@article{fresnedo-ramirez_anderson_d'amico-willman_gradziel_2023, title={A review of plant epigenetics through the lens of almond}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20367}, abstractNote={While genomes were originally seen as static entities that stably held and organized genetic information, recent advances in sequencing have uncovered the dynamic nature of the genome. New conceptualizations of the genome include complex relationships between the environment and gene expression that must be maintained, regulated, and sometimes even transmitted over generations. The discovery of epigenetic mechanisms has allowed researchers to understand how traits like phenology, plasticity, and fitness can be altered without changing the underlying deoxyribonucleic acid sequence. While many discoveries were first made in animal systems, plants provide a particularly complex set of epigenetic mechanisms due to unique aspects of their biology and interactions with human selective breeding and cultivation. In the plant kingdom, annual plants have received the most attention; however, perennial plants endure and respond to their environment and human management in distinct ways. Perennials include crops such as almond, for which epigenetic effects have long been linked to phenomena and even considered relevant for breeding. Recent discoveries have elucidated epigenetic phenomena that influence traits such as dormancy and self-compatibility, as well as disorders like noninfectious bud failure, which are known to be triggered by the environment and influenced by inherent aspects of the plant. Thus, epigenetics represents fertile ground to further understand almond biology and production and optimize its breeding. Here, we provide our current understanding of epigenetic regulation in plants and use almond as an example of how advances in epigenetics research can be used to understand biological fitness and agricultural performance in crop plants.}, journal={PLANT GENOME}, author={Fresnedo-Ramirez, Jonathan and Anderson, Elizabeth S. and D'Amico-Willman, Katherine and Gradziel, Thomas M.}, year={2023}, month={Jul} }
 @article{katherine m. d'amico-willman_joglekar_luna_ritchie_fagen_huerta_2022, title={Complete Genome Sequence of Xanthomonas arboricola pv. pruni Strain Xcp1 Isolated in 1984 from a Bacterial Spot Spring Canker on Prunus persica var. nucipersica cv. "Redgold"}, volume={11}, ISSN={["2576-098X"]}, DOI={10.1128/mra.00209-22}, abstractNote={Xanthomonas arboricola pv. pruni is an important plant pathogen and the causal agent of bacterial spot of stone fruits (Prunus spp). Here, we report a complete genome of X. arboricola pv. pruni strain Xcp1 generated from hybrid PacBio Sequel and Illumina NextSeq2000 sequencing.}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Katherine M. D'Amico-Willman and Joglekar, Prasanna and Luna, Emily K. and Ritchie, David F. and Fagen, Jennie and Huerta, Alejandra I.}, year={2022}, month={Nov} }
 @article{katherine m. d'amico-willman_sideli_allen_anderson_gradziel_fresnedo-ramirez_2022, title={Identification of Putative Markers of Non-infectious Bud Failure in Almond [Prunus dulcis (Mill.) DA Webb] Through Genome Wide DNA Methylation Profiling and Gene Expression Analysis in an Almond x Peach Hybrid Population}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.804145}, abstractNote={Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important nut crop susceptible to the genetic disorder, Non-infectious Bud Failure (NBF). Despite the severity of exhibition in several prominent almond cultivars, no causal mechanism has been identified underlying NBF development. The disorder is hypothesized to be associated with differential DNA methylation patterns based on patterns of inheritance (i.e., via sexual reproduction and clonal propagation) and previous work profiling methylation in affected trees. Peach (Prunus persica L. Batsch) is a closely related species that readily hybridizes with almond; however, peach is not known to exhibit NBF. A cross between an NBF-exhibiting 'Carmel' cultivar and early flowering peach ('40A17') produced an F1 where ∼50% of progeny showed signs of NBF, including canopy die-back, erratic branching patterns (known as "crazy-top"), and rough bark. In this study, whole-genome DNA methylation profiles were generated for three F1 progenies exhibiting NBF and three progenies considered NBF-free. Subsequent alignment to both the almond and peach reference genomes showed an increase in genome-wide methylation levels in NBF hybrids in CG and CHG contexts compared to no-NBF hybrids when aligned to the almond genome but no difference in methylation levels when aligned to the peach genome. Significantly differentially methylated regions (DMRs) were identified by comparing methylation levels across the genome between NBF- and no-NBF hybrids in each methylation context. In total, 115,635 DMRs were identified based on alignment to the almond reference genome, and 126,800 DMRs were identified based on alignment to the peach reference genome. Nearby genes were identified as associated with the 39 most significant DMRs occurring either in the almond or peach alignments alone or occurring in both the almond and peach alignments. These DMR-associated genes include several uncharacterized proteins and transposable elements. Quantitative PCR was also performed to analyze the gene expression patterns of these identified gene targets to determine patterns of differential expression associated with differential DNA methylation. These DMR-associated genes, particularly those showing corresponding patterns of differential gene expression, represent key targets for almond breeding for future cultivars and mitigating the effects of NBF-exhibition in currently affected cultivars.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Katherine M. D'Amico-Willman and Sideli, Gina M. and Allen, Brian J. and Anderson, Elizabeth S. and Gradziel, Thomas M. and Fresnedo-Ramirez, Jonathan}, year={2022}, month={Feb} }