Defining the genetic components of callus formation: A GWAS approach

Abstract

A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture propagation of recalcitrant plant species and genetic engineering for desired phenotypes typically depends on efficient in vitro callus generation. Callus formation is under genetic regulation, and consequently, a molecular understanding of this process underlies successful generation for propagation materials and/or introduction of genetic elements in experimental or industrial applications. Herein, we identified 11 genetic loci significantly associated with callus formation in Populus trichocarpa using a genome-wide association study (GWAS) approach. Eight of the 11 significant gene associations were consistent across biological replications, exceeding a chromosome-wide–log10 (p) = 4.46 [p = 3.47E−05] Bonferroni-adjusted significance threshold. These eight genes were used as hub genes in a high-resolution co-expression network analysis to gain insight into the genome-wide basis of callus formation. A network of positively and negatively co-expressed genes, including several transcription factors, was identified. As proof-of-principle, a transient protoplast assay confirmed the negative regulation of a Chloroplast Nucleoid DNA-binding-related gene (Potri.018G014800) by the LEC2 transcription factor. Many of the candidate genes and co-expressed genes were 1) linked to cell division and cell cycling in plants and 2) showed homology to tumor and cancer-related genes in humans. The GWAS approach based on a high-resolution marker set, and the ability to manipulate targets genes in vitro, provided a catalog of high-confidence genes linked to callus formation that can serve as an important resource for successful manipulation of model and non-model plant species, and likewise, suggests a robust method of discovering common homologous functions across organisms.

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

“…However, this fungus has been difficult to study phylogenetically, and further work is needed to delineate its phylogenetic and functional relationships within what may be a highly heterogenous species complex. Our team has set a long-term goal to build a genetically diverse collection of C. geophilum isolates from across the Populus trichocarpa range, mirroring prior host GWAS population studies which have proven valuable for understanding the biology of these host trees [36][37][38][39][40][41][42][43]. Towards this goal we have isolated 229 new C. geophilum strains from beneath P. trichocarpa stands over a range of approximately 283 miles of the host range in the United States Pacific Northwest (PNW) states of Oregon and Washington and confirmed their identity using sequencing of the internal transcribed spacer (ITS) region and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene.…”

The genetic framework of shoot regeneration in Arabidopsis comprises master regulators and conditional fine-tuning factors

“…Accordingly, a GWAS on embryonic callus regeneration in maize showed that only 15 out of 63 QTNs were retained in multiple environments and highlighted WUSCHEL-RELATED HOMEOBOX 2 (WOX2) , although other candidates are distinct from ours 37 . Most QTGs we identified are also new compared to association studies on adventitious shoot regeneration in roses 38 , callus formation in poplar 39 and rice 40 and in vitro regeneration of cucumber 41 and tomato 42 . However, these studies do report similar functional classes of candidates (e.g., embryogenesis and meristem genes, reprogramming factors, hormone-related proteins, receptor-like kinases, and TFs from the LBD, ERF, MYB, and WOX families) 37 – 40 and in cases where multiple traits, protocols or techniques are evaluated, overlap between them is limited 37 , 38 , suggesting that the difference in experimental systems could be part of the cause.…”

Natural Variation in Plant Pluripotency and Regeneration

“…Poplar is another valuable commodity crop (e.g., for timber, plywood, pulp, and paper) that has also been proposed as a model system for woody species. Association mapping of callus formation from parenchyma cells in 280 poplar genotypes uncovered 8 QTGs, and a transcriptional network indicated that these were coexpressed with a multitude of cell cycle components, as well as homologs of LBD16 , LEC1&2 , WUS , TSD1, and CLF ( Table 3 ) [ 128 ]. Another recent study reported 83 loci linked to 275 QTGs underlying in vivo shoot traits in poplar [ 129 ].…”