Biology subjects

Anderson, E. S.

Publications and source records attributed to Anderson, E. S..

3 recordsLinked to original sources

bioRxiv2026

From chromosome-scale assembly to the mappable genome of rubber dandelion: chromosome reorganization, rubber-pathway coordination, and domestication traits

Natural rubber supply depends almost entirely on one tropical tree, motivating development of temperate alternatives. Rubber dandelion (Taraxacum kok-saghyz Rodin) is the leading candidate, with comparatively well characterized rubber biosynthesis pathways, but its large, repeat-rich genome has left breeding genomics far behind pathway biology. In response, we assembled OSU TarKok 3.0, a 1.19-Gb nuclear reference in which eight chromosome-scale scaffolds contain 98% of the sequence. Continuity within chromosomes improved markedly, with contig N50 rising from 1.3 to 37.8 Mb, and conserved gene-space recovery improved accordingly. Macrosynteny showed strong chromosome conservation within Taraxacum and, when compared to lettuce, displayed four nearly intact and four composite chromosomes, a signature compatible with descending dysploidy accompanied by rearrangement rather than a single end-to-end fusion. Across nine Cichorieae genomes, none of six surveyed rubber-related gene families was uniquely enlarged in rubber dandelion. Instead, a cis-prenyltransferase locus, a rubber transferase activator, and three small rubber particle protein genes were enriched in underground tissues and grouped with rubber elongation factor in a latex-associated co-expression module, favoring coordinated pathway deployment over species-specific family expansion. Intersecting uniquely mappable and nonrepetitive sequence defined the mappable genome, approximately 210 Mb or 18% of the assembly, within which markers can be interpreted allelically. Mapping in an independent F2 family of 83 plants identified a chromosome 1 locus for filled-seed production under restricted cross-pollination, whereas herbicide response yielded no significant locus in this design. OSU TarKok 3.0 links chromosome reorganization, pathway deployment, and domestication traits into one framework for improving an outcrossing crop.

plant biology↗

bioRxiv2021

Hypermethylation is associated with increased age in almond (Prunus dulcis D.A. Webb) accessions

O_LIThe focus of this study is to profile changes in DNA methylation and small RNA expression occurring with increased age in almond breeding germplasm to identify possible biomarkers of age that can be used to assess the potential of individuals to develop aging-related disorders. C_LIO_LITo profile DNA methylation in almond germplasm, 70 methylomes were generated from almond individuals representing three age cohorts (11, 7, and 2 years old) using an enzymatic methyl-seq approach followed by analysis to call differentially methylated regions (DMRs) within these cohorts. Small RNA (sRNA) expression was profiled in three breeding selections, each from two age cohorts (1 and 6 years old) using sRNA-Seq followed by differential expression analysis. C_LIO_LIWeighted chromosome-level methylation analysis reveals hypermethylation in 11-year old almond breeding selections when compared to 2-year-old selections in the CG and CHH contexts. Seventeen consensus DMRs were identified in all age contrasts. sRNA expression differed significantly between the two age cohorts tested, with significantly decreased expression in sRNAs in the 6-year-old selections compared to the 1-year-old. C_LIO_LIAlmond shows a pattern of hypermethylation and decreased sRNA expression with increased age. Identified DMRs and differentially expressed sRNAs could function as putative biomarkers of age following validation in additional age groups. C_LI

plant biology↗

bioRxiv2020

Telomere length and TERT expression are associated with age in almond (Prunus dulcis)

While it is well known that all organisms age, our understanding of how aging occurs varies dramatically among species. The aging process in perennial plants is not well defined, yet can have implications on production and yield of valuable fruit and nut crops. Almond, a relevant nut crop, exhibits an age-related disorder known as non-infectious bud failure (BF) that affects vegetative bud development, indirectly affecting kernel-yield. This species and disorder present an opportunity to address aging in a commercially-relevant and vegetatively-propagated, perennial crop threatened by an aging-related disorder. In this study, we tested the hypothesis that telomere length and/or TERT expression can serve as biomarkers of aging in almond using both whole-genome sequencing data and leaf samples collected from distinct age cohorts over a two-year period. To measure telomere lengths, we employed both in silico and molecular approaches. We also measured expression of TERT, a subunit of the enzyme telomerase, which is responsible for maintaining telomere lengths. Results from this work show a marginal but significant association between both telomere length measured by monochrome multiplex quantitative PCR and TERT expression, and age of almond seedlings. These results suggest that as almonds age, TERT expression decreases and telomeres shorten. This work provides valuable information on potential biomarkers of perennial plant aging, contributing to our limited knowledge of this process. In addition, translation of this information will provide opportunities to address BF in almond breeding and nursery propagation.

plant biology↗