Foxtail mosaic virus: A tool for gene function analysis in maize and other monocots

Many plant viruses have been engineered into vectors for use in functional genomics studies, expression of heterologous proteins, and, most recently, gene editing applications. The use of viral vectors overcomes bottlenecks associated with mutagenesis and transgenesis approaches often implemented for analysis of gene function. There are several engineered viruses that are demonstrated or suggested to be useful in maize through proof-of-concept studies. However, foxtail mosaic virus (FoMV), which has a relatively broad host range, is emerging as a particularly useful virus for gene function studies in maize and other monocot crop or weed species. A few clones of FoMV have been independently engineered, and they have different features and capabilities for virus-induced gene silencing (VIGS) and virus-mediated overexpression (VOX) of proteins. In addition, FoMV can be used to deliver functional guide RNAs in maize and other plants expressing the Cas9 protein, demonstrating its potential utility in virus-induced gene editing applications. There is a growing number of studies in which FoMV vectors are being applied for VIGS or VOX in maize and the vast majority of these are related to maize–microbe interactions. In this review, we highlight the biology and engineering of FoMV as well as its applications in maize–microbe interactions and more broadly in the context of the monocot functional genomics toolbox.     

Genetic variation associated with chronic water and nutrient stress in pinyon pine

We examined how genotypic variation at the glycerate dehydrogenase (GLY) locus in pinyon pine might be affected by environmental stress and herbivory. We compared GLY allelic and genotypic frequencies among mature and juvenile trees growing in stressful cinder soil and adjacent sandy-loam soil. While no association was found with herbivory, three lines of evidence support the hypothesis that GLY slow homozygotes (SS) are selected for under conditions of environmental stress. 1) We found no differences at the GLY locus between juvenile and mature trees growing in sandy-loam soil. 2) However, in the stressful cinder soil we found a lower frequency of SS homozygotes in juvenile trees than in mature trees, suggesting that selection has occurred in one generation. 3) Using biomass as a measure of fitness, SS homozygotes were superior to other GLY genotypes in cinder soil. Two lines of evidence were inconsistent with the hypothesis of selection for SS homozygotes in stressful environments. 1) SS homozygote frequency between habitats was not significantly different, suggesting that too few generations have passed for differentiation to occur, and/or insufficient selection pressure. 2) The low frequency of SS homozygote juvenile trees growing in cinder soil suggests that counterbalancing selection may prevent SS homozygotes from increasing in the population.     

Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

Studies of genetic variation can clarify the role of geography and spatio-temporal variation of climate in shaping demography, particularly in temperate zone tree species with large latitudinal ranges. Here, we examined genetic variation in narrowleaf cottonwood, Populus angustifolia, a dominant riparian tree. Using multi-locus surveys of polymorphism in 363 individuals across the species'' 1800 km latitudinal range, we found that, first, P. angustifolia has stronger neutral genetic structure than many forest trees (simple sequence repeat (SSR) F_ST=0.21), with major genetic groups corresponding to large apparent geographical barriers to gene flow. Second, using SSRs and putatively neutral sequenced loci, coalescent simulations indicated that populations diverged before the last glacial maximum (LGM), suggesting the presence of population structure before the LGM. Third, the LGM and subsequent warming appear to have had different influences on each of these distinct populations, with effective population size reduction in the southern extent of the range but major expansion in the north. These results are consistent with the hypothesis that climate and geographic barriers have jointly affected the demographic history of P. angustifolia, and point the importance of both factors as being instrumental in shaping genetic variation and structure in widespread forest trees.