Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize
The root-associated microbiome (rhizobiome) affects plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2022-07-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/75790 |
| _version_ | 1811181658531954688 |
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| author | Michael A Meier Gen Xu Martha G Lopez-Guerrero Guangyong Li Christine Smith Brandi Sigmon Joshua R Herr James R Alfano Yufeng Ge James C Schnable Jinliang Yang |
| author_facet | Michael A Meier Gen Xu Martha G Lopez-Guerrero Guangyong Li Christine Smith Brandi Sigmon Joshua R Herr James R Alfano Yufeng Ge James C Schnable Jinliang Yang |
| author_sort | Michael A Meier |
| collection | DOAJ |
| description | The root-associated microbiome (rhizobiome) affects plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here, we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize (Zea mays L.) genotypes grown in agronomically relevant conditions under high N (+N) and low N (-N) treatments. We analyze the maize rhizobiome in terms of 150 abundant and consistently reproducible microbial groups and we show that the abundance of many root-associated microbes is explainable by natural genetic variation in the host plant, with a greater proportion of microbial variance attributable to plant genetic variation in -N conditions. Population genetic approaches identify signatures of purifying selection in the maize genome associated with the abundance of several groups of microbes in the maize rhizobiome. Genome-wide association study was conducted using the abundance of microbial groups as rhizobiome traits, and n=622 plant loci were identified that are linked to the abundance of n=104 microbial groups in the maize rhizosphere. In 62/104 cases, which is more than expected by chance, the abundance of these same microbial groups was correlated with variation in plant vigor indicators derived from high throughput phenotyping of the same field experiment. We provide comprehensive datasets about the three-way interaction of host genetics, microbe abundance, and plant performance under two N treatments to facilitate targeted experiments toward harnessing the full potential of root-associated microbial symbionts in maize production. |
| first_indexed | 2024-04-11T09:21:20Z |
| format | Article |
| id | doaj.art-4985814c06ed441898567b4a80352b89 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T09:21:20Z |
| publishDate | 2022-07-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-4985814c06ed441898567b4a80352b892022-12-22T04:32:12ZengeLife Sciences Publications LtdeLife2050-084X2022-07-011110.7554/eLife.75790Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maizeMichael A Meier0https://orcid.org/0000-0002-7727-6561Gen Xu1Martha G Lopez-Guerrero2Guangyong Li3Christine Smith4Brandi Sigmon5Joshua R Herr6https://orcid.org/0000-0003-3425-292XJames R Alfano7Yufeng Ge8James C Schnable9Jinliang Yang10https://orcid.org/0000-0002-0999-3518Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States; Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, United StatesDepartment of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States; Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, United StatesDepartment of Biochemistry, University of Nebraska-Lincoln, Lincoln, United StatesDepartment of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States; Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, United StatesCenter for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, United StatesDepartment of Plant Pathology, University of Nebraska-Lincoln, Lincoln, United StatesCenter for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, United States; Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, United StatesCenter for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, United States; Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, United StatesBiological Systems Engineering Department, University of Nebraska-Lincoln, Lincoln, United StatesDepartment of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States; Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, United StatesDepartment of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States; Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, United StatesThe root-associated microbiome (rhizobiome) affects plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here, we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize (Zea mays L.) genotypes grown in agronomically relevant conditions under high N (+N) and low N (-N) treatments. We analyze the maize rhizobiome in terms of 150 abundant and consistently reproducible microbial groups and we show that the abundance of many root-associated microbes is explainable by natural genetic variation in the host plant, with a greater proportion of microbial variance attributable to plant genetic variation in -N conditions. Population genetic approaches identify signatures of purifying selection in the maize genome associated with the abundance of several groups of microbes in the maize rhizobiome. Genome-wide association study was conducted using the abundance of microbial groups as rhizobiome traits, and n=622 plant loci were identified that are linked to the abundance of n=104 microbial groups in the maize rhizosphere. In 62/104 cases, which is more than expected by chance, the abundance of these same microbial groups was correlated with variation in plant vigor indicators derived from high throughput phenotyping of the same field experiment. We provide comprehensive datasets about the three-way interaction of host genetics, microbe abundance, and plant performance under two N treatments to facilitate targeted experiments toward harnessing the full potential of root-associated microbial symbionts in maize production.https://elifesciences.org/articles/75790microbiomerhizobiomeGWAShost-microbe interactionpopulation geneticsnitrogen |
| spellingShingle | Michael A Meier Gen Xu Martha G Lopez-Guerrero Guangyong Li Christine Smith Brandi Sigmon Joshua R Herr James R Alfano Yufeng Ge James C Schnable Jinliang Yang Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize eLife microbiome rhizobiome GWAS host-microbe interaction population genetics nitrogen |
| title | Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize |
| title_full | Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize |
| title_fullStr | Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize |
| title_full_unstemmed | Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize |
| title_short | Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize |
| title_sort | association analyses of host genetics root colonizing microbes and plant phenotypes under different nitrogen conditions in maize |
| topic | microbiome rhizobiome GWAS host-microbe interaction population genetics nitrogen |
| url | https://elifesciences.org/articles/75790 |
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