MSH1 is a plant-specific protein. RNAi suppression of MSH1 results in phenotype variability for developmental and stress response pathways. Segregation of the RNAi transgene produces non-genetic msh1 ‘memory’ with multi-generational inheritance. First-generation memory versus non-memory comparison, and six-generation inheritance studies, identifies gene-associated, heritable methylation repatterning. Genome-wide methylome analysis integrated with RNAseq and network-based enrichment studies identifies altered circadian clock networks, and phytohormone and stress response pathways that intersect with circadian control. A total of 373 differentially methylated loci comprising these networks are sufficient to discriminate memory from nonmemory full sibs. Methylation inhibitor 5-azacytidine diminishes the differences between memory and wild type for growth, gene expression and methylation patterning. The msh1 reprogramming is dependent on functional HISTONE DEACETYLASE 6 and methyltransferase MET1, and transition to memory requires the RNA-directed DNA methylation pathway. This system of phenotypic plasticity may serve as a potent model for defining accelerated plant adaptation during environmental change.

Anthracnose of strawberry, caused primarily by the fungal pathogens belonging to Colletotrichum acutatum species complex (CASC) and C. gloeosporioides species complex (CGSC) is an economically important disease in the Southeast United States. Quiescently infected (QI) planting stock is one of the most important sources of inoculum in the fruiting field that can only be reliably detected by highly sensitive real time quantitative PCR (q-PCR) assay. In this study, a q-PCR assay was developed and optimized that can discriminate anthracnose fruit rot (AFR) and anthracnose crown rot (ACR) causing species based on the difference in post PCR melting temperatures of amplicons. Controlled environment grown plants artificially inoculated with different levels of CASC and CGSC showed a significant (P < 0.001) correlation with levels of quantification expressed by C t values in q-PCR from petioles and leaf blades. The leaf blade was a significantly larger reservoir of QI than that of the petiole. Both TaqMan and SYBR Green assay showed similar sensitivity and specificity. Detection of QI on leaves at young middle and older stages from inoculation with same number of conidia indicated that middle aged leaves were the best for assessing QI. Quantification of QI from middle aged leaf samples from a strawberry fruiting field that has been planted with pre-inoculated plants at both ends of rows and let inoculum spread showed higher sensitivity and precision by q-PCR compared to that of a traditional How to cite this paper: