken A, Guerra W, Al-Rifaï M, Lewandowski M, Sanin N, Rymenants M, Didelot F, Dujak C, Font i Forcada C, Knauf A, Laurens F, Studer B, Muranty H, Patocchi A. Genetic architecture and genomic predictive ability of apple quantitative traits across environments. Hortic Res 2022; 9:uhac028. [PMID: 35184165 PMCID: PMC8976694 DOI: 10.1093/hr/uhac028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/09/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Implementation of genomic tools is desirable to increase the efficiency of apple breeding. Recently, the multi-environment apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using the apple REFPOP, although the population may be valuable when dissecting genetic architecture and reporting predictive abilities for additional key traits in apple breeding. Here we show contrasting genetic architecture and genomic predictive abilities for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic predictive abilities of 0.18-0.88 were estimated using main-effect univariate, main-effect multivariate, multi-environment univariate, and multi-environment multivariate models. The G × E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.
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Affiliation(s)
- Michaela Jung
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Beat Keller
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Morgane Roth
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- GAFL, INRAE, 84140 Montfavet, France
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140 Caldes de Montbui, Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | | | | | - Mehdi Al-Rifaï
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Mariusz Lewandowski
- The National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | | | - Marijn Rymenants
- Better3fruit N.V., 3202 Rillaar, Belgium
- Laboratory for Plant Genetics and Crop Improvement, KU Leuven, B-3001 Leuven, Belgium
| | | | - Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Carolina Font i Forcada
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140 Caldes de Montbui, Barcelona, Spain
| | - Andrea Knauf
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - François Laurens
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Hélène Muranty
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Andrea Patocchi
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
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18
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Russo A, Mayjonade B, Frei D, Potente G, Kellenberger RT, Frachon L, Copetti D, Studer B, Frey JE, Grossniklaus U, Schlüter PM. Low-Input High-Molecular-Weight DNA Extraction for Long-Read Sequencing From Plants of Diverse Families. Front Plant Sci 2022; 13:883897. [PMID: 35665166 PMCID: PMC9161206 DOI: 10.3389/fpls.2022.883897] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/21/2022] [Indexed: 05/16/2023]
Abstract
Long-read DNA sequencing technologies require high molecular weight (HMW) DNA of adequate purity and integrity, which can be difficult to isolate from plant material. Plant leaves usually contain high levels of carbohydrates and secondary metabolites that can impact DNA purity, affecting downstream applications. Several protocols and kits are available for HMW DNA extraction, but they usually require a high amount of input material and often lead to substantial DNA fragmentation, making sequencing suboptimal in terms of read length and data yield. We here describe a protocol for plant HMW DNA extraction from low input material (0.1 g) which is easy to follow and quick (2.5 h). This method successfully enabled us to extract HMW from four species from different families (Orchidaceae, Poaceae, Brassicaceae, Asteraceae). In the case of recalcitrant species, we show that an additional purification step is sufficient to deliver a clean DNA sample. We demonstrate the suitability of our protocol for long-read sequencing on the Oxford Nanopore Technologies PromethION® platform, with and without the use of a short fragment depletion kit.
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Affiliation(s)
- Alessia Russo
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
- Department of Systematic and Evolutionary Botany and Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
- *Correspondence: Alessia Russo,
| | - Baptiste Mayjonade
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), INRAE, Toulouse, France
| | - Daniel Frei
- Department of Method Development and Analytics, Agroscope, Wädenswil, Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany and Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
| | | | - Léa Frachon
- Department of Systematic and Evolutionary Botany and Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
| | - Dario Copetti
- Institute of Agricultural Sciences and Zurich-Basel Plant Science Centre, ETH Zürich, Zurich, Switzerland
| | - Bruno Studer
- Institute of Agricultural Sciences and Zurich-Basel Plant Science Centre, ETH Zürich, Zurich, Switzerland
| | - Jürg E. Frey
- Department of Method Development and Analytics, Agroscope, Wädenswil, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
| | - Philipp M. Schlüter
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
- Department of Systematic and Evolutionary Botany and Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
- Philipp M. Schlüter,
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19
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Loera-Sánchez M, Studer B, Kölliker R. A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species. Mol Ecol Resour 2021; 22:1725-1745. [PMID: 34918474 PMCID: PMC9305562 DOI: 10.1111/1755-0998.13577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/02/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Abstract
Grasslands are widespread and economically relevant ecosystems at the basis of sustainable roughage production. Plant genetic diversity (PGD; i.e., within‐species diversity) is related to many beneficial effects on the ecosystem functioning of grasslands. The monitoring of PGD in temperate grasslands is complicated by the multiplicity of species present and by a shortage of methods for large‐scale assessments. However, the continuous advancement of high‐throughput DNA sequencing approaches has improved the prospects of broad, multispecies PGD monitoring. Among them, amplicon sequencing stands out as a robust and cost‐effective method. Here, we report a set of 12 multispecies primer pairs that can be used for high‐throughput PGD assessments in multiple grassland plant species. The target loci were selected and tested in two phases: a “discovery phase” based on a sequence capture assay (611 nuclear loci assessed in 16 grassland plant species), which resulted in the selection of 11 loci; and a “validation phase”, in which the selected loci were targeted and sequenced using multispecies primers in test populations of Dactylis glomerata L., Lolium perenne L., Festuca pratensis Huds., Trifolium pratense L. and T. repens L. The multispecies amplicons had nucleotide diversities per species from 5.19 × 10−3 to 1.29 × 10−2, which is in the range of flowering‐related genes but slightly lower than pathogen resistance genes. We conclude that the methodology, the DNA sequence resources, and the primer pairs reported in this study provide the basis for large‐scale, multispecies PGD monitoring in grassland plants.
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Affiliation(s)
- Miguel Loera-Sánchez
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
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20
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Cropano C, Manzanares C, Yates S, Copetti D, Do Canto J, Lübberstedt T, Koch M, Studer B. Identification of Candidate Genes for Self-Compatibility in Perennial Ryegrass ( Lolium perenne L.). Front Plant Sci 2021; 12:707901. [PMID: 34721449 PMCID: PMC8554087 DOI: 10.3389/fpls.2021.707901] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/30/2021] [Indexed: 05/10/2023]
Abstract
Self-incompatibility (SI) is a genetic mechanism preventing self-pollination in ~40% of plant species. Two multiallelic loci, called S and Z, control the gametophytic SI system of the grass family (Poaceae), which contains all major forage grasses. Loci independent from S and Z have been reported to disrupt SI and lead to self-compatibility (SC). A locus causing SC in perennial ryegrass (Lolium perenne L.) was previously mapped on linkage group (LG) 5 in an F2 population segregating for SC. Using a subset of the same population (n = 68), we first performed low-resolution quantitative trait locus (QTL) mapping to exclude the presence of additional, previously undetected contributors to SC. The previously reported QTL on LG 5 explained 38.4% of the phenotypic variation, and no significant contribution from other genomic regions was found. This was verified by the presence of significantly distorted markers in the region overlapping with the QTL. Second, we fine mapped the QTL to 0.26 centimorgan (cM) using additional 2,056 plants and 23 novel sequence-based markers. Using Italian ryegrass (Lolium multiflorum Lam.) genome assembly as a reference, the markers flanking SC were estimated to span a ~3 Mb region encoding for 57 predicted genes. Among these, seven genes were proposed as relevant candidate genes based on their annotation and function described in previous studies. Our study is a step forward to identify SC genes in forage grasses and provides diagnostic markers for marker-assisted introgression of SC into elite germplasm.
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Affiliation(s)
- Claudio Cropano
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Deutsche Saatveredelung AG, Lippstadt, Germany
| | - Chloé Manzanares
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Dario Copetti
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Javier Do Canto
- Instituto Nacional de Investigación Agropecuaria, Tacuarembó, Uruguay
| | | | | | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
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21
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Wille L, Kurmann M, Messmer MM, Studer B, Hohmann P. Untangling the Pea Root Rot Complex Reveals Microbial Markers for Plant Health. Front Plant Sci 2021; 12:737820. [PMID: 34712258 PMCID: PMC8545811 DOI: 10.3389/fpls.2021.737820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Plant health is recognised as a key element to ensure global food security. While plant breeding has substantially improved crop resistance against individual pathogens, it showed limited success for diseases caused by the interaction of multiple pathogens such as root rot in pea (Pisum sativum L.). To untangle the causal agents of the pea root rot complex and determine the role of the plant genotype in shaping its own detrimental or beneficial microbiome, fungal and oomycete root rot pathogens, as well as previously identified beneficials, i.e., arbuscular mycorrhizal fungi (AMF) and Clonostachys rosea, were qPCR quantified in diseased roots of eight differently resistant pea genotypes grown in four agricultural soils under controlled conditions. We found that soil and pea genotype significantly determined the microbial compositions in diseased pea roots. Despite significant genotype x soil interactions and distinct soil-dependent pathogen complexes, our data revealed key microbial taxa that were associated with plant fitness. Our study indicates the potential of fungal and oomycete markers for plant health and serves as a precedent for other complex plant pathosystems. Such microbial markers can be used to complement plant phenotype- and genotype-based selection strategies to improve disease resistance in one of the world's most important pulse crops of the world.
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Affiliation(s)
- Lukas Wille
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Mario Kurmann
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Monika M. Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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22
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Frei D, Veekman E, Grogg D, Stoffel-Studer I, Morishima A, Shimizu-Inatsugi R, Yates S, Shimizu KK, Frey JE, Studer B, Copetti D. Erratum to: Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly. Genome Biol Evol 2021; 13:6409998. [PMID: 34695194 PMCID: PMC8545041 DOI: 10.1093/gbe/evab203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Frei D, Veekman E, Grogg D, Stoffel-Studer I, Morishima A, Shimizu-Inatsugi R, Yates S, Shimizu KK, Frey JE, Studer B, Copetti D. Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly. Genome Biol Evol 2021; 13:evab159. [PMID: 34247248 PMCID: PMC8358221 DOI: 10.1093/gbe/evab159] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/24/2022] Open
Abstract
Despite the progress made in DNA sequencing over the last decade, reconstructing telomere-to-telomere genome assemblies of large and repeat-rich eukaryotic genomes is still difficult. More accurate basecalls or longer reads could address this issue, but no current sequencing platform can provide both simultaneously. Perennial ryegrass (Lolium perenne L.) is an example of an important species for which the lack of a reference genome assembly hindered a swift adoption of genomics-based methods into breeding programs. To fill this gap, we optimized the Oxford Nanopore Technologies' sequencing protocol, obtaining sequencing reads with an N50 of 62 kb-a very high value for a plant sample. The assembly of such reads produced a highly complete (2.3 of 2.7 Gb), correct (QV 45), and contiguous (contig N50 and N90 11.74 and 3.34 Mb, respectively) genome assembly. We show how read length was key in determining the assembly contiguity. Sequence annotation revealed the dominance of transposable elements and repeated sequences (81.6% of the assembly) and identified 38,868 protein coding genes. Almost 90% of the bases could be anchored to seven pseudomolecules, providing the first high-quality haploid reference assembly for perennial ryegrass. This protocol will enable producing longer Oxford Nanopore Technology reads for more plant samples and ushering forage grasses into modern genomics-assisted breeding programs.
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Affiliation(s)
- Daniel Frei
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | | | - Daniel Grogg
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Ingrid Stoffel-Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Aki Morishima
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka-ward, Yokohama, Japan
| | - Jürg E Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Dario Copetti
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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24
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Glombik M, Copetti D, Bartos J, Stoces S, Zwierzykowski Z, Ruttink T, Wendel JF, Duchoslav M, Dolezel J, Studer B, Kopecky D. Reciprocal allopolyploid grasses (Festuca × Lolium) display stable patterns of genome dominance. Plant J 2021; 107:1166-1182. [PMID: 34152039 PMCID: PMC8518873 DOI: 10.1111/tpj.15375] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/21/2021] [Accepted: 06/11/2021] [Indexed: 05/19/2023]
Abstract
Allopolyploidization entailing the merger of two distinct genomes in a single hybrid organism, is an important process in plant evolution and a valuable tool in breeding programs. Newly established hybrids often experience massive genomic perturbations, including karyotype reshuffling and gene expression modifications. These phenomena may be asymmetric with respect to the two progenitors, with one of the parental genomes being "dominant." Such "genome dominance" can manifest in several ways, including biased homoeolog gene expression and expression level dominance. Here we employed a k-mer-based approach to study gene expression in reciprocal Festuca pratensis Huds. × Lolium multiflorum Lam. allopolyploid grasses. Our study revealed significantly more genes where expression mimicked that of the Lolium parent compared with the Festuca parent. This genome dominance was heritable to successive generation and its direction was only slightly modified by environmental conditions and plant age. Our results suggest that Lolium genome dominance was at least partially caused by its more efficient trans-acting gene expression regulatory factors. Unraveling the mechanisms responsible for propagation of parent-specific traits in hybrid crops contributes to our understanding of allopolyploid genome evolution and opens a way to targeted breeding strategies.
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Affiliation(s)
- Marek Glombik
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 3177900OlomoucCzech Republic
- National Centre for Biomolecular ResearchFaculty of ScienceMasaryk UniversityKotlářská 261137BrnoCzech Republic
| | - Dario Copetti
- Molecular Plant BreedingInstitute of Agricultural SciencesETH ZurichUniversitaetstrasse 28092ZurichSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Jan Bartos
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 3177900OlomoucCzech Republic
| | - Stepan Stoces
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 3177900OlomoucCzech Republic
| | - Zbigniew Zwierzykowski
- Department of Environmental Stress BiologyInstitute of Plant GeneticsPolish Academy of SciencesStrzeszyńska 3460‐479PoznańPoland
| | - Tom Ruttink
- Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)Caritasstraat 399090MelleBelgium
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIA50011USA
| | - Martin Duchoslav
- Department of BotanyFaculty of SciencePalacký University in OlomoucŠlechtitelů 2778371OlomoucCzech Republic
| | - Jaroslav Dolezel
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 3177900OlomoucCzech Republic
| | - Bruno Studer
- Molecular Plant BreedingInstitute of Agricultural SciencesETH ZurichUniversitaetstrasse 28092ZurichSwitzerland
| | - David Kopecky
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 3177900OlomoucCzech Republic
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25
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Kronenberg L, Yates S, Ghiasi S, Roth L, Friedli M, Ruckle ME, Werner RA, Tschurr F, Binggeli M, Buchmann N, Studer B, Walter A. Rethinking temperature effects on leaf growth, gene expression and metabolism: Diel variation matters. Plant Cell Environ 2021; 44:2262-2276. [PMID: 33230869 PMCID: PMC8359295 DOI: 10.1111/pce.13958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 06/11/2023]
Abstract
Plants have evolved to grow under prominently fluctuating environmental conditions. In experiments under controlled conditions, temperature is often set to artificial, binary regimes with constant values at day and at night. This study investigated how such a diel (24 hr) temperature regime affects leaf growth, carbohydrate metabolism and gene expression, compared to a temperature regime with a field-like gradual increase and decline throughout 24 hr. Soybean (Glycine max) was grown under two contrasting diel temperature treatments. Leaf growth was measured in high temporal resolution. Periodical measurements were performed of carbohydrate concentrations, carbon isotopes as well as the transcriptome by RNA sequencing. Leaf growth activity peaked at different times under the two treatments, which cannot be explained intuitively. Under field-like temperature conditions, leaf growth followed temperature and peaked in the afternoon, whereas in the binary temperature regime, growth increased at night and decreased during daytime. Differential gene expression data suggest that a synchronization of cell division activity seems to be evoked in the binary temperature regime. Overall, the results show that the coordination of a wide range of metabolic processes is markedly affected by the diel variation of temperature, which emphasizes the importance of realistic environmental settings in controlled condition experiments.
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Affiliation(s)
- Lukas Kronenberg
- Crop ScienceInstitute of Agricultural Sciences, ETH ZurichZurichSwitzerland
| | - Steven Yates
- Molecular Plant BreedingInstitute of Agricultural Sciences, ETH ZurichZurichSwitzerland
| | - Shiva Ghiasi
- Grassland SciencesInstitute of Agricultural Sciences, ETH ZurichZurichSwitzerland
| | - Lukas Roth
- Crop ScienceInstitute of Agricultural Sciences, ETH ZurichZurichSwitzerland
| | - Michael Friedli
- Crop ScienceInstitute of Agricultural Sciences, ETH ZurichZurichSwitzerland
| | - Michael E. Ruckle
- Molecular Plant BreedingInstitute of Agricultural Sciences, ETH ZurichZurichSwitzerland
| | - Roland A. Werner
- Grassland SciencesInstitute of Agricultural Sciences, ETH ZurichZurichSwitzerland
| | - Flavian Tschurr
- Crop ScienceInstitute of Agricultural Sciences, ETH ZurichZurichSwitzerland
| | - Melanie Binggeli
- Crop ScienceInstitute of Agricultural Sciences, ETH ZurichZurichSwitzerland
| | - Nina Buchmann
- Grassland SciencesInstitute of Agricultural Sciences, ETH ZurichZurichSwitzerland
| | - Bruno Studer
- Molecular Plant BreedingInstitute of Agricultural Sciences, ETH ZurichZurichSwitzerland
| | - Achim Walter
- Crop ScienceInstitute of Agricultural Sciences, ETH ZurichZurichSwitzerland
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26
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Cropano C, Place I, Manzanares C, Do Canto J, Lübberstedt T, Studer B, Thorogood D. Characterization and practical use of self-compatibility in outcrossing grass species. Ann Bot 2021; 127:841-852. [PMID: 33755100 PMCID: PMC8225281 DOI: 10.1093/aob/mcab043] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Self-incompatibility (SI) systems prevent self-fertilization in several species of Poaceae, many of which are economically important forage, bioenergy and turf grasses. Self-incompatibility ensures cross-pollination and genetic diversity but restricts the ability to fix useful genetic variation. In most inbred crops it is possible to develop high-performing homozygous parental lines by self-pollination, which then enables the creation of F1 hybrid varieties with higher performance, a phenomenon known as heterosis. The inability to fully exploit heterosis in outcrossing grasses is partially responsible for lower levels of improvement in breeding programmes compared with inbred crops. However, SI can be overcome in forage grasses to create self-compatible populations. This is generating interest in understanding the genetical basis of self-compatibility (SC), its significance for reproductive strategies and its exploitation for crop improvement, especially in the context of F1 hybrid breeding. SCOPE We review the literature on SI and SC in outcrossing grass species. We review the currently available genomic tools and approaches used to discover and characterize novel SC sources. We discuss opportunities barely explored for outcrossing grasses that SC facilitates. Specifically, we discuss strategies for wide SC introgression in the context of the Lolium-Festuca complex and the use of SC to develop immortalized mapping populations for the dissection of a wide range of agronomically important traits. The germplasm available is a valuable practical resource and will aid understanding the basis of inbreeding depression and hybrid vigour in key temperate forage grass species. CONCLUSIONS A better understanding of the genetic control of additional SC loci offers new insight into SI systems, their evolutionary origins and their reproductive significance. Heterozygous outcrossing grass species that can be readily selfed facilitate studies of heterosis. Moreover, SC introduction into a range of grass species will enable heterosis to be exploited in innovative ways in genetic improvement programmes.
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Affiliation(s)
- Claudio Cropano
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Deutsche Saatveredelung AG, Lippstadt, Germany
| | - Iain Place
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Chloé Manzanares
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Javier Do Canto
- Instituto Nacional de Investigación Agropecuaria (INIA), 4500 Tacuarembó, Uruguay
| | | | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Daniel Thorogood
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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27
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Wille L, Messmer MM, Bodenhausen N, Studer B, Hohmann P. Heritable Variation in Pea for Resistance Against a Root Rot Complex and Its Characterization by Amplicon Sequencing. Front Plant Sci 2020; 11:542153. [PMID: 33224157 PMCID: PMC7669989 DOI: 10.3389/fpls.2020.542153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
Soil-borne pathogens cause severe root rot of pea (Pisum sativum L.) and are a major constraint to pea cultivation worldwide. Resistance against individual pathogen species is often ineffective in the field where multiple pathogens form a pea root rot complex (PRRC) and conjointly infect pea plants. On the other hand, various beneficial plant-microbe interactions are known that offer opportunities to strengthen plant health. To account for the whole rhizosphere microbiome in the assessment of root rot resistance in pea, an infested soil-based resistance screening assay was established. The infested soil originated from a field that showed severe pea root rot in the past. Initially, amplicon sequencing was employed to characterize the fungal microbiome of diseased pea roots grown in the infested soil. The amplicon sequencing evidenced a diverse fungal community in the roots including pea pathogens Fusarium oxysporum, F. solani, Didymella sp., and Rhizoctonia solani and antagonists such as Clonostachys rosea and several mycorrhizal species. The screening system allowed for a reproducible assessment of disease parameters among 261 pea cultivars, breeding lines, and landraces grown for 21 days under controlled conditions. A sterile soil control treatment was used to calculate relative shoot and root biomass in order to compare growth performance of pea lines with highly different growth morphologies. Broad sense heritability was calculated from linear mixed model estimated variance components for all traits. Emergence on the infested soil showed high (H 2 = 0.89), root rot index (H 2 = 0.43), and relative shoot dry weight (H 2 = 0.51) medium heritability. The resistance screening allowed for a reproducible distinction between PRRC susceptible and resistant pea lines. The combined assessment of root rot index and relative shoot dry weight allowed to identify resistant (low root rot index) and tolerant pea lines (low relative shoot dry weight at moderate to high root rot index). We conclude that relative shoot dry weight is a valuable trait to select disease tolerant pea lines. Subsequently, the resistance ranking was verified in an on-farm experiment with a subset of pea lines. We found a significant correlation (r s = 0.73, p = 0.03) between the controlled conditions and the resistance ranking in a field with high PRRC infestation. The screening system allows to predict PRRC resistance for a given field site and offers a tool for selection at the seedling stage in breeding nurseries. Using the complexity of the infested field soil, the screening system provides opportunities to study plant resistance in the light of diverse plant-microbe interactions occurring in the rhizosphere.
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Affiliation(s)
- Lukas Wille
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Monika M. Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Natacha Bodenhausen
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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28
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Jung M, Roth M, Aranzana MJ, Auwerkerken A, Bink M, Denancé C, Dujak C, Durel CE, Font I Forcada C, Cantin CM, Guerra W, Howard NP, Keller B, Lewandowski M, Ordidge M, Rymenants M, Sanin N, Studer B, Zurawicz E, Laurens F, Patocchi A, Muranty H. The apple REFPOP-a reference population for genomics-assisted breeding in apple. Hortic Res 2020; 7:189. [PMID: 33328447 PMCID: PMC7603508 DOI: 10.1038/s41438-020-00408-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/25/2020] [Accepted: 09/06/2020] [Indexed: 05/16/2023]
Abstract
Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates. Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs, and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions. Here we present an apple reference population: the apple REFPOP, a large collection formed of 534 genotypes planted in six European countries, as a unique tool to accelerate apple breeding. The population consisted of 269 accessions and 265 progeny from 27 parental combinations, representing the diversity in cultivated apple and current European breeding material, respectively. A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95. Based on the genotypic data, linkage disequilibrium was low and population structure was weak. Two well-studied phenological traits of horticultural importance were measured. We found marker-trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date, respectively. With decreasing SNP density, the detection of significant marker-trait associations varied depending on trait architecture. Regardless of the trait, 10,000 SNPs sufficed to maximize genomic prediction ability. We confirm the suitability of the apple REFPOP design for genomics-assisted breeding, especially for breeding programs using related germplasm, and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.
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Affiliation(s)
- Michaela Jung
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | - Morgane Roth
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
- GAFL, INRAE, 84140, Montfavet, France
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | | | - Marco Bink
- Biometris, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Hendrix Genetics Research, Technology and Services B.V., PO Box 114, 5830AC, Boxmeer, The Netherlands
| | - Caroline Denancé
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Charles-Eric Durel
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Carolina Font I Forcada
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Celia M Cantin
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
- ARAID (Fundación Aragonesa para la Investigación y el Desarrollo), 50018, Zaragoza, Spain
| | | | - Nicholas P Howard
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA
- Institute of Biology and Environmental Sciences, University of Oldenburg, 26129, Oldenburg, Germany
| | - Beat Keller
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | | | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, RG6 6AR, Reading, UK
| | - Marijn Rymenants
- Better3fruit N.V., 3202, Rillaar, Belgium
- Biometris, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Laboratory for Plant Genetics and Crop Improvement, KU Leuven, B-3001, Leuven, Belgium
| | - Nadia Sanin
- Research Centre Laimburg, 39040, Auer, Italy
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Edward Zurawicz
- Research Institute of Horticulture, 96-100, Skierniewice, Poland
| | - François Laurens
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Andrea Patocchi
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | - Hélène Muranty
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France.
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Frey LA, Baumann P, Aasen H, Studer B, Kölliker R. A Non-destructive Method to Quantify Leaf Starch Content in Red Clover. Front Plant Sci 2020; 11:569948. [PMID: 33178239 PMCID: PMC7593268 DOI: 10.3389/fpls.2020.569948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
Grassland-based ruminant livestock production provides a sustainable alternative to intensive production systems relying on concentrated feeds. However, grassland-based roughage often lacks the energy content required to meet the productivity potential of modern livestock breeds. Forage legumes, such as red clover, with increased starch content could partly replace maize and cereal supplements. However, breeding for increased starch content requires efficient phenotyping methods. This study is unique in evaluating a non-destructive hyperspectral imaging approach to estimate leaf starch content in red clover for enabling efficient development of high starch red clover genotypes. We assessed prediction performance of partial least square regression models (PLSR) using cross-validation, and validated model performance with an independent test set under controlled conditions. Starch content of the training set ranged from 0.1 to 120.3 mg g-1 DW. The best cross-validated PLSR model explained 56% of the measured variation and yielded a root mean square error (RMSE) of 17 mg g-1 DW. Model performance decreased when applying the trained model on the independent test set (RMSE = 29 mg g-1 DW, R 2 = 0.36). Different variable selection methods did not increase model performance. Once validated in the field, the non-destructive spectral method presented here has the potential to detect large differences in leaf starch content of red clover genotypes. Breeding material could be sampled and selected according to their starch content without destroying the plant.
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Affiliation(s)
- Lea Antonia Frey
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Philipp Baumann
- Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Helge Aasen
- Crop Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
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30
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Keller B, Ariza-Suarez D, de la Hoz J, Aparicio JS, Portilla-Benavides AE, Buendia HF, Mayor VM, Studer B, Raatz B. Genomic Prediction of Agronomic Traits in Common Bean ( Phaseolus vulgaris L.) Under Environmental Stress. Front Plant Sci 2020; 11:1001. [PMID: 32774338 PMCID: PMC7381332 DOI: 10.3389/fpls.2020.01001] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/18/2020] [Indexed: 05/19/2023]
Abstract
In plant and animal breeding, genomic prediction models are established to select new lines based on genomic data, without the need for laborious phenotyping. Prediction models can be trained on recent or historic phenotypic data and increasingly available genotypic data. This enables the adoption of genomic selection also in under-used legume crops such as common bean. Beans are an important staple food in the tropics and mainly grown by smallholders under limiting environmental conditions such as drought or low soil fertility. Therefore, genotype-by-environment interactions (G × E) are an important consideration when developing new bean varieties. However, G × E are often not considered in genomic prediction models nor are these models implemented in current bean breeding programs. Here we show the prediction abilities of four agronomic traits in common bean under various environmental stresses based on twelve field trials. The dataset includes 481 elite breeding lines characterized by 5,820 SNP markers. Prediction abilities over all twelve trials ranged between 0.6 and 0.8 for yield and days to maturity, respectively, predicting new lines into new seasons. In all four evaluated traits, the prediction abilities reached about 50-80% of the maximum accuracies given by phenotypic correlations and heritability. Predictions under drought and low phosphorus stress were up to 10 and 20% improved when G × E were included in the model, respectively. Our results demonstrate the potential of genomic selection to increase the genetic gain in common bean breeding. Prediction abilities improved when more phenotypic data was available and G × E could be accounted for. Furthermore, the developed models allowed us to predict genotypic performance under different environmental stresses. This will be a key factor in the development of common bean varieties adapted to future challenging conditions.
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Affiliation(s)
- Beat Keller
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Daniel Ariza-Suarez
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Juan de la Hoz
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Johan Steven Aparicio
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Hector Fabio Buendia
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Victor Manuel Mayor
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Bodo Raatz
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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31
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Loera-Sánchez M, Studer B, Kölliker R. DNA barcode trnH-psbA is a promising candidate for efficient identification of forage legumes and grasses. BMC Res Notes 2020; 13:35. [PMID: 31952556 PMCID: PMC6969398 DOI: 10.1186/s13104-020-4897-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/08/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Grasslands are widespread ecosystems that fulfil many functions. Plant species richness (PSR) is known to have beneficial effects on such functions and monitoring PSR is crucial for tracking the effects of land use and agricultural management on these ecosystems. Unfortunately, traditional morphology-based methods are labor-intensive and cannot be adapted for high-throughput assessments. DNA barcoding could aid increasing the throughput of PSR assessments in grasslands. In this proof-of-concept work, we aimed at determining which of three plant DNA barcodes (rbcLa, matK and trnH-psbA) best discriminates 16 key grass and legume species common in temperate sub-alpine grasslands. RESULTS Barcode trnH-psbA had a 100% correct assignment rate (CAR) in the five analyzed legumes, followed by rbcLa (93.3%) and matK (55.6%). Barcode trnH-psbA had a 100% CAR in the grasses Cynosurus cristatus, Dactylis glomerata and Trisetum flavescens. However, the closely related Festuca, Lolium and Poa species were not always correctly identified, which led to an overall CAR in grasses of 66.7%, 50.0% and 46.4% for trnH-psbA, matK and rbcLa, respectively. Barcode trnH-psbA is thus the most promising candidate for PSR assessments in permanent grasslands and could greatly support plant biodiversity monitoring on a larger scale.
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Affiliation(s)
- Miguel Loera-Sánchez
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland.
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Jaškūnė K, Aleliūnas A, Statkevičiūtė G, Kemešytė V, Studer B, Yates S. Genome-Wide Association Study to Identify Candidate Loci for Biomass Formation Under Water Deficit in Perennial Ryegrass. Front Plant Sci 2020; 11:570204. [PMID: 33519834 PMCID: PMC7841438 DOI: 10.3389/fpls.2020.570204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 11/12/2020] [Indexed: 05/21/2023]
Abstract
Global warming is predicted to impact many agricultural areas, which will suffer from reduced water availability. Due to precipitation changes, mild summer droughts are expected to become more frequent, even in temperate regions. For perennial ryegrass (Lolium perenne L.), an important forage grass of the Poaceae family, leaf growth is a crucial factor determining biomass accumulation and hence forage yield. Although leaf elongation has been shown to be temperature-dependent under normal conditions, the genetic regulation of leaf growth under water deficit in perennial ryegrass is poorly understood. Herein, we evaluated the response to water deprivation in a diverse panel of perennial ryegrass genotypes, employing a high-precision phenotyping platform. The study revealed phenotypic variation for growth-related traits and significant (P < 0.05) differences in leaf growth under normal conditions within the subgroups of turf and forage type cultivars. The phenotypic data was combined with genotypic variants identified using genotyping-by-sequencing to conduct a genome-wide association study (GWAS). Using GWAS, we identified DNA polymorphisms significantly associated with leaf growth reduction under water deprivation. These polymorphisms were adjacent to genes predicted to encode for phytochrome B and a MYB41 transcription factor. The result obtained in the present study will increase our understanding on the complex molecular mechanisms involved in plant growth under water deficit. Moreover, the single nucleotide polymorphism (SNP) markers identified will serve as a valuable resource in future breeding programs to select for enhanced biomass formation under mild summer drought conditions.
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Affiliation(s)
- Kristina Jaškūnė
- Laboratory of Genetics and Physiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
- *Correspondence: Kristina Jaškūnė, ;
| | - Andrius Aleliūnas
- Laboratory of Genetics and Physiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Gražina Statkevičiūtė
- Laboratory of Genetics and Physiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Vilma Kemešytė
- Department of Grass Breeding, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Bruno Studer
- Department of Environmental Systems Science, Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Steven Yates
- Department of Environmental Systems Science, Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Steven Yates,
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Nay MM, Mukankusi CM, Studer B, Raatz B. Haplotypes at the Phg-2 Locus Are Determining Pathotype-Specificity of Angular Leaf Spot Resistance in Common Bean. Front Plant Sci 2019; 10:1126. [PMID: 31572421 PMCID: PMC6753878 DOI: 10.3389/fpls.2019.01126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/15/2019] [Indexed: 05/11/2023]
Abstract
Angular leaf spot (ALS) is one of the most devastating diseases of common bean (Phaseolus vulgaris L.) and causes serious yield losses worldwide. ALS resistance is reportedly pathotype-specific, but little is known about the efficacy of resistance loci against different pathotypes. Here, we report on ALS resistance evaluations of 316 bean lines under greenhouse and field conditions at multiple sites in Colombia and Uganda. Surprisingly, genome-wide association studies revealed only two of the five previously described resistance loci to be significantly associated with ALS resistance. Phg-2 on chromosome eight was crucial for ALS resistance in all trials, while the resistance locus Phg-4 on chromosome 4 was effective against one particular pathotype. Further dissection of Phg-2 uncovered an unprecedented diversity of functional haplotypes for a resistance locus in common bean. DNA sequence-based clustering identified eleven haplotype groups at Phg-2. One haplotype group conferred broad-spectrum ALS resistance, six showed pathotype-specific effects, and the remaining seven did not exhibit clear resistance patterns. Our research highlights the importance of ALS pathotype-specificity for durable resistance management strategies in common bean. Molecular markers co-segregating with resistance loci and haplotypes will increase breeding efficiency for ALS resistance and allow to react faster to future changes in pathogen pressure and composition.
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Affiliation(s)
- Michelle M. Nay
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Clare M. Mukankusi
- Bean Program, International Center for Tropical Agriculture (CIAT), Kampala, Uganda
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Bodo Raatz
- Bean Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Veeckman E, Van Glabeke S, Haegeman A, Muylle H, van Parijs FRD, Byrne SL, Asp T, Studer B, Rohde A, Roldán-Ruiz I, Vandepoele K, Ruttink T. Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne). DNA Res 2019; 26:1-12. [PMID: 30325414 PMCID: PMC6379033 DOI: 10.1093/dnares/dsy033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 06/26/2018] [Accepted: 09/06/2018] [Indexed: 11/13/2022] Open
Abstract
Revealing DNA sequence variation within the Lolium perenne genepool is important for genetic analysis and development of breeding applications. We reviewed current literature on plant development to select candidate genes in pathways that control agronomic traits, and identified 503 orthologues in L. perenne. Using targeted resequencing, we constructed a comprehensive catalogue of genomic variation for a L. perenne germplasm collection of 736 genotypes derived from current cultivars, breeding material and wild accessions. To overcome challenges of variant calling in heterogeneous outbreeding species, we used two complementary strategies to explore sequence diversity. First, four variant calling pipelines were integrated with the VariantMetaCaller to reach maximal sensitivity. Additional multiplex amplicon sequencing was used to empirically estimate an appropriate precision threshold. Second, a de novo assembly strategy was used to reconstruct divergent alleles for each gene. The advantage of this approach was illustrated by discovery of 28 novel alleles of LpSDUF247, a polymorphic gene co-segregating with the S-locus of the grass self-incompatibility system. Our approach is applicable to other genetically diverse outbreeding species. The resulting collection of functionally annotated variants can be mined for variants causing phenotypic variation, either through genetic association studies, or by selecting carriers of rare defective alleles for physiological analyses.
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Affiliation(s)
- Elisabeth Veeckman
- ILVO, Plant Sciences Unit, B Melle, Belgium.,Bioinformatics Institute Ghent, Ghent University, B Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, B Ghent, Belgium
| | | | | | | | | | | | - Torben Asp
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Center Flakkebjerg Aarhus University, DK Slagelse, Denmark
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, CH Zurich, Switzerland
| | | | - Isabel Roldán-Ruiz
- ILVO, Plant Sciences Unit, B Melle, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, B Ghent, Belgium
| | - Klaas Vandepoele
- Bioinformatics Institute Ghent, Ghent University, B Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, B Ghent, Belgium.,Center for Plant Systems Biology, VIB, B Ghent, Belgium
| | - Tom Ruttink
- ILVO, Plant Sciences Unit, B Melle, Belgium.,Bioinformatics Institute Ghent, Ghent University, B Ghent, Belgium
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35
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Knorst V, Byrne S, Yates S, Asp T, Widmer F, Studer B, Kölliker R. Pooled DNA sequencing to identify SNPs associated with a major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.). Theor Appl Genet 2019; 132:947-958. [PMID: 30506318 PMCID: PMC6449324 DOI: 10.1007/s00122-018-3250-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/23/2018] [Indexed: 05/27/2023]
Abstract
SNPs and candidate genes associated with bacterial wilt resistance in Italian ryegrass were identified by sequencing the parental plants and pooled F1 progeny of a segregating population. Italian ryegrass (Lolium multiflorum Lam.) is one of the most important forage grass species in temperate regions. Its yield, quality and persistency can significantly be reduced by bacterial wilt, a serious disease caused by Xanthomonas translucens pv. graminis. Although a major QTL for bacterial wilt resistance has previously been reported, detailed knowledge on underlying genes and DNA markers to allow for efficient resistance breeding strategies is currently not available. We used pooled DNA sequencing to characterize a major QTL for bacterial wilt resistance of Italian ryegrass and to develop inexpensive sequence-based markers to efficiently target resistance alleles for marker-assisted recurrent selection. From the mapping population segregating for the QTL, DNA of 44 of the most resistant and 44 of the most susceptible F1 individuals was pooled and sequenced using the Illumina HiSeq 2000 platform. Allele frequencies of 18 × 106 single nucleotide polymorphisms (SNP) were determined in the resistant and susceptible pool. A total of 271 SNPs on 140 scaffold sequences of the reference parental genome showed significantly different allele frequencies in both pools. We converted 44 selected SNPs to KASP™ markers, genetically mapped these proximal to the major QTL and thus validated their association with bacterial wilt resistance. This study highlights the power of pooled DNA sequencing to efficiently target binary traits in biparental mapping populations. It delivers genome sequence data, SNP markers and potential candidate genes which will allow to implement marker-assisted strategies to fix bacterial wilt resistance in outcrossing breeding populations of Italian ryegrass.
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Affiliation(s)
- Verena Knorst
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Stephen Byrne
- Crops Science Department, Teagasc, Oak Park, Carlow, R93 XE12, Ireland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland
| | - Torben Asp
- Department of Molecular Biology and Genetics, Section for Crop Genetics and Biotechnology, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Franco Widmer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland.
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland.
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36
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Yates S, Jaškūnė K, Liebisch F, Nagelmüller S, Kirchgessner N, Kölliker R, Walter A, Brazauskas G, Studer B. Phenotyping a Dynamic Trait: Leaf Growth of Perennial Ryegrass Under Water Limiting Conditions. Front Plant Sci 2019; 10:344. [PMID: 30967891 PMCID: PMC6440318 DOI: 10.3389/fpls.2019.00344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 03/05/2019] [Indexed: 05/30/2023]
Abstract
Water limitation is one of the major factors reducing crop productivity worldwide. In order to develop efficient breeding strategies to improve drought tolerance, accurate methods to identify when a plant reduces growth as a consequence of water deficit have yet to be established. In perennial ryegrass (Lolium perenne L.), an important forage grass of the Poaceae family, leaf elongation is a key factor determining plant growth and hence forage yield. Although leaf elongation has been shown to be temperature-dependent under non-stress conditions, the impact of water limitation on leaf elongation in perennial ryegrass is poorly understood. We describe a method for quantifying tolerance to water deficit based on leaf elongation in relation to temperature and soil moisture in perennial ryegrass. With decreasing soil moisture, three growth response phases were identified: first, a "normal" phase where growth is mainly determined by temperature, second a "slow" phase where leaf elongation decreases proportionally to soil water potential and third an "arrest" phase where leaf growth terminates. A custom R function was able to quantify the points which demarcate these phases and can be used to describe the response of plants to water deficit. Applied to different perennial ryegrass genotypes, this function revealed significant genotypic variation in the response of leaf growth to temperature and soil moisture. Dynamic phenotyping of leaf elongation can be used as a tool to accurately quantify tolerance to water deficit in perennial ryegrass and to improve this trait by breeding. Moreover, the tools presented here are applicable to study the plant response to other stresses in species with linear, graminoid leaf morphology.
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Affiliation(s)
- Steven Yates
- Molecular Plant Breeding, Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Kristina Jaškūnė
- Laboratory of Genetics and Physiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Frank Liebisch
- Crop Science, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Sebastian Nagelmüller
- Crop Science, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Norbert Kirchgessner
- Crop Science, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Achim Walter
- Crop Science, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Gintaras Brazauskas
- Laboratory of Genetics and Physiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Bruno Studer
- Molecular Plant Breeding, Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
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Wille L, Messmer MM, Studer B, Hohmann P. Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes. Plant Cell Environ 2019; 42:20-40. [PMID: 29645277 DOI: 10.1111/pce.13214] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [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: 12/31/2017] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 05/19/2023]
Abstract
Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant-microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant-associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant-microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil-borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere-related traits, (c) the role of root exudation in microbe-mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.
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Affiliation(s)
- Lukas Wille
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), 5070, Frick, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, 8092, Zurich, Switzerland
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), 5070, Frick, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, 8092, Zurich, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), 5070, Frick, Switzerland
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38
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Yates S, Mikaberidze A, Krattinger SG, Abrouk M, Hund A, Yu K, Studer B, Fouche S, Meile L, Pereira D, Karisto P, McDonald BA. Precision Phenotyping Reveals Novel Loci for Quantitative Resistance to Septoria Tritici Blotch. Plant Phenomics 2019; 2019:3285904. [PMID: 33313526 PMCID: PMC7706307 DOI: 10.34133/2019/3285904] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/02/2019] [Indexed: 05/19/2023]
Abstract
Accurate, high-throughput phenotyping for quantitative traits is a limiting factor for progress in plant breeding. We developed an automated image analysis to measure quantitative resistance to septoria tritici blotch (STB), a globally important wheat disease, enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance. 335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen population. More than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform the GWAS. We identified 26 chromosome intervals explaining 1.9-10.6% of the variance associated with four independent resistance traits. Sixteen of the intervals overlapped with known STB resistance intervals, suggesting that our phenotyping approach can identify simultaneously (i.e., in a single experiment) many previously defined STB resistance intervals. Seventeen of the intervals were less than 5 Mbp in size and encoded only 173 genes, including many genes associated with disease resistance. Five intervals contained four or fewer genes, providing high priority targets for functional validation. Ten chromosome intervals were not previously associated with STB resistance, perhaps representing resistance to pathogen strains that had not been tested in earlier experiments. The SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance genes. Our experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance.
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Affiliation(s)
- Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Alexey Mikaberidze
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Simon G. Krattinger
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Michael Abrouk
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Andreas Hund
- Crop Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Kang Yu
- Crop Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Simone Fouche
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Lukas Meile
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Danilo Pereira
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Petteri Karisto
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Bruce A. McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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Begheyn RF, Yates SA, Sykes T, Studer B. Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass ( Lolium perenne L.). G3 (Bethesda) 2018; 8:1897-1908. [PMID: 29626084 PMCID: PMC5982819 DOI: 10.1534/g3.117.300550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/29/2018] [Indexed: 01/17/2023]
Abstract
Immature pollen can be induced to switch developmental pathways from gametogenesis to embryogenesis and subsequently regenerate into homozygous, diploid plants. Such androgenic production of doubled haploids is particularly useful for species where inbreeding is hampered by effective self-incompatibility systems. Therefore, increasing the generally low androgenic capacity of perennial ryegrass (Lolium perenne L.) germplasm would enable the efficient production of homozygous plant material, so that a more effective exploitation of heterosis through hybrid breeding schemes can be realized. Here, we present the results of a genome-wide association study in a heterozygous, multiparental population of perennial ryegrass (n = 391) segregating for androgenic capacity. Genotyping-by-sequencing was used to interrogate gene- dense genomic regions and revealed over 1,100 polymorphic sites. Between one and 10 quantitative trait loci (QTL) were identified for anther response, embryo and total plant production, green and albino plant production and regeneration. Most traits were under polygenic control, although a major QTL on linkage group 5 was associated with green plant regeneration. Distinct genetic factors seem to affect green and albino plant recovery. Two intriguing candidate genes, encoding chromatin binding domains of the developmental phase transition regulator, Polycomb Repressive Complex 2, were identified. Our results shed the first light on the molecular mechanisms behind perennial ryegrass microspore embryogenesis and enable marker-assisted introgression of androgenic capacity into recalcitrant germplasm of this forage crop of global significance.
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Affiliation(s)
- Rachel F Begheyn
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Steven A Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Timothy Sykes
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
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Do Canto J, Studer B, Frei U, Lübberstedt T. Fine mapping a self-fertility locus in perennial ryegrass. Theor Appl Genet 2018; 131:817-827. [PMID: 29247258 DOI: 10.1007/s00122-017-3038-6] [Citation(s) in RCA: 4] [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: 08/02/2017] [Accepted: 12/11/2017] [Indexed: 05/25/2023]
Abstract
A self-fertility locus was fine mapped to a 1.6 cM region on linkage group 5 in a perennial ryegrass population. This locus was the main determinant of pollen self-compatibility. In grasses, self-incompatibility (SI) is characterized by a two-loci gametophytic (S and Z) mechanism acting together in the recognition and inhibition of self-pollen. Mutations affecting the expression of SI have been reported in a few grass species. In perennial ryegrass (Lolium perenne L.), a mutation independent from S and Z, and mapping on linkage group 5 (LG 5), was previously reported to produce self-fertile plants. Here, we describe fine mapping of the self-fertility (SF) gene in a perennial ryegrass population and determine whether there is any effect of other genomic regions on the pollen compatibility. The phenotypic segregation of SF showed a bimodal distribution with one mean at 49% pollen compatibility and the other at 91%. Marker-trait association analysis showed that only markers on LG 5 were significantly associated with the trait. A single gene model explained 82% of the observed variability and no effects of the other regions were detected. Using segregation and linkage analysis, the SF locus was located to a 1.6 cM region on LG 5. The flanking marker sequences were aligned to rice and Brachypodium distachyon reference genomes to estimate the physical distance. We provide markers tightly linked to SF that can be used for introgression of this trait into advanced breeding germplasm. Moreover, our results represent a further step towards the identification of the SF gene in LG 5.
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Affiliation(s)
- Javier Do Canto
- Department of Agronomy, Iowa State University, 1204 Agronomy Hall, Ames, IA, 50011‑1010, USA.
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Tacuarembó, Ruta 5 km 386, Tacuarembó, Uruguay.
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Ursula Frei
- Department of Agronomy, Iowa State University, 1204 Agronomy Hall, Ames, IA, 50011‑1010, USA
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University, 1204 Agronomy Hall, Ames, IA, 50011‑1010, USA
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Leng P, Ji Q, Asp T, Frei UK, Ingvardsen CR, Xing Y, Studer B, Redinbaugh M, Jones M, Gajjar P, Liu S, Li F, Pan G, Xu M, Lübberstedt T. Auxin Binding Protein 1 Reinforces Resistance to Sugarcane Mosaic Virus in Maize. Mol Plant 2017; 10:1357-1360. [PMID: 28827193 DOI: 10.1016/j.molp.2017.07.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 07/08/2017] [Accepted: 07/31/2017] [Indexed: 05/21/2023]
Affiliation(s)
- Pengfei Leng
- National Maize Improvement Center, China Agricultural University, Beijing 100193, China; Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Qing Ji
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Torben Asp
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Ursula K Frei
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Christina R Ingvardsen
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Bruno Studer
- Institute of Agricultural Sciences, Molecular Plant Breeding, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Margaret Redinbaugh
- USDA, Agricultural Research Service, Corn, Soybean and Wheat Quality Research Unit and Department of Plant Pathology, Ohio State University, Wooster, OH 44691, USA
| | - Mark Jones
- USDA, Agricultural Research Service, Corn, Soybean and Wheat Quality Research Unit and Department of Plant Pathology, Ohio State University, Wooster, OH 44691, USA
| | - Priyanka Gajjar
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Sisi Liu
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA; Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Fei Li
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA; School of Life Sciences, Guizhou Normal University, Laboratory of Plant Physiology and Developmental Regulation, Guiyang 550000, China
| | - Guangtang Pan
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingliang Xu
- National Maize Improvement Center, China Agricultural University, Beijing 100193, China.
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Sykes T, Yates S, Nagy I, Asp T, Small I, Studer B. In Silico Identification of Candidate Genes for Fertility Restoration in Cytoplasmic Male Sterile Perennial Ryegrass (Lolium perenne L.). Genome Biol Evol 2017; 9:351-362. [PMID: 26951780 PMCID: PMC5499803 DOI: 10.1093/gbe/evw047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2016] [Indexed: 12/24/2022] Open
Abstract
Perennial ryegrass (Lolium perenne L.) is widely used for forage production in both permanent and temporary grassland systems. To increase yields in perennial ryegrass, recent breeding efforts have been focused on strategies to more efficiently exploit heterosis by hybrid breeding. Cytoplasmic male sterility (CMS) is a widely applied mechanism to control pollination for commercial hybrid seed production and although CMS systems have been identified in perennial ryegrass, they are yet to be fully characterized. Here, we present a bioinformatics pipeline for efficient identification of candidate restorer of fertility (Rf) genes for CMS. From a high-quality draft of the perennial ryegrass genome, 373 pentatricopeptide repeat (PPR) genes were identified and classified, further identifying 25 restorer of fertility-like PPR (RFL) genes through a combination of DNA sequence clustering and comparison to known Rf genes. This extensive gene family was targeted as the majority of Rf genes in higher plants are RFL genes. These RFL genes were further investigated by phylogenetic analyses, identifying three groups of perennial ryegrass RFLs. These three groups likely represent genomic regions of active RFL generation and identify the probable location of perennial ryegrass PPR-Rf genes. This pipeline allows for the identification of candidate PPR-Rf genes from genomic sequence data and can be used in any plant species. Functional markers for PPR-Rf genes will facilitate map-based cloning of Rf genes and enable the use of CMS as an efficient tool to control pollination for hybrid crop production.
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Affiliation(s)
- Timothy Sykes
- Institute of Agricultural Sciences, Forage Crop Genetics, ETH Zurich, Zurich, Switzerland
| | - Steven Yates
- Institute of Agricultural Sciences, Forage Crop Genetics, ETH Zurich, Zurich, Switzerland
| | - Istvan Nagy
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Torben Asp
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Ian Small
- Plant Energy Biology, ARC Centre of Excellence, the University of Western Australia, Crawley, Western Australia, Australia
| | - Bruno Studer
- Institute of Agricultural Sciences, Forage Crop Genetics, ETH Zurich, Zurich, Switzerland
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Thorogood D, Yates S, Manzanares C, Skot L, Hegarty M, Blackmore T, Barth S, Studer B. A Novel Multivariate Approach to Phenotyping and Association Mapping of Multi-Locus Gametophytic Self-Incompatibility Reveals S, Z, and Other Loci in a Perennial Ryegrass (Poaceae) Population. Front Plant Sci 2017; 8:1331. [PMID: 28824669 PMCID: PMC5539123 DOI: 10.3389/fpls.2017.01331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/17/2017] [Indexed: 05/18/2023]
Abstract
Self-incompatibility (SI) is a mechanism that many flowering plants employ to prevent fertilisation by self- and self-like pollen ensuring heterozygosity and hybrid vigour. Although a number of single locus mechanisms have been characterised in detail, no multi-locus systems have been fully elucidated. Historically, examples of the genetic analysis of multi-locus SI, to make analysis tractable, are either made on the progeny of bi-parental crosses, where the number of alleles at each locus is restricted, or on crosses prepared in such a way that only one of the SI loci segregates. Perennial ryegrass (Lolium perenne L.) possesses a well-documented two locus (S and Z) gametophytic incompatibility system. A more universal, realistic proof of principle study was conducted in a perennial ryegrass population in which allelic and non-allelic diversity was not artificially restricted. A complex pattern of pollinations from a diallel cross was revealed which could not possibly be interpreted easily per se, even with an already established genetic model. Instead, pollination scores were distilled into principal component scores described as Compatibility Components (CC1-CC3). These were then subjected to a conventional genome-wide association analysis. CC1 associated with markers on linkage groups (LGs) 1, 2, 3, and 6, CC2 exclusively with markers in a genomic region on LG 2, and CC3 with markers on LG 1. BLAST alignment with the Brachypodium physical map revealed highly significantly associated markers with peak associations with genes adjacent and four genes away from the chromosomal locations of candidate SI genes, S- and Z-DUF247, respectively. Further significant associations were found in a Brachypodium distachyon chromosome 3 region, having shared synteny with Lolium LG 1, suggesting further SI loci linked to S or extensive micro-re-arrangement of the genome between B. distachyon and L. perenne. Significant associations with gene sequences aligning with marker sequences on Lolium LGs 3 and 6 were also identified. We therefore demonstrate the power of a novel association genetics approach to identify the genes controlling multi-locus gametophytic SI systems and to identify novel loci potentially involved in already established SI systems.
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Affiliation(s)
- Daniel Thorogood
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
- *Correspondence: Daniel Thorogood
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH ZurichZurich, Switzerland
| | - Chloé Manzanares
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH ZurichZurich, Switzerland
| | - Leif Skot
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Matthew Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Tina Blackmore
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Susanne Barth
- Teagasc Crops Environment and Land Use Programme, Oak Park Research CentreCarlow, Ireland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH ZurichZurich, Switzerland
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Malisch CS, Salminen JP, Kölliker R, Engström MT, Suter D, Studer B, Lüscher A. Drought Effects on Proanthocyanidins in Sainfoin (Onobrychis viciifolia Scop.) Are Dependent on the Plant's Ontogenetic Stage. J Agric Food Chem 2016; 64:9307-9316. [PMID: 27960281 DOI: 10.1021/acs.jafc.6b02342] [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] [Indexed: 05/15/2023]
Abstract
Sainfoin (Onobrychis viciifolia Scop.) is a forage legume, which improves animal health and the environmental impact of livestock farming due to its proanthocyanidin content. To identify the impact of drought on acetone/water-extractable proanthocyanidin (PA) concentration and composition in the generative and vegetative stages, a rain exclosure experiment was established. Leaves of 120 plants from 5 different sainfoin accessions were sampled repeatedly and analyzed by UPLC-ESI-MS/MS. The results showed distinct differences in response to drought between vegetative and generative plants. Whereas vegetative plants showed a strong response to drought in growth (-56%) and leaf PA concentration (+46%), generative plants showed no response in growth (-2%) or PA concentration (-9%). The PA composition was stable across environments. The five accessions varied in PA concentrations and composition but showed the same pattern of response to the experimental treatments. These results show that the ontogenetic stage at which drought occurs significantly affects the plant's response.
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Affiliation(s)
- Carsten S Malisch
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich , 8092 Zurich, Switzerland
| | - Juha-Pekka Salminen
- Laboratory of Organic Chemistry and Chemical Biology, Department of Chemistry, University of Turku , 20500 Turku, Finland
| | | | - Marica T Engström
- Laboratory of Organic Chemistry and Chemical Biology, Department of Chemistry, University of Turku , 20500 Turku, Finland
| | | | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich , 8092 Zurich, Switzerland
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Stočes Š, Ruttink T, Bartoš J, Studer B, Yates S, Zwierzykowski Z, Abrouk M, Roldán-Ruiz I, Książczyk T, Rey E, Doležel J, Kopecký D. Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-Nucleotide Polymorphism Discovery. Plant Genome 2016; 9. [PMID: 27902806 DOI: 10.3835/plantgenome2016.02.0017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) represent natural DNA sequence variation. They can be used for various applications including the construction of high-density genetic maps, analysis of genetic variability, genome-wide association studies, and map-based cloning. Here we report on transcriptome sequencing in the two forage grasses, meadow fescue ( Huds.) and Italian ryegrass ( Lam.), and identification of various classes of SNPs. Using the Orthology Guided Assembly (OGA) strategy, we assembled and annotated a total of 18,952 and 19,036 transcripts for Italian ryegrass and meadow fescue, respectively. In addition, we used transcriptome sequence data of perennial ryegrass ( L.) from a previous study to identify 16,613 transcripts shared across all three species. Large numbers of intraspecific SNPs were identified in all three species: 248,000 in meadow fescue, 715,000 in Italian ryegrass, and 529,000 in perennial ryegrass. Moreover, we identified almost 25,000 interspecific SNPs located in 5343 genes that can distinguish meadow fescue from Italian ryegrass and 15,000 SNPs located in 3976 genes that discriminate meadow fescue from both species. All identified SNPs were positioned in silico on the seven linkage groups (LGs) of using the GenomeZipper approach. With the identification and positioning of interspecific SNPs, our study provides a valuable resource for the grass research and breeding community and will enable detailed characterization of genomic composition and gene expression analysis in prospective × hybrids.
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Do Canto J, Studer B, Lubberstedt T. Overcoming self-incompatibility in grasses: a pathway to hybrid breeding. Theor Appl Genet 2016; 129:1815-29. [PMID: 27577253 DOI: 10.1007/s00122-016-2775-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/24/2016] [Indexed: 05/24/2023]
Abstract
Allogamous grasses exhibit an effective two-locus gametophytic self-incompatibility (SI) system, limiting the range of breeding techniques applicable for cultivar development. Current breeding methods based on populations are characterized by comparably low genetic gains for important traits such as biomass yield. To implement more efficient breeding schemes, the overall understanding of the SI system is crucial as are the mechanisms involved in the breakdown of SI. Self-fertile variants in outcrossing grasses have been studied, and the current level of knowledge includes approximate gene locations, linked molecular markers and first hypotheses on their mode of action. Environmental conditions increasing seed set upon self-pollination have also been described. Even though some strategies were proposed to take advantage of self-fertility, there have, so far, not been changes in the methods applied in cultivar development for allogamous grasses. In this review, we describe the current knowledge about self-fertility in allogamous grasses and outline strategies to incorporate this trait for implementation in synthetic and hybrid breeding schemes.
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Affiliation(s)
- Javier Do Canto
- Department of Agronomy, Iowa State University, 2104 Agronomy Hall, Ames, IA, 50011-1010, USA.
- National Institute of Agricultural Research, INIA, Route 5 km 386, Tacuarembo, Uruguay.
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, LFW Building, University Street 2, Zurich, 8092, Switzerland
| | - Thomas Lubberstedt
- Department of Agronomy, Iowa State University, 2104 Agronomy Hall, Ames, IA, 50011-1010, USA
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Abstract
This final chapter deliberates three overarching topics and conclusions of the research presented in this volume: the endurance of the concept of extrinsic vs intrinsic motivation, the importance of considering subjective costs of activities when aiming to understand and enhance motivation, and current knowledge of the neurobiological underpinnings of motivation. Furthermore, three topics for future motivation research are outlined, namely the assessment and determinants of intrinsic benefits, the reconciliation of activity-specific motivation models with generalized motivation impairments in clinical populations, and the motivational dynamics of groups.
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Affiliation(s)
- B Studer
- Mauritius Hospital, Meerbusch, Germany; Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
| | - S Knecht
- Mauritius Hospital, Meerbusch, Germany; Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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Abstract
How can an individual be motivated to perform a target exercise or activity? This question arises in training, therapeutic, and education settings alike, yet despite-or even because of-the large range of extant motivation theories, finding a clear answer to this question can be challenging. Here we propose an application-friendly framework of motivation for a specific activity or exercise that incorporates core concepts from several well-regarded psychological and economic theories of motivation. The key assumption of this framework is that motivation for performing a given activity is determined by the expected benefits and the expected costs of (performance of) the activity. Benefits comprise positive feelings, gains, and rewards experienced during performance of the activity (intrinsic benefits) or achieved through the activity (extrinsic benefits). Costs entail effort requirements, time demands, and other expenditure (intrinsic costs) as well as unwanted associated outcomes and missing out on alternative activities (extrinsic costs). The expected benefits and costs of a given exercise are subjective and state dependent. We discuss convergence of the proposed framework with a selection of extant motivation theories and briefly outline neurobiological correlates of its main components and assumptions. One particular strength of our framework is that it allows to specify five pathways to increasing motivation for a target exercise, which we illustrate and discuss with reference to previous empirical data.
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Affiliation(s)
- B Studer
- Mauritius Hospital, Meerbusch, Germany; Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
| | - S Knecht
- Mauritius Hospital, Meerbusch, Germany; Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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Studer B, Van Dijk H, Handermann R, Knecht S. Increasing self-directed training in neurorehabilitation patients through competition. Prog Brain Res 2016; 229:367-388. [PMID: 27926448 DOI: 10.1016/bs.pbr.2016.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This proof-of-concept study aimed to test whether competition could be a useful tool to increase intensity and amount of self-directed training in neurorehabilitation. Stroke patients undergoing inpatient neurorehabilitation (n=93) conducted self-directed endurance training on a (wheelchair-compatible) bicycle trainer under three experimental conditions: a "Competition" condition and two noncompetition control conditions (repeated randomized within-subject design). Training performance and perceived exertion were recorded and statistically analyzed. Three motivational effects of competition were found. First, competition led to an increase in self-directed training. Patients exercised significantly more intensively under competition than in the two noncompetition control conditions. Second, (winning a) competition had a positive influence on performance in the subsequent training session. Third, training performance was particularly high during rematch competitions; that is to say, during second encounter competitions against an opponent that the patient had just beaten. No systematic effect of competition upon perceived exertion (controlled for training performance) was found. Together, our results demonstrate that competition is a potent motivational tool to increase self-directed training in neurorehabilitation.
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Affiliation(s)
- B Studer
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Mauritius Hospital, Meerbusch, Germany.
| | - H Van Dijk
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | | | - S Knecht
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Mauritius Hospital, Meerbusch, Germany
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50
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Paina C, Byrne SL, Studer B, Rognli OA, Asp T. Using a Candidate Gene-Based Genetic Linkage Map to Identify QTL for Winter Survival in Perennial Ryegrass. PLoS One 2016; 11:e0152004. [PMID: 27010567 PMCID: PMC4807000 DOI: 10.1371/journal.pone.0152004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 03/06/2016] [Indexed: 11/25/2022] Open
Abstract
Important agronomical traits in perennial ryegrass (Lolium perenne) breeding programs such as winter survival and heading date, are quantitative traits that are generally controlled by multiple loci. Individually, these loci have relatively small effects. The aim of this study was to develop a candidate gene based Illumina GoldenGate 1,536-plex assay, containing single nucleotide polymorphism markers designed from transcripts involved in response to cold acclimation, vernalization, and induction of flowering. The assay was used to genotype a mapping population that we have also phenotyped for winter survival to complement the heading date trait previously mapped in this population. A positive correlation was observed between strong vernalization requirement and winter survival, and some QTL for winter survival and heading date overlapped on the genetic map. Candidate genes were located in clusters along the genetic map, some of which co-localized with QTL for winter survival and heading date. These clusters of candidate genes may be used in candidate gene based association studies to identify alleles associated with winter survival and heading date.
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Affiliation(s)
- Cristiana Paina
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Slagelse, Denmark
| | - Stephen L. Byrne
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Slagelse, Denmark
| | - Bruno Studer
- Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Odd Arne Rognli
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Torben Asp
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Slagelse, Denmark
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