1
|
Zhang S, Wu Y, Skaro M, Cheong JH, Bouffier-Landrum A, Torrres I, Guo Y, Stupp L, Lincoln B, Prestel A, Felt C, Spann S, Mandal A, Johnson N, Arnold J. Computer vision models enable mixed linear modeling to predict arbuscular mycorrhizal fungal colonization using fungal morphology. Sci Rep 2024; 14:10866. [PMID: 38740920 DOI: 10.1038/s41598-024-61181-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
The presence of Arbuscular Mycorrhizal Fungi (AMF) in vascular land plant roots is one of the most ancient of symbioses supporting nitrogen and phosphorus exchange for photosynthetically derived carbon. Here we provide a multi-scale modeling approach to predict AMF colonization of a worldwide crop from a Recombinant Inbred Line (RIL) population derived from Sorghum bicolor and S. propinquum. The high-throughput phenotyping methods of fungal structures here rely on a Mask Region-based Convolutional Neural Network (Mask R-CNN) in computer vision for pixel-wise fungal structure segmentations and mixed linear models to explore the relations of AMF colonization, root niche, and fungal structure allocation. Models proposed capture over 95% of the variation in AMF colonization as a function of root niche and relative abundance of fungal structures in each plant. Arbuscule allocation is a significant predictor of AMF colonization among sibling plants. Arbuscules and extraradical hyphae implicated in nutrient exchange predict highest AMF colonization in the top root section. Our work demonstrates that deep learning can be used by the community for the high-throughput phenotyping of AMF in plant roots. Mixed linear modeling provides a framework for testing hypotheses about AMF colonization phenotypes as a function of root niche and fungal structure allocations.
Collapse
Affiliation(s)
- Shufan Zhang
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Yue Wu
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Michael Skaro
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | | | | | - Isaac Torrres
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Yinping Guo
- Genetics Department, University of Georgia, Athens, GA, USA
| | - Lauren Stupp
- Genetics Department, University of Georgia, Athens, GA, USA
| | - Brooke Lincoln
- Genetics Department, University of Georgia, Athens, GA, USA
| | - Anna Prestel
- Genetics Department, University of Georgia, Athens, GA, USA
| | - Camryn Felt
- Genetics Department, University of Georgia, Athens, GA, USA
| | - Sedona Spann
- School of Earth and Sustainability and Department of Biological Sciences, North Arizona University, Flagstaff, AZ, USA
| | - Abhyuday Mandal
- Statistics Department, University of Georgia, Athens, GA, USA
| | - Nancy Johnson
- School of Earth and Sustainability and Department of Biological Sciences, North Arizona University, Flagstaff, AZ, USA
| | - Jonathan Arnold
- Genetics Department, University of Georgia, Athens, GA, USA.
| |
Collapse
|
2
|
Eck JL, Kytöviita M, Laine A. Arbuscular mycorrhizal fungi influence host infection during epidemics in a wild plant pathosystem. THE NEW PHYTOLOGIST 2022; 236:1922-1935. [PMID: 36093733 PMCID: PMC9827988 DOI: 10.1111/nph.18481] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/15/2022] [Indexed: 05/29/2023]
Abstract
While pathogenic and mutualistic microbes are ubiquitous across ecosystems and often co-occur within hosts, how they interact to determine patterns of disease in genetically diverse wild populations is unknown. To test whether microbial mutualists provide protection against pathogens, and whether this varies among host genotypes, we conducted a field experiment in three naturally occurring epidemics of a fungal pathogen, Podosphaera plantaginis, infecting a host plant, Plantago lanceolata, in the Åland Islands, Finland. In each population, we collected epidemiological data on experimental plants from six allopatric populations that had been inoculated with a mixture of mutualistic arbuscular mycorrhizal fungi or a nonmycorrhizal control. Inoculation with arbuscular mycorrhizal fungi increased growth in plants from every population, but also increased host infection rate. Mycorrhizal effects on disease severity varied among host genotypes and strengthened over time during the epidemic. Host genotypes that were more susceptible to the pathogen received stronger protective effects from inoculation. Our results show that arbuscular mycorrhizal fungi introduce both benefits and risks to host plants, and shift patterns of infection in host populations under pathogen attack. Understanding how mutualists alter host susceptibility to disease will be important for predicting infection outcomes in ecological communities and in agriculture.
Collapse
Affiliation(s)
- Jenalle L. Eck
- Department of Evolutionary Biology and Environmental StudiesUniversity of Zurich8057ZurichSwitzerland
| | - Minna‐Maarit Kytöviita
- Department of Biological and Environmental ScienceUniversity of Jyväskylä40014JyväskyläFinland
| | - Anna‐Liisa Laine
- Department of Evolutionary Biology and Environmental StudiesUniversity of Zurich8057ZurichSwitzerland
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental SciencesUniversity of Helsinki00790HelsinkiFinland
| |
Collapse
|
3
|
Arbuscular Mycorrhizal Fungi Increase Nutritional Quality of Soilless Grown Lettuce while Overcoming Low Phosphorus Supply. Foods 2022; 11:foods11223612. [PMID: 36429202 PMCID: PMC9689368 DOI: 10.3390/foods11223612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Lettuce is widely used for its healthy properties, and it is of interest to increase them with minimal environmental impact. The purpose of this work was to evaluate the effect of the arbuscular mycorrhizal fungus (AMF) Funneliformis mosseae in lettuce plants (Lactuca sativa L. cv. Salinas) cultivated in a soilless system with sub-optimal phosphorus (P) compared with non-inoculated controls at two different P concentrations. Results show that lettuce inoculation with the selected AMF can improve the growth and the nutritional quality of lettuce even at sub-optimal P. Leaf content of chlorophylls, carotenoids, and phenols, known as important bioactive compounds for human health, was higher in mycorrhizal lettuce plants compared with non-mycorrhizal plants. The antioxidant capacity in AMF plants showed higher values compared with control plants grown at optimal P nutrition level. Moreover, leaf gas exchanges were higher in inoculated plants than in non-inoculated ones. Nitrogen, P, and magnesium leaf content was significantly higher in mycorrhizal plants compared with non-mycorrhizal plants grown with the same P level. These findings suggest that F. mosseae can stimulate plants growth, improving the nutritional quality of lettuce leaves even when grown with sub-optimal P concentration.
Collapse
|
4
|
Marsh JI, Hu H, Petereit J, Bayer PE, Valliyodan B, Batley J, Nguyen HT, Edwards D. Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1443-1455. [PMID: 35141762 PMCID: PMC9033719 DOI: 10.1007/s00122-022-04045-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/22/2022] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE The major soy protein QTL, cqProt-003, was analysed for haplotype diversity and global distribution, and results indicate 304 bp deletion and variable tandem repeats in protein coding regions are likely causal candidates. Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait-associated region within a 173 kb linkage block was identified, and variants in the region were characterized, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the second exon of gene Glyma.20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304 bp deletion and have identified additional nested variation present in high-protein individuals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximize protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterization and modification.
Collapse
Affiliation(s)
- Jacob I Marsh
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Jakob Petereit
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Babu Valliyodan
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, MO, 65101, USA
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia.
| |
Collapse
|
5
|
Genome-Wide Profiling of Alternative Splicing and Gene Fusion during Rice Black-Streaked Dwarf Virus Stress in Maize (Zea mays L.). Genes (Basel) 2022; 13:genes13030456. [PMID: 35328010 PMCID: PMC8955601 DOI: 10.3390/genes13030456] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 12/26/2022] Open
Abstract
Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease (MRDD), which is a viral disease that significantly affects maize yields worldwide. Plants tolerate stress through transcriptional reprogramming at the alternative splicing (AS), transcriptional, and fusion gene (FG) levels. However, it is unclear whether and how AS and FG interfere with transcriptional reprogramming in MRDD. In this study, we performed global profiling of AS and FG on maize response to RBSDV and compared it with transcriptional changes. There are approximately 1.43 to 2.25 AS events per gene in maize infected with RBSDV. GRMZM2G438622 was only detected in four AS modes (A3SS, A5SS, RI, and SE), whereas GRMZM2G059392 showed downregulated expression and four AS events. A total of 106 and 176 FGs were detected at two time points, respectively, including six differentially expressed genes and five differentially spliced genes. The gene GRMZM2G076798 was the only FG that occurred at two time points and was involved in two FG events. Among these, 104 GOs were enriched, indicating that nodulin-, disease resistance-, and chloroplastic-related genes respond to RBSDV stress in maize. These results provide new insights into the mechanisms underlying post-transcriptional and transcriptional regulation of maize response to RBSDV stress.
Collapse
|
6
|
Thirkell TJ, Grimmer M, James L, Pastok D, Allary T, Elliott A, Paveley N, Daniell T, Field KJ. Variation in mycorrhizal growth response among a spring wheat mapping population shows potential to breed for symbiotic benefit. Food Energy Secur 2022; 11:e370. [PMID: 35865673 PMCID: PMC9286679 DOI: 10.1002/fes3.370] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/09/2021] [Accepted: 12/15/2021] [Indexed: 12/12/2022] Open
Affiliation(s)
- Tom J. Thirkell
- Plants, Photosynthesis and Soil School of Biosciences University of Sheffield Sheffield UK
| | | | | | - Daria Pastok
- School of Biology Centre for Plant Sciences University of Leeds Leeds UK
| | - Théa Allary
- Plants, Photosynthesis and Soil School of Biosciences University of Sheffield Sheffield UK
| | - Ashleigh Elliott
- School of Biology Centre for Plant Sciences University of Leeds Leeds UK
| | | | - Tim Daniell
- Plants, Photosynthesis and Soil School of Biosciences University of Sheffield Sheffield UK
| | - Katie J. Field
- Plants, Photosynthesis and Soil School of Biosciences University of Sheffield Sheffield UK
| |
Collapse
|
7
|
Stahlhut KN, Dowell JA, Temme AA, Burke JM, Goolsby EW, Mason CM. Genetic control of arbuscular mycorrhizal colonization by Rhizophagus intraradices in Helianthus annuus (L.). MYCORRHIZA 2021; 31:723-734. [PMID: 34480215 DOI: 10.1007/s00572-021-01050-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Plant symbiosis with arbuscular mycorrhizal (AM) fungi provides many benefits, including increased nutrient uptake, drought tolerance, and belowground pathogen resistance. To develop a better understanding of the genetic architecture of mycorrhizal symbiosis, we conducted a genome-wide association study (GWAS) of this plant-fungal interaction in cultivated sunflower. A diversity panel of cultivated sunflower (Helianthus annuus L.) was phenotyped for root colonization under inoculation with the AM fungus Rhizophagus intraradices. Using a mixed linear model approach with a high-density genetic map, we identified genomic regions that are likely associated with R. intraradices colonization in sunflower. Additionally, we used a set of twelve diverse lines to assess the effect that inoculation with R. intraradices has on dried shoot biomass and macronutrient uptake. Colonization among lines in the mapping panel ranged from 0-70% and was not correlated with mycorrhizal growth response, shoot phosphorus response, or shoot potassium response among the Core 12 lines. Association mapping yielded three single-nucleotide polymorphisms (SNPs) that were significantly associated with R. intraradices colonization. This is the first study to use GWAS to identify genomic regions associated with AM colonization in an Asterid eudicot species. Three genes of interest identified from the regions containing these SNPs are likely related to plant defense.
Collapse
Affiliation(s)
| | - Jordan A Dowell
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
| | - Andries A Temme
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Eric W Goolsby
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
| | - Chase M Mason
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA.
| |
Collapse
|
8
|
Genetic variability assessment of 127 Triticum turgidum L. accessions for mycorrhizal susceptibility-related traits detection. Sci Rep 2021; 11:13426. [PMID: 34183734 PMCID: PMC8239029 DOI: 10.1038/s41598-021-92837-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Positive effects of arbuscular mycorrhizal fungi (AMF)-wheat plant symbiosis have been well discussed by research, while the actual role of the single wheat genotype in establishing this type of association is still poorly investigated. In this work, the genetic diversity of Triticum turgidum wheats was exploited to detect roots susceptibility to AMF and to identify genetic markers in linkage with chromosome regions involved in this symbiosis. A tetraploid wheat collection of 127 accessions was genotyped using 35K single-nucleotide polymorphism (SNP) array and inoculated with the AMF species Funneliformis mosseae (F. mosseae) and Rhizoglomus irregulare (R. irregulare), and a genome-wide association study (GWAS) was conducted. Six clusters of genetically related accessions were identified, showing a different mycorrhizal colonization among them. GWAS revealed four significant quantitative trait nucleotides (QTNs) involved in mycorrhizal symbiosis, located on chromosomes 1A, 2A, 2B and 6A. The results of this work enrich future breeding activities aimed at developing new grains on the basis of genetic diversity on low or high susceptibility to mycorrhization, and, possibly, maximizing the symbiotic effects.
Collapse
|
9
|
Ramírez-Flores MR, Perez-Limon S, Li M, Barrales-Gamez B, Albinsky D, Paszkowski U, Olalde-Portugal V, Sawers RJH. The genetic architecture of host response reveals the importance of arbuscular mycorrhizae to maize cultivation. eLife 2020; 9:e61701. [PMID: 33211006 PMCID: PMC7676867 DOI: 10.7554/elife.61701] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are ubiquitous in cultivated soils, forming symbiotic relationships with the roots of major crop species. Studies in controlled conditions have demonstrated the potential of AMF to enhance the growth of host plants. However, it is difficult to estimate the actual benefit in the field, not least because of the lack of suitable AMF-free controls. Here we implement a novel strategy using the selective incorporation of AMF-resistance into a genetic mapping population to evaluate maize response to AMF. We found AMF to account for about one-third of the grain production in a medium input field, as well as to affect the relative performance of different plant genotypes. Characterization of the genetic architecture of the host response indicated a trade-off between mycorrhizal dependence and benefit. We identified several QTL linked to host benefit, supporting the feasibility of breeding crops to maximize profit from symbiosis with AMF.
Collapse
Affiliation(s)
- M Rosario Ramírez-Flores
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN)IrapuatoMexico
| | - Sergio Perez-Limon
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN)IrapuatoMexico
| | - Meng Li
- Department of Plant Science, The Pennsylvania State UniversityState CollegeUnited States
| | - Benjamín Barrales-Gamez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN)IrapuatoMexico
| | - Doris Albinsky
- Crop Science Centre and Department of Plant Sciences, University of CambridgeCambridgeUnited Kingdom
| | - Uta Paszkowski
- Crop Science Centre and Department of Plant Sciences, University of CambridgeCambridgeUnited Kingdom
| | - Víctor Olalde-Portugal
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN)IrapuatoMexico
| | - Ruairidh JH Sawers
- Department of Plant Science, The Pennsylvania State UniversityState CollegeUnited States
| |
Collapse
|