Genetic Regulation of Vessel Morphology in Populus

Induced and natural variation affect traits independently in hybrid Populus

The genetic control of many plant traits can be highly complex. Both allelic variation (sequence change) and dosage variation (copy number change) contribute to a plant's phenotype. While numerous studies have investigated the effect of allelic or dosage variation, very few have documented both within the same system, leaving their relative contribution to phenotypic effects unclear. The Populus genome is highly polymorphic, and poplars are fairly tolerant of gene dosage variation. Here, using a previously established Populus hybrid F1 population, we assessed and compared the effect of natural allelic variation and induced dosage variation on biomass, phenology, and leaf morphology traits. We identified QTLs for many of these traits, but our results indicate limited overlap between the QTLs associated with natural allelic variation and induced dosage variation. Additionally, the integration of data from both allelic and dosage variation identifies a larger set of QTLs that together explain a larger percentage of the phenotypic variance. Finally, our results suggest that the effect of the large indels might mask that of allelic QTLs. Our study helps clarify the relationship between allelic and dosage variation and their effects on quantitative traits.

The transcriptional integration of environmental cues with root cell type development

Plant roots navigate the soil ecosystem with each cell type uniquely responding to environmental stimuli. Below ground, the plant's response to its surroundings is orchestrated at the cellular level, including morphological and molecular adaptations that shape root system architecture as well as tissue and organ functionality. Our understanding of the transcriptional responses at cell type resolution has been profoundly enhanced by studies of the model plant Arabidopsis thaliana. However, both a comprehensive view of the transcriptional basis of these cellular responses to single and combinatorial environmental cues in diverse plant species remains elusive. In this review, we highlight the ability of root cell types to undergo specific anatomical or morphological changes in response to abiotic and biotic stresses or cues and how they collectively contribute to the plant's overall physiology. We further explore interconnections between stress and the temporal nature of developmental pathways and discuss examples of how this transcriptional reprogramming influences cell type identity and function. Finally, we highlight the power of single-cell and spatial transcriptomic approaches to refine our understanding of how environmental factors fine tune root spatiotemporal development. These complex root system responses underscore the importance of spatiotemporal transcriptional mapping, with significant implications for enhanced agricultural resilience.

Influence of IAA and ABA on maize stem vessel diameter and stress resistance in variable environments

The plasticity of the xylem and its associated hydraulic properties play crucial roles in plant acclimation to environmental changes, with vessel diameter (Dv) being the most functionally prominent trait. While the effects of external environmental factors on xylem formation and Dv are not fully understood, the endogenous hormones indole-3-acetic acid (IAA) and abscisic acid (ABA) are known to play significant signalling roles under stress conditions. This study investigates how these hormones impact Dv under various environmental changes. Experiments were conducted in maize plants subjected to drought, soil salinity, and high CO2 concentration treatments. We found that drought and soil salinity significantly reduced Dv at the same stem internode, while an elevated CO2 concentration can mitigate this decrease in Dv. Remarkably, significant negative correlations were observed between Dv and the contents of IAA and ABA when considering the different treatments. Moreover, appropriate foliar application of either IAA or ABA on well-watered and stressed plants led to a decrease in Dv, while the application of corresponding inhibitors resulted in an increase in Dv. This finding underscores the causal relationship between Dv and the levels of both IAA and ABA, offering a promising approach to manipulating xylem vessel size.

A systems genetic analysis identifies putative mechanisms and candidate genes regulating vessel traits in poplar wood

Wood is the water conducting tissue of tree stems. Like most angiosperm trees, poplar wood contains water-conducting vessel elements whose functional properties affect water transport and growth rates, as well as susceptibility to embolism and hydraulic failure during water stress and drought. Here we used a unique hybrid poplar pedigree carrying genomically characterized chromosomal insertions and deletions to undertake a systems genomics analysis of vessel traits. We assayed gene expression in wood forming tissues from clonal replicates of genotypes covering dosage quantitative trait loci with insertions and deletions, genotypes with extreme vessel trait phenotypes, and control genotypes. A gene co-expression analysis was used to assign genes to modules, which were then used in integrative analyses to identify modules associated with traits, to identify putative molecular and cellular processes associated with each module, and finally to identify candidate genes using multiple criteria including dosage responsiveness. These analyses identified known processes associated with vessel traits including stress response, abscisic acid and cell wall biosynthesis, and in addition identified previously unexplored processes including cell cycle and protein ubiquitination. We discuss our findings relative to component processes contributing to vessel trait variation including signaling, cell cycle, cell expansion, and cell differentiation.

Temperature and Turgor "Limitation" and Environmental "Control" in Xylem Biology and Dendrochronology

Trees and other woody plants are immensely ecologically important, making it essential to understand the causes of relationships between tree structure and function. To help these efforts, we highlight persistent traditions in plant biology of appealing to environmental factors "limiting" or "controlling" woody plant features. Examples include the idea that inevitable drops in cell turgor with plant height limit cell expansion and thus leaf size and tree height; that low temperatures prohibit lignification of cells and thus the growth of woody plants at high elevation; and notions from dendrochronology and related fields that climate factors such as rainfall and temperature "control" growth ring features. We show that notions of "control," "limitation," and the like imply that selection would favor a given trait value, but that these would-be favored values are developmentally impossible to produce. Such "limitation" scenarios predict trait frequency distributions that are very narrow and are abruptly curtailed at the upper limit of developmental possibility (the right-hand side of the distribution). Such distributions have, to our knowledge, never been observed, so we see little empirical support for "limitation" hypotheses. We suggest that, as a more productive starting point, plant biologists should examine adaptation hypotheses, in which developmental possibility is wide (congruent with the wide ranges of trait variation that really are observed), but only some of the possible variants are favored. We suggest that (1) the traditional the proximate/ultimate causation distinction, (2) purging scenarios of teleology/anthropomorphism, and (3) stating hypotheses in terms of developmental potential and natural selection are three simple ways of making "limitation" hypotheses clearer with regard to biological process and thus empirically testable.

Chromoanagenesis in plants: triggers, mechanisms, and potential impact

Chromoanagenesis is a single catastrophic event that involves, in most cases, localized chromosomal shattering and reorganization, resulting in a dramatically restructured chromosome. First discovered in cancer cells, it has since been observed in various other systems, including plants. In this review, we discuss the origin, characteristics, and potential mechanisms underlying chromoanagenesis in plants. We report that multiple processes, including mutagenesis and genetic engineering, can trigger chromoanagenesis via a variety of mechanisms such as micronucleation, breakage-fusion-bridge (BFB) cycles, or chain-like translocations. The resulting rearranged chromosomes can be preserved during subsequent plant growth, and sometimes inherited to the next generation. Because of their high tolerance to genome restructuring, plants offer a unique system for investigating the evolutionary consequences and potential practical applications of chromoanagenesis.

Variation of Chromosome Composition in a Full-Sib Population Derived From 2x × 3x Interploidy Cross of Populus

Interploidy cross commonly results in complex chromosome number and structural variations. In our previous study, a progeny with segregated ploidy levels was produced by an interploidy cross between diploid female parent Populus tomentosa × Populus bolleana clone TB03 and triploid male parent Populus alba × Populus berolinensis 'Yinzhong'. However, the chromosome compositions of aneuploid genotypes in the progeny were still unclear. In the present study, a microsatellite DNA allele counting-peak ratios (MAC-PR) method was employed to analyze allelic configurations of each genotype to clarify their chromosome compositions, while 45S rDNA fluorescence in situ hybridization (FISH) analysis was used to reveal the mechanism of chromosome number variation. Based on the MAC-PR analysis of 47 polymorphic simple sequence repeat (SSR) markers distributed across all 19 chromosomes of Populus, both chromosomal number and structural variations were detected for the progeny. In the progeny, 26 hypo-triploids, 1 hyper-triploid, 16 hypo-tetraploids, 10 tetraploids, and 5 hyper-tetraploids were found. A total of 13 putative structural variation events (duplications and/or deletions) were detected in 12 genotypes, involved in chromosomes 3, 6, 7, 14, 15, 16, and 18. The 46.2% (six events) structural variation events occurred on chromosome 6, suggesting that there probably is a chromosome breakpoint near the SSR loci of chromosome 6. Based on calculation of the allelic information, the transmission of paternal heterozygosity in the hypo-triploids, hyper-triploid, hypo-tetraploids, tetraploids, and hyper-tetraploids were 0.748, 0.887, 0.830, 0.833, and 0.836, respectively, indicating that the viable pollen gains of the male parent 'Yinzhong' were able to transmit high heterozygosity to progeny. Furthermore, 45S rDNA-FISH analysis showed that specific-chromosome segregation feature during meiosis and chromosome appointment in normal and fused daughter nuclei of telophase II of 'Yinzhong,' which explained that the formation of aneuploids and tetraploids in the progeny could be attributed to imbalanced meiotic chromosomal segregation and division restitution of 'Yinzhong,' The data of chromosomal composition and structural variation of each aneuploid in the full-sib progeny of TB03 × 'Yinzhong' lays a foundation for analyzing mechanisms of trait variation relying on chromosome or gene dosages in Populus.