Epigenetic Memory in Mammals

Epigenetic information can be passed on from one generation to another via DNA methylation, histone modifications, and changes in small RNAs, a process called epigenetic memory. During a mammal’s lifecycle epigenetic reprogramming, or the resetting of most epigenetic marks, occurs twice. The first instance of reprogramming occurs in primordial germ cells and the second occurs following fertilization. These processes may be both passive and active. In order for epigenetic inheritance to occur the epigenetic modifications must be able to escape reprogramming. There are several examples supporting this non-Mendelian mechanism of inheritance including the prepacking of early developmental genes in histones instead of protamines in sperm, genomic imprinting via methylation marks, the retention of CenH3 in mammalian sperm and the inheritance of piwi-associated interfering RNAs. The ability of mammals to pass on epigenetic information to their progeny provides clear evidence that inheritance is not restricted to DNA sequence and epigenetics plays a key role in producing viable offspring

Epigenetic Modifications during Angiosperm Gametogenesis

Angiosperms do not contain a distinct germline, but rather develop gametes from gametophyte initials that undergo cell division. These gametes contain cells that give rise to an endosperm and the embryo. DNA methylation is decreased in the vegetative nucleus (VN) and central cell nuclei (CCN) resulting in expression of transposable elements (TEs). It is thought that the siRNAs produced in response to TE expression are able to travel to the sperm cells and egg cells (EC) from VN and CCN, respectively, in order to enforce silencing there. Demethylation during gametogenesis helps ensure that even newly integrated TEs are expressed and therefore silenced by the resulting siRNA production. A final form of epigenetic control is modification of histones, which includes accumulation of the H3 variant HTR10 in mature sperm that is then completely replaced following fertilization. In females, the histone isoforms present in the EC and CCN differ, potentially helping to differentiate the two components during gametogenesis

Transgenerational inheritance of epigenetic response to abiotic stress in Arabidopsis thaliana

xiv, 246 leaves : ill. ; 29 cmAbiotic stresses are one of the major limiting factors of plant growth and thus crop productivity. Exposure to these stresses, including temperature and UV, cause physiological and epigenetic changes in plants. Such changes may be inherited in the progeny of stressed plants, and may change their ability to respond to stress. To understand the ability of plants to inherit an epigenetic stress memory as well as the physiological manifestations of such a memory, we propagated both stressed and control plants and compared the progeny under both normal and stressed conditions. In addition to wild-type plants we used Dicer-like mutants dcl2, dcl3 and dcl4, as Dicers have been linked to RNA-directed DNA methylation, a form of epigenetic memory. These studies revealed that leaf number decreases in the progeny of stressed plants, and bolting occurs earlier in the progeny of temperature stressed plants but later in the progeny of UV-C stressed plants. Transposons were also re-activated in the progeny of stressed plants. While heat shock transcription factor 2A increased expression in the progeny of heat stressed plants, many genes involved in DNA repair and histone modifications decreased. DCL2 and DCL3 appeared to be more important in transgenerational stress memory than DCL4. However, all dcl plants were generally not significantly different than wild-type plants, indicating that a single DCL deficiency may be compensated for by another DCL

Transgenerational Adaptation to Heavy Metal Salts in Arabidopsis

Exposure to abiotic and biotic stress results in changes in plant physiology and triggers genomic instability. Recent reports suggest that the progeny of stressed plants also exhibit changes in genome stability, stress tolerance, and methylation. Here we analyzed whether exposure to Ni2+, Cd2+, and Cu2+ salts leads to transgenerational changes in homologous recombination frequency and stress tolerance. We found that the immediate progeny of stressed plants exhibited an increased rate of recombination. However, when the progeny of stressed plants was propagated without stress, recombination reverted to normal levels. Exposure of plants to heavy metals for five consecutive generations (S1–S5) resulted in recombination frequency being maintained at a high level. Skipping stress following two to three generations of propagation with 50 mM Ni2+ or Cd2+ did not decrease the recombination frequency, suggesting plant acclimation to upregulated recombination. Analysis of the progeny of plants exposed to Cu2+ and Ni2+ indicated higher stress tolerance to the heavy metal parental plants were exposed to. Tolerance was higher in plants propagated with stress for three to five generations, which resulted in longer roots than plants propagated on heavy metals for only one to two generations. Tolerance was also more prominent upon exposure to a higher concentration of salts. The progeny of stressed plants were also more tolerant to NaCl and methyl methane sulfonate

Patterns of genomic and phenomic diversity in wine and table grapes.

Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes. By pairing publicly available historical phenotype data with genome-wide polymorphism data, we identify large effect loci controlling traits that have been targeted during domestication and breeding, including hermaphroditism, lighter skin pigmentation and muscat aroma. Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited, whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions. We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries. Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes

Genomic insights into apple aroma diversity

An apple's aroma is a major determinant of its desirability by consumers. To better understand the aroma of apples, 2-dimensional gas-chromatography mass-spectrometry (2D-GCMS) was used to quantify 106 volatile organic compounds (VOCs) from 515 apple varieties. We identified esters and aldehydes as the most abundant classes of VOCs, with butyl acetate and hexyl acetate being present in nearly every variety. Principal component analysis (PCA) revealed that the primary axis of variation in the apple volatilome is correlated with harvest date, with early-harvested apples expressing a greater number and higher concentration of VOCs compared to late-harvested apples. Genome-wide association studies (GWAS) using 250,579 single nucleotide polymorphisms (SNPs) identified a significant association between SNPs near the alcohol acyltransferase (AAT1) locus and the abundance of several esters. Additionally, strong associations were observed between SNPs at the NAC18.1 transcription factor locus and the abundances of 1-hexanol and 1-butanol, which serve as precursors for hexyl acetate and butyl acetate, respectively. These findings provide a foundation for understanding the genetic basis of apple aroma production and pave the way for the genomics-assisted enhancement of the aroma profiles of apple varieties to meet consumer preferences

Increases in Vein Length Compensate for Leaf Area Lost to Lobing in Grapevine

Premise:Leaf lobing and leaf size vary considerably across and within species,including among grapevines (Vitisspp.), some of the best‐studied leaves. Weexamined the relationship between leaf lobing and leaf area across grapevinepopulations that varied in extent of leaf lobing.Methods:We used homologous landmarking techniques to measure 2632 leavesacross 2 years in 476 unique, genetically distinct grapevines fromfive biparentalcrosses that vary primarily in the extent of lobing. We determined to what extent leafarea explained variation in lobing, vein length, and vein to blade ratio.Results:Although lobing was the primary source of variation in shape across theleaves we measured, leaf area varied only slightly as a function of lobing. Rather, leafarea increases as a function of total major vein length, total branching vein length, andvein to blade ratio. These relationships are stronger for more highly lobed leaves, withthe residuals for each model differing as a function of distal lobing.Conclusions:For leaves with different extents of lobing but the same area, the morehighly lobed leaves have longer veins and higher vein to blade ratios, allowing themto maintain similar leaf areas despite increased lobing. Thesefindings show howmore highly lobed leaves may compensate for what would otherwise result in areduced leaf area, allowing for increasedphotosynthetic capacity through similarleaf siz

Rootstock Effects on Scion Phenotypes in a ‘Chambourcin’ Experimental Vineyard

Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops. Grafting is a common horticultural practice that joins the roots (rootstock) of one plant to the shoot (scion) of another, providing an excellent method for investigating how these two organ systems affect each other. In this study, we used the French-American hybrid grapevine ‘Chambourcin’ (Vitis L.) as a model to explore the rootstock–scion relationship. We examined leaf shape, ion concentrations, and gene expression in ‘Chambourcin’ grown ungrafted as well as grafted to three different rootstocks (‘SO4’, ‘1103P’ and ‘3309C’) across 2 years and three different irrigation treatments. We found that a significant amount of the variation in leaf shape could be explained by the interaction between rootstock and irrigation. For ion concentrations, the primary source of variation identified was the position of a leaf in a shoot, although rootstock and rootstock by irrigation interaction also explained a significant amount of variation for most ions. Lastly, we found rootstock-specific patterns of gene expression in grafted plants when compared to ungrafted vines. Thus, our work reveals the subtle and complex effect of grafting on ‘Chambourcin’ leaf morphology, ionomics, and gene expression

Berries as a case study for crop wild relative conservation, use, and public engagement in Canada

Conservation of plant biodiversity, in particular crop wild relatives including those tended and cultivated by Indigenous Peoples, is critical to food security and agricul ture. Building on the 2019 road map for crop wild relatives, we examine berries as a case study for crop wild relative conservation, use, and public engagement. We focus on berries due not only to their economic, cultural, and nutritional importance but also because they are consumed fresh, providing a unique opportunity for individuals and communities to connect with plants. We outline health benefits, geographic dis tribution, and species at risk for Canadian berries. We describe practices, strategies, and approaches used by Indigenous Peoples to steward berries and emphasize the importance of traditional knowledge. We highlight opportunities for in situ and ex situ berry conservation and use of berries in plant breeding and Indigenous foodways. Our aim is to lay the groundwork for future collaborative efforts in these areas and to showcase berries as a useful case study for conservation of food plant biodiversity and public engagement