A select-and-resequence approach reveals strain-specific effects of Medicago nodule-specific PLAT-domain genes

Genetic studies of legume symbiosis with nitrogen-fixing rhizobial
bacteria have traditionally focused on nodule and nitrogen-fixation
phenotypes when hosts are inoculated with a single rhizobial strain. These
approaches overlook the potential effect of host genes on rhizobial
fitness (i.e., how many rhizobia are released from host nodules) and
strain-specific effects of host genes (i.e., genome x genome
interactions). Using Medicago truncatula mutants in the recently described
Nodule-specific PLAT Domain (NPD) gene family, we show how inoculating
plants with a mixed inoculum of 68 rhizobial strains (Ensifer meliloti)
via a Select and Resequence (S&R) approach can be used to
efficiently assay host mutants for strain-specific effects of late-acting
host genes on interacting bacteria. The deletion of a single NPD gene
(npd2) or all five members of the NPD gene family (npd1-5) differentially
altered the frequency of rhizobial strains in nodules even though npd2
mutants had no visible nodule morphology or N-fixation phenotype. Also,
npd1-5 nodules were less diverse and had larger populations of
colony-forming rhizobia despite their smaller size. Lastly, NPD mutations
disrupt a positive correlation between strain fitness and wild type host
biomass. These changes indicate that the effects of NPD proteins are
strain-dependent and that NPD gene family members are not redundant with
regard to their effects on rhizobial strains. Association analyses of the
rhizobial strains in the mixed inoculation indicate that rhizobial genes
involved in chromosome segregation, cell division, GABA metabolism, efflux
systems, and stress tolerance play an important role in the
strain-specific effects of NPD genes.