Plant Scientist
Research
Loblolly pine nuclei - © Lilian Matallana
Towards the Multidimensional Annotation of Pine Genomes
Chromatin accessibility in the loblolly pine genome
The nucleus of a diploid loblolly pine cell is less than 15 microns in diameter but contains double-stranded DNA with a contour length of about 14 meters. Packing that amount of DNA into the cell nucleus requires an efficient organization of DNA into chromatin, a protein-DNA complex with a higher-order structure. Regions of accessible chromatin have been associated with regulatory DNA sequences, transcription start sites, and phenotypic variation across plant and animal species from humans to maize. We are establishing methods to explore chromatin structure in the loblolly pine genome, using nuclei isolated from different tissues. Preliminary results suggest that chromatin accessibility can add value to genome annotation efforts, improving the ability to discriminate between functional genes and processed pseudogenes in conifer genomes.
© Lilian Matallana
Postharvest Needle Retention
An exploratory Journey of the Christmas Tree Genome
Postharvest needle abscission (PNA) is the physiological process of needle separation from the main body of the tree after harvest. Due to their use as Christmas trees, there is a growing demand for firs that can hold their needles for long periods while display in rooms. While there is remarkable intra- and inter-specific variation in needle retention across cultivated firs, long breeding cycles make it difficult to breed superior phenotypes using traditional methods. In this study, we performed deep transcriptome sequencing of abscission zones (AZs) from three fir species (Abies fraseri, Abies balsamea, and Abies balsamea var. phanerolepis) that exhibit good (G) and poor (P) needle retention based on previous phenotypic data. We are building a pipeline for the de novo assembly and transcriptome analysis of these endemic North American firs. Our goal is to expand the
knowledge about Christmas tree genomes and develop genetic marker systems to predict NR variation and other important traits that support farmers and the real Christmas tree industry competitiveness.
Fraser fir somatic embryos on solid media © Lilian Matallana
Somatic Embryogenesis of Fraser fir
Christmas trees for the future
Fraser fir trees are one of North Carolina’s largest specialty crops, producing revenue of over $100 million annually. Genetic improvement efforts are underway using traditional plant breeding methods to increase growth, quality, pest resistance, and post-harvest needle retention. However, progress is slow due to the intrinsic challenges of breeding a conifer species with a long generation cycle (8-15 years). We implemented some techniques that improve the induction and maintenance of somatic embryogenic cultures in solid and liquid media. The best lines were cryopreserved for future genetic engineering.
© Lilian Matallana
NAZ
Needle
Twig
Histological Characterization of the needle abscission zone in firs
Biological divorce: How Christmas tree needles go their own way
Adhesion and separation of plant cells constitute essential features of plant development. The physiological process of an organ separation is called abscission. Although there are several histological studies that describe abscission in different models and non-model plants, needle abscission zones (NAZ)s are vaguely described in most conifer and are almost completely absent for firs. I have combined and simplified current methods for cell wall component visualization to determine morphological changes during NA and differences between phenotypes while reducing cost and time.
Fantastic bugs and where to find them: the biology of chalcid seed predation
The study of tiny wasps
Seed chalcids (Megastigmus spp.) are tiny wasps whose larvae destroy seeds of various plant species by consuming the megagametophyte (or endosperm) and embryo. We implemented a method for rearing chalcid adults under lab conditions and provided direct evidence that Mesopolobus cf. pinus is an ectoparasitoid of M. specularis. We proposed a model that linked different aspects of the biology of these species and discussed host–insect phenological relationships. The infestation of seeds in some clones across surveys suggested a potential genetic component to chalcid wasp's prevalence. Furthermore, we demonstrated the effectiveness of a simple gravitation method to separate Fraser fir seeds infested with Megastigmus larvae from healthy seeds.
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