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1. Genome-Wide Association Analyses in the Model Rhizobium Ensifer meliloti

   https://doi.org/10.1128/mSphere.00386-18  

   Epstein, Brendan ; Abou-Shanab, Reda A. ; Shamseldin, Abdelaal ; Taylor, Margaret R. ; Guhlin, Joseph ; Burghardt, Liana T. ; Nelson, Matthew ; Sadowsky, Michael J. ; Tiffin, Peter ; Oh, Julia ( October 2018 , mSphere)

   ABSTRACT Genome-wide association studies (GWAS) can identify genetic variants responsible for naturally occurring and quantitative phenotypic variation. Association studies therefore provide a powerful complement to approaches that rely on de novo mutations for characterizing gene function. Although bacteria should be amenable to GWAS, few GWAS have been conducted on bacteria, and the extent to which nonindependence among genomic variants (e.g., linkage disequilibrium [LD]) and the genetic architecture of phenotypic traits will affect GWAS performance is unclear. We apply association analyses to identify candidate genes underlying variation in 20 biochemical, growth, and symbiotic phenotypes among 153 strains of Ensifer meliloti . For 11 traits, we find genotype-phenotype associations that are stronger than expected by chance, with the candidates in relatively small linkage groups, indicating that LD does not preclude resolving association candidates to relatively small genomic regions. The significant candidates show an enrichment for nucleotide polymorphisms (SNPs) over gene presence-absence variation (PAV), and for five traits, candidates are enriched in large linkage groups, a possible signature of epistasis. Many of the variants most strongly associated with symbiosis phenotypes were in genes previously identified as being involved in nitrogen fixation or nodulation. For other traits, apparently strong associations were not stronger thanmore »the range of associations detected in permuted data. In sum, our data show that GWAS in bacteria may be a powerful tool for characterizing genetic architecture and identifying genes responsible for phenotypic variation. However, careful evaluation of candidates is necessary to avoid false signals of association. IMPORTANCE Genome-wide association analyses are a powerful approach for identifying gene function. These analyses are becoming commonplace in studies of humans, domesticated animals, and crop plants but have rarely been conducted in bacteria. We applied association analyses to 20 traits measured in Ensifer meliloti , an agriculturally and ecologically important bacterium because it fixes nitrogen when in symbiosis with leguminous plants. We identified candidate alleles and gene presence-absence variants underlying variation in symbiosis traits, antibiotic resistance, and use of various carbon sources; some of these candidates are in genes previously known to affect these traits whereas others were in genes that have not been well characterized. Our results point to the potential power of association analyses in bacteria, but also to the need to carefully evaluate the potential for false associations.« less
2. The role of microRNAs in the legume–Rhizobium nitrogen-fixing symbiosis

   https://doi.org/10.1093/jxb/eraa018  

   Hoang, Nhung T ; Tóth, Katalin ; Stacey, Gary ; Mittler, Ron ( March 2020 , Journal of Experimental Botany)

   Abstract Under nitrogen starvation, most legume plants form a nitrogen-fixing symbiosis with Rhizobium bacteria. The bacteria induce the formation of a novel organ called the nodule in which rhizobia reside as intracellular symbionts and convert atmospheric nitrogen into ammonia. During this symbiosis, miRNAs are essential for coordinating the various plant processes required for nodule formation and function. miRNAs are non-coding, endogenous RNA molecules, typically 20–24 nucleotides long, that negatively regulate the expression of their target mRNAs. Some miRNAs can move systemically within plant tissues through the vascular system, which mediates, for example, communication between the stem/leaf tissues and the roots. In this review, we summarize the growing number of miRNAs that function during legume nodulation focusing on two model legumes, Lotus japonicus and Medicago truncatula, and two important legume crops, soybean (Glycine max) and common bean (Phaseolus vulgaris). This regulation impacts a variety of physiological processes including hormone signaling and spatial regulation of gene expression. The role of mobile miRNAs in regulating legume nodule number is also highlighted.
3. Novel plant–microbe interactions: Rapid evolution of a legume–rhizobium mutualism in restored prairies

   https://doi.org/10.1111/1365-2745.13366  

   Magnoli, Susan M. ; Lau, Jennifer A. ; Thrall, Peter ( July 2020 , Journal of Ecology)
4. Long-term agricultural management does not alter the evolution of a soybean-rhizobium mutualism

   https://doi.org/10.1002/eap.1625  

   Schmidt, Jennifer E. ; Weese, Dylan J. ; Lau, Jennifer A. ( December 2017 , Ecological Applications)
5. Discordant population structure among rhizobium divided genomes and their legume hosts

   https://doi.org/10.1111/mec.16704  

   Riley, Alex B. ; Grillo, Michael A. ; Epstein, Brendan ; Tiffin, Peter ; Heath, Katy D. ( October 2022 , Molecular Ecology)