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Svendsen ASL, Nielsen LB, Schmidt JB, Bruhn D, Andersen LH, Pertoldi C. eDNA Metabarcoding- and Microscopic Analysis for Diet Determination in Waterfowl, a Comparative Study in Vejlerne, Denmark. BIOLOGY 2023; 12:1272. [PMID: 37759671 PMCID: PMC10525441 DOI: 10.3390/biology12091272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
Understanding diets and structural food webs are keys to the apprehension of ecological communities, upon which conservation and management biology are based. The understanding of grazing and habitat choice for waterfowl is one of the most important topics for avian ecologists today and can, to some degree, be answered by dietary analysis. Droppings collected from four waterfowl, the Eurasian wigeon (Anas penelope), Greylag goose (Anser anser), pink-footed goose (Anser brachyrhynchus) and Barnacle goose (Branta leucopsis) in Vejlerne (Denmark), were analysed microscopically and through eDNA metabarcoding with the use of next generation sequencing (NGS) to accumulate knowledge about the diet of these waterfowl. In total, 120 dropping samples were microscopically analysed, of which the eDNA metabarcoding analysis was done on 79 samples. The prey items were identified according to the taxonomic level of species, and a qualitative method, frequency of occurrence (FO) and FO calculated as a percentage, was used in order to compare the results from the two methods. As neither of the methods was able to encompass all species discovered when combining the two methods, it was concluded in this study that the two methods can support each other in a dietary analysis of waterfowl, but not replace one another.
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Affiliation(s)
- Anna-Sofie Lützhøft Svendsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg Øst, Denmark; (L.B.N.); (J.B.S.); (D.B.); (L.H.A.); (C.P.)
| | - Louise Bach Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg Øst, Denmark; (L.B.N.); (J.B.S.); (D.B.); (L.H.A.); (C.P.)
| | - Jakob Braüner Schmidt
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg Øst, Denmark; (L.B.N.); (J.B.S.); (D.B.); (L.H.A.); (C.P.)
| | - Dan Bruhn
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg Øst, Denmark; (L.B.N.); (J.B.S.); (D.B.); (L.H.A.); (C.P.)
| | - Line Holm Andersen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg Øst, Denmark; (L.B.N.); (J.B.S.); (D.B.); (L.H.A.); (C.P.)
| | - Cino Pertoldi
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg Øst, Denmark; (L.B.N.); (J.B.S.); (D.B.); (L.H.A.); (C.P.)
- Department of Zoology, Aalborg Zoo, Mølleparkvej 63, DK-9000 Aalborg, Denmark
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2
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Ferguson JN, Fernandes SB, Monier B, Miller ND, Allen D, Dmitrieva A, Schmuker P, Lozano R, Valluru R, Buckler ES, Gore MA, Brown PJ, Spalding EP, Leakey ADB. Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. PLANT PHYSIOLOGY 2021; 187:1481-1500. [PMID: 34618065 PMCID: PMC9040483 DOI: 10.1093/plphys/kiab346] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/29/2021] [Indexed: 05/04/2023]
Abstract
Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.
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Affiliation(s)
- John N Ferguson
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Samuel B Fernandes
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Brandon Monier
- Institute for Genomic Diversity, Cornell University, Ithaca, New
York 14853, USA
| | - Nathan D Miller
- Department of Botany, University of Wisconsin, Madison, Wisconsin
53706, USA
| | - Dylan Allen
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Anna Dmitrieva
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Peter Schmuker
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, New York 14853, USA
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, New
York 14853, USA
- Present address: Lincoln Institute for Agri-Food Technology,
University of Lincoln, Lincoln LN2 2LG, UK
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New
York 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, New York 14853, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, New York 14853, USA
| | - Patrick J Brown
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
- Present address: Section of Agricultural Plant Biology,
Department of Plant Sciences, University of California Davis, California 95616,
USA
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin, Madison, Wisconsin
53706, USA
| | - Andrew D B Leakey
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
- Department of Crop Sciences, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
- Department of Plant Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
- Author for communication: ,
Present address: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA,
UK
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3
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Xie J, Fernandes SB, Mayfield-Jones D, Erice G, Choi M, E Lipka A, Leakey ADB. Optical topometry and machine learning to rapidly phenotype stomatal patterning traits for maize QTL mapping. PLANT PHYSIOLOGY 2021; 187:1462-1480. [PMID: 34618057 PMCID: PMC8566313 DOI: 10.1093/plphys/kiab299] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 05/26/2021] [Indexed: 05/03/2023]
Abstract
Stomata are adjustable pores on leaf surfaces that regulate the tradeoff of CO2 uptake with water vapor loss, thus having critical roles in controlling photosynthetic carbon gain and plant water use. The lack of easy, rapid methods for phenotyping epidermal cell traits have limited discoveries about the genetic basis of stomatal patterning. A high-throughput epidermal cell phenotyping pipeline is presented here and used for quantitative trait loci (QTL) mapping in field-grown maize (Zea mays). The locations and sizes of stomatal complexes and pavement cells on images acquired by an optical topometer from mature leaves were automatically determined. Computer estimated stomatal complex density (SCD; R2 = 0.97) and stomatal complex area (SCA; R2 = 0.71) were strongly correlated with human measurements. Leaf gas exchange traits were genetically correlated with the dimensions and proportions of stomatal complexes (rg = 0.39-0.71) but did not correlate with SCD. Heritability of epidermal traits was moderate to high (h2 = 0.42-0.82) across two field seasons. Thirty-six QTL were consistently identified for a given trait in both years. Twenty-four clusters of overlapping QTL for multiple traits were identified, with univariate versus multivariate single marker analysis providing evidence consistent with pleiotropy in multiple cases. Putative orthologs of genes known to regulate stomatal patterning in Arabidopsis (Arabidopsis thaliana) were located within some, but not all, of these regions. This study demonstrates how discovery of the genetic basis for stomatal patterning can be accelerated in maize, a C4 model species where these processes are poorly understood.
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Affiliation(s)
- Jiayang Xie
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Samuel B Fernandes
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Dustin Mayfield-Jones
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Gorka Erice
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Min Choi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Andrew D B Leakey
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Author for communication: , cor2">Present address: Agrotecnologías Naturales S.L., 43762 Tarragona, Spain
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4
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Ferguson JN, Fernandes SB, Monier B, Miller ND, Allen D, Dmitrieva A, Schmuker P, Lozano R, Valluru R, Buckler ES, Gore MA, Brown PJ, Spalding EP, Leakey ADB. Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. PLANT PHYSIOLOGY 2021; 187:1481-1500. [PMID: 34618065 DOI: 10.1093/plphys/kiab34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/29/2021] [Indexed: 05/27/2023]
Abstract
Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.
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Affiliation(s)
- John N Ferguson
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Samuel B Fernandes
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Brandon Monier
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - Nathan D Miller
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Dylan Allen
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Anna Dmitrieva
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Peter Schmuker
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Patrick J Brown
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Andrew D B Leakey
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
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5
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Prakash PT, Banan D, Paul RE, Feldman MJ, Xie D, Freyfogle L, Baxter I, Leakey ADB. Correlation and co-localization of QTL for stomatal density, canopy temperature, and productivity with and without drought stress in Setaria. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5024-5037. [PMID: 33893796 PMCID: PMC8219040 DOI: 10.1093/jxb/erab166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 04/23/2021] [Indexed: 05/04/2023]
Abstract
Mechanistic modeling indicates that stomatal conductance could be reduced to improve water use efficiency (WUE) in C4 crops. Genetic variation in stomatal density and canopy temperature was evaluated in the model C4 genus, Setaria. Recombinant inbred lines (RILs) derived from a Setaria italica×Setaria viridis cross were grown with ample or limiting water supply under field conditions in Illinois. An optical profilometer was used to rapidly assess stomatal patterning, and canopy temperature was measured using infrared imaging. Stomatal density and canopy temperature were positively correlated but both were negatively correlated with total above-ground biomass. These trait relationships suggest a likely interaction between stomatal density and the other drivers of water use such as stomatal size and aperture. Multiple quantitative trait loci (QTL) were identified for stomatal density and canopy temperature, including co-located QTL on chromosomes 5 and 9. The direction of the additive effect of these QTL on chromosome 5 and 9 was in accordance with the positive phenotypic relationship between these two traits. This, along with prior experiments, suggests a common genetic architecture between stomatal patterning and WUE in controlled environments with canopy transpiration and productivity in the field, while highlighting the potential of Setaria as a model to understand the physiology and genetics of WUE in C4 species.
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Affiliation(s)
- Parthiban Thathapalli Prakash
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- International Rice Research Institute, Los Baños, Philippines
| | - Darshi Banan
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rachel E Paul
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Dan Xie
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Luke Freyfogle
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Andrew D B Leakey
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Haus MJ, Li M, Chitwood DH, Jacobs TW. Long-Distance and Trans-Generational Stomatal Patterning by CO 2 Across Arabidopsis Organs. FRONTIERS IN PLANT SCIENCE 2018; 9:1714. [PMID: 30559750 PMCID: PMC6287203 DOI: 10.3389/fpls.2018.01714] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/05/2018] [Indexed: 05/20/2023]
Abstract
Stomata control water loss and carbon dioxide uptake by both altering pore aperture and developmental patterning. Stomatal patterning is regulated by environmental factors including atmospheric carbon dioxide (p[CO2]), which is increasing globally at an unprecedented rate. Mature leaves are known to convey developmental cues to immature leaves in response to p[CO2], but the developmental mechanisms are unknown. To characterize changes in stomatal patterning resulting from signals moving from mature to developing leaves, we constructed a dual-chamber growth system in which rosette and cauline leaves of Arabidopsis thaliana were subjected to differing p[CO2]. Young rosette tissue was found to adjust stomatal index (SI, the proportion of stomata to total cell number) in response to both the current environment and the environment experienced by mature rosette tissue, whereas cauline leaves appear to be insensitive to p[CO2] treatment. It is likely that cauline leaves and cotyledons deploy mechanisms for controlling stomatal development that share common but also deploy distinctive mechanisms to that operating in rosette leaves. The effect of p[CO2] on stomatal development is retained in cotyledons of the next generation, however, this effect does not occur in pre-germination stomatal lineage cells but only after germination. Finally, these data suggest that p[CO2] affects regulation of stomatal development specifically through the development of satellite stomata (stomata induced by signals from a neighboring stomate) during spacing divisions and not the basal pathway. To our knowledge, this is the first report identifying developmental steps responsible for altered stomatal patterning to p[CO2] and its trans-generational inheritance.
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Affiliation(s)
- Miranda J. Haus
- Department of Plant Biology, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Mao Li
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Daniel H. Chitwood
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, United States
| | - Thomas W. Jacobs
- Department of Plant Biology, University of Illinois at Urbana–Champaign, Urbana, IL, United States
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