Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil Environments
Root development is crucial for plant growth and therefore a key factor in plant performance and food production. <i>Arabidopsis thaliana</i> is the most commonly used system to study root system architecture (RSA). Growing plants on agar-based media has always been routine practice, but...
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| Format: | Article |
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MDPI AG
2021-07-01
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| Online Access: | https://www.mdpi.com/2073-4425/12/7/1028 |
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| author | Merijn Kerstens Vera Hesen Kavya Yalamanchili Andrea Bimbo Stephen Grigg Davy Opdenacker Tom Beeckman Renze Heidstra Viola Willemsen |
| author_facet | Merijn Kerstens Vera Hesen Kavya Yalamanchili Andrea Bimbo Stephen Grigg Davy Opdenacker Tom Beeckman Renze Heidstra Viola Willemsen |
| author_sort | Merijn Kerstens |
| collection | DOAJ |
| description | Root development is crucial for plant growth and therefore a key factor in plant performance and food production. <i>Arabidopsis thaliana</i> is the most commonly used system to study root system architecture (RSA). Growing plants on agar-based media has always been routine practice, but this approach poorly reflects the natural situation, which fact in recent years has led to a dramatic shift toward studying RSA in soil. Here, we directly compare RSA responses to agar-based medium (plates) and potting soil (rhizotrons) for a set of redundant loss-of-function <i>plethora</i> (<i>plt</i>) CRISPR mutants with variable degrees of secondary root defects. We demonstrate that <i>plt3plt7</i> and <i>plt3plt5plt7</i> plants, which produce only a handful of emerged secondary roots, can be distinguished from other genotypes based on both RSA shape and individual traits on plates and rhizotrons. However, in rhizotrons the secondary root density and the total contribution of the side root system to the RSA is increased in these two mutants, effectively rendering their phenotypes less distinct compared to WT. On the other hand, <i>plt3</i>, <i>plt3plt5</i>, and <i>plt5plt7</i> mutants showed an opposite effect by having reduced secondary root density in rhizotrons. This leads us to believe that plate versus rhizotron responses are genotype dependent, and these differential responses were also observed in unrelated mutants <i>short-root</i> and <i>scarecrow</i>. Our study demonstrates that the type of growth system affects the RSA differently across genotypes, hence the optimal choice of growth conditions to analyze RSA phenotype is not predetermined. |
| first_indexed | 2024-03-10T09:39:26Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T09:39:26Z |
| publishDate | 2021-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-9b87334e46134be79a790aff7ca7180b2023-11-22T03:50:32ZengMDPI AGGenes2073-44252021-07-01127102810.3390/genes12071028Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil EnvironmentsMerijn Kerstens0Vera Hesen1Kavya Yalamanchili2Andrea Bimbo3Stephen Grigg4Davy Opdenacker5Tom Beeckman 6Renze Heidstra7Viola Willemsen8Cluster of Plant Developmental Biology Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The NetherlandsCluster of Plant Developmental Biology Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The NetherlandsCluster of Plant Developmental Biology Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The NetherlandsCluster of Plant Developmental Biology Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The NetherlandsCluster of Plant Developmental Biology Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The NetherlandsDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, BelgiumCluster of Plant Developmental Biology Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The NetherlandsCluster of Plant Developmental Biology Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The NetherlandsRoot development is crucial for plant growth and therefore a key factor in plant performance and food production. <i>Arabidopsis thaliana</i> is the most commonly used system to study root system architecture (RSA). Growing plants on agar-based media has always been routine practice, but this approach poorly reflects the natural situation, which fact in recent years has led to a dramatic shift toward studying RSA in soil. Here, we directly compare RSA responses to agar-based medium (plates) and potting soil (rhizotrons) for a set of redundant loss-of-function <i>plethora</i> (<i>plt</i>) CRISPR mutants with variable degrees of secondary root defects. We demonstrate that <i>plt3plt7</i> and <i>plt3plt5plt7</i> plants, which produce only a handful of emerged secondary roots, can be distinguished from other genotypes based on both RSA shape and individual traits on plates and rhizotrons. However, in rhizotrons the secondary root density and the total contribution of the side root system to the RSA is increased in these two mutants, effectively rendering their phenotypes less distinct compared to WT. On the other hand, <i>plt3</i>, <i>plt3plt5</i>, and <i>plt5plt7</i> mutants showed an opposite effect by having reduced secondary root density in rhizotrons. This leads us to believe that plate versus rhizotron responses are genotype dependent, and these differential responses were also observed in unrelated mutants <i>short-root</i> and <i>scarecrow</i>. Our study demonstrates that the type of growth system affects the RSA differently across genotypes, hence the optimal choice of growth conditions to analyze RSA phenotype is not predetermined.https://www.mdpi.com/2073-4425/12/7/1028root system architecture<i>Arabidopsis thaliana</i>rhizotronPLETHORAgeometric morphometrics |
| spellingShingle | Merijn Kerstens Vera Hesen Kavya Yalamanchili Andrea Bimbo Stephen Grigg Davy Opdenacker Tom Beeckman Renze Heidstra Viola Willemsen Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil Environments Genes root system architecture <i>Arabidopsis thaliana</i> rhizotron PLETHORA geometric morphometrics |
| title | Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil Environments |
| title_full | Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil Environments |
| title_fullStr | Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil Environments |
| title_full_unstemmed | Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil Environments |
| title_short | Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil Environments |
| title_sort | nature and nurture genotype dependent differential responses of root architecture to agar and soil environments |
| topic | root system architecture <i>Arabidopsis thaliana</i> rhizotron PLETHORA geometric morphometrics |
| url | https://www.mdpi.com/2073-4425/12/7/1028 |
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