Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Mar 29;11(4):879.
doi: 10.3390/microorganisms11040879.

Effects of Inbreeding on Microbial Community Diversity of Zea mays

Corey R Schultz  1 , Matthew Johnson  2 , Jason G Wallace  2   3
Affiliations

Effects of Inbreeding on Microbial Community Diversity of Zea mays

Corey R Schultz et al. Microorganisms. .

Abstract

Heterosis, also known as hybrid vigor, is the basis of modern maize production. The effect of heterosis on maize phenotypes has been studied for decades, but its effect on the maize-associated microbiome is much less characterized. To determine the effect of heterosis on the maize microbiome, we sequenced and compared the bacterial communities of inbred, open pollinated, and hybrid maize. Samples covered three tissue types (stalk, root, and rhizosphere) in two field experiments and one greenhouse experiment. Bacterial diversity was more affected by location and tissue type than genetic background for both within-sample (alpha) and between-sample (beta) diversity. PERMANOVA analysis similarly showed that tissue type and location had significant effects on the overall community structure, whereas the intraspecies genetic background and individual plant genotypes did not. Differential abundance analysis identified only 25 bacterial ASVs that significantly differed between inbred and hybrid maize. Predicted metagenome content was inferred with Picrust2, and it also showed a significantly larger effect of tissue and location than genetic background. Overall, these results indicate that the bacterial communities of inbred and hybrid maize are often more similar than they are different and that non-genetic effects are generally the largest influences on the maize microbiome.

Keywords: genetic variation; heterosis; inbreeding; maize; microbiome.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
Shared ASVs across plant tissues (A) compared to relative abundance of reads in plant tissues (B) colored by phylum.
Figure 2
Figure 2
UpSet plot [65] showing intersections of common genera (those found in >50% of samples) based on genetic background and tissue. Intersections with zero counts are not shown. Open pollinated lines share genera in some but not all of these intersections.
Figure 3
Figure 3
Weighted UniFrac diversity principal coordinates colorized by experiment (A), tissue type (B), and genetic background (C).
Figure 4
Figure 4
Volcano plots of differentially abundant ASVs. ASVs were more abundant in inbred (blue) or hybrid (red) determined by DESeq2 with an alpha of 0.001. Dots represent individual ASVs, which are labeled according to their taxonomic family. The full list of differentially abundant ASVs is presented in Supplemental Table S4.
See this image and copyright information in PMC

References

    1. Wallace J.G., May G. Endophytes: The Other Maize Genome. In: Bennetzen J., Flint-Garcia S., Hirsch C., Tuberosa R., editors. The Maize Genome. Springer International Publishing; Cham, Switzerland: 2018. pp. 213–246. Compendium of Plant Genomes.
    1. Compant S., Samad A., Faist H., Sessitsch A. A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application. J. Adv. Res. 2019;19:29–37. doi: 10.1016/j.jare.2019.03.004. - DOI - PMC - PubMed
    1. Peiffer J.A., Spor A., Koren O., Jin Z., Tringe S.G., Dangl J.L., Buckler E.S., Ley R.E. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc. Natl. Acad. Sci. USA. 2013;110:6548–6553. doi: 10.1073/pnas.1302837110. - DOI - PMC - PubMed
    1. Innerebner G., Knief C., Vorholt J.A. Protection of Arabidopsis thaliana against Leaf-Pathogenic Pseudomonas syringae by Sphingomonas Strains in a Controlled Model System. Appl. Environ. Microbiol. 2011;77:3202–3210. doi: 10.1128/AEM.00133-11. - DOI - PMC - PubMed
    1. Cagnano G., Lenk I., Roulund N., Jensen C.S., Cox M.P., Asp T. Mycelial biomass and concentration of loline alkaloids driven by complex population structure in Epichloë uncinata and meadow fescue (Schedonorus pratensis) Mycologia. 2020;112:474–490. doi: 10.1080/00275514.2020.1746607. - DOI - PubMed

LinkOut - more resources