Mutation is the ultimate source of genetic variation in natural populations and crops. To study mechanisms determining mutation rate variation within plant genomes, we analyzed 43,483 de novo germline single base substitutions in 1,504 fast neutron mutation lines of the model rice cultivar Kitaake (Oryza sativa ssp japonica) (from Li et al. 2017). We find that, like previously observed for de novo germline mutations in Arabidopsis. thaliana, mutation rates are significantly lower in genomic regions marked by H3K4me1, a histone modification found in the gene bodies of actively expressed genes in plants. We also observed conservation in rice for PDS5C, a cohesion cofactor involved in the homology-directed repair pathway that in A. thaliana binds to H3K4me1 via its Tudor domain. By examining existing ChIP-seq data for PDS5C in A. thaliana, we find that it localizes to genome regions marked by H3K4me1: regions of low mutation rates, coding regions, essential genes, constitutively expressed genes, and genes under stronger purifying selection, mirroring mutation biases observed in rice as well. We searched the A. thaliana proteome for genes containing similar Tudor domains and found that they are significantly enriched for DNA repair functions (p<1×10-11), including the mismatch repair MSH6 gene (in both rice and A. thaliana ), suggesting the potential for multiple DNA repair pathways to specifically target gene bodies and essential genes through H3K4me1 reading. These findings inspire further research to characterize mechanisms that localize DNA repair via histone interactions, leading to hypomutation in functionally constrained regions and potentially tuning the evolutionary trajectories of plant genomes.

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Mutation is the source of all heritable diversity, the essential material of evolution and breeding. While mutation rates are often regarded as constant, variability in mutation rates has been observed at nearly every level—varying across mutation types, genome locations, gene functions, epigenomic contexts, environmental conditions, genotypes, and species. This mutation rate variation arises from differential rates of DNA damage, repair, and transposable element activation and insertion that together produce what is measured by DNA mutation rates. We review historical and recent investigations into the causes and consequences of mutation rate variability in plants by focusing on the mechanisms shaping this variation. Emerging mechanistic models point to the evolvability of mutation rate variation across genomes via mechanisms that target DNA repair, shaping the diversification of plants at phenotypic and genomic scales. Expected final online publication date for the Annual Review of Plant Biology, Volume 74 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

No abstract

Grapevine leafroll-associated virus (GLRaV) infections are accompanied by symptoms with varying severity. Using a dedicated experimental vineyard, we studied the responses to GLRaVs in ripening berries from Cabernet franc grapevines grafted to different rootstocks and with zero, one, or pairs of leafroll infection(s). RNA sequencing data were mapped to a high-quality Cabernet franc genome reference assembled to carry out this study and integrated with hormone and metabolite abundance data. This study identified several molecular levers that participate in responses to GLRaVs, including those that are condition-dependent. This included describing common responses to GLRaVs that were reproduced in two consecutive years, in plants grafted to different rootstocks, and in more than one infection condition. Though different infections were inconsistently distinguishable from one another overall, the effects of infections in plants grafted to different rootstocks were distinct at each developmental stage. Conserved responses included the modulation of pathogen detecting genes, increases in abscisic acid signaling and cytoskeleton remodeling gene expression. The abundance of abscisic acid (ABA), related metabolites, ABA and hormone signaling-related gene expression, and the expression of several transcription factor families differentiated rootstocks overall. These data show that rootstock influences the effect of GLRaVs in ripening berries.