Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range

Edwards, Joseph A.; Saran, Usha Bishnoi; Bonnette, Jason; MacQueen, Alice; Yin, Jun; Nguyen, Tu uyen; Schmutz, Jeremy; Grimwood, Jane; Pennacchio, Len A.; Daum, Chris; Glavina del Rio, Tijana; Fritschi, Felix B.; Lowry, David B.; Juenger, Thomas E.

doi:10.1016/j.cub.2023.03.078

Title: Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range

Journal Article · Wed Apr 19 00:00:00 EDT 2023 · Current Biology

DOI:https://doi.org/10.1016/j.cub.2023.03.078· OSTI ID:1970495

^[1]; Saran, Usha Bishnoi ^[1]; Bonnette, Jason ^[1]; MacQueen, Alice ^[1]; Yin, Jun ^[1]; Nguyen, Tu uyen ^[1]; Schmutz, Jeremy ^[2]; Grimwood, Jane ^[3]; Pennacchio, Len A. ^[4]; Daum, Chris ^[4]; Glavina del Rio, Tijana ^[4]; Fritschi, Felix B. ^[5]; Lowry, David B. ^[6]; Juenger, Thomas E. ^[1]

Univ. of Texas at Austin, TX (United States)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of Missouri, Columbia, MO (United States)
Michigan State Univ., East Lansing, MI (United States)

A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. Furthermore, this study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.

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Research Organization:: Univ. of Texas at Austin, TX (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDA National Institute of Food and Agriculture

Grant/Contract Number:: SC0014156; SC0021126; AC02-05CH11231; SC0018409; 2019-67012-2971

OSTI ID:: 1970495

Journal Information:: Current Biology, Vol. 33, Issue 10; ISSN 0960-9822

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Title: Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range

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