Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis

Epstein, Brendan; Burghardt, Liana T.; Heath, Katy D.; Grillo, Michael A.; Kostanecki, Adam; Hämälä, Tuomas; Young, Nevin D.; Tiffin, Peter

doi:10.1111/mec.16602

Title: Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis

Journal Article · Thu Jul 21 00:00:00 EDT 2022 · Molecular Ecology

DOI:https://doi.org/10.1111/mec.16602· OSTI ID:1877426

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^[3]; Grillo, Michael A. ^[4]; Kostanecki, Adam ^[1]; Hämälä, Tuomas ^[5];

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Department of Plant and Microbial Biology University of Minnesota St. Paul Minnesota USA
Department of Plant Sciences The University of Pennsylvania University Park Pennsylvania USA
Department of Plant Biology University of Illinois Urbana Illinois USA, Carl R. Woese Institute for Genomic Biology University of Illinois Urbana Illinois USA
Department of Biology Loyola University Chicago Chicago Illinois USA
Department of Plant and Microbial Biology University of Minnesota St. Paul Minnesota USA, School of Life Sciences University of Nottingham Nottingham UK
Department of Plant and Microbial Biology University of Minnesota St. Paul Minnesota USA, Department of Plant Pathology University of Minnesota St. Paul Minnesota USA

Abstract The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two‐species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host Medicago truncatula with a community of 88 Sinorhizobia (Ensifer) meliloti strains. Multistrain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single‐strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, that is, genotype‐by‐genotype, effects on rhizobial fitness and some annotated rhizobial genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation‐selection balance. Consistent with the lack of positive selection acting on host genes, we found that among‐host variation in growth was similar whether plants were grown with rhizobia or N‐fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multistrain contexts.

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Research Organization:: Univ. of Minnesota, Minneapolis, MN (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: CSP‐503446

OSTI ID:: 1877426

Alternate ID(s):: OSTI ID: 1877429; OSTI ID: 1982917

Journal Information:: Molecular Ecology, Journal Name: Molecular Ecology Vol. 32 Journal Issue: 14; ISSN 0962-1083

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
bacteria
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mutualism
population genomics

Title: Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis

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