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Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance.

SUMMARY: To improve our understanding of genetic mechanisms underlying complex traits in plants, a comprehensive analysis of gene variants is required. Eucalyptus is an important forest plantation genus that is highly outbred. Trait dissection and molecular breeding in eucalypts currently relies on biallelic single‐nucleotide polymorphism (SNP) markers. These markers fail to capture the large amount of haplotype diversity in these species, and thus multi‐allelic markers are required. We aimed to develop a gene‐based haplotype mining panel for Eucalyptus species. We generated 17 999 oligonucleotide probe sets for targeted sequencing of selected regions of 6293 genes implicated in growth and wood properties, pest and disease resistance, and abiotic stress responses. We identified and phased 195 834 SNPs using a read‐based phasing approach to reveal SNP‐based haplotypes. A total of 8915 target regions (at 4637 gene loci) passed tests for Mendelian inheritance. We evaluated the haplotype panel in four Eucalyptus species (E. grandis, E. urophylla, E. dunnii and E. nitens) to determine its ability to capture diversity across eucalypt species. This revealed an average of 3.13–4.52 haplotypes per target region in each species, and 33.36% of the identified haplotypes were shared by at least two species. This haplotype mining panel will enable the analysis of haplotype diversity within and between species, and provide multi‐allelic markers that can be used for genome‐wide association studies and gene‐based breeding approaches. Significance Statement: We developed a haplotype sequencing panel for Eucalyptus targeting 8915 regions at 4637 gene loci associated with growth and wood properties, pest and disease resistance, and abiotic stress response providing a genome‐wide, multi‐allelic, gene‐centric genotyping resource for eucalypts. We tested the panel in four Eucalyptus species (E. grandis, E. dunnii, E. nitens and E. urophylla), and found an average of 3.65 haplotypes per target region per species, and 9.98 across all four species. [ABSTRACT FROM AUTHOR]

The appearance of lignin, 400 million-years ago, has been crucial for the successful land colonization by plants. This complex phenolic polymer which confers hydrophobicity and resistance to degradation to secondary cell walls, is also neosynthesized in response to both biotic and abiotic stresses. Lignin biosynthesis during development is regulated by a complex hierarchical transcriptional gene regulatory network. Notably, distinct abiotic stresses can co-opt different genes of this network, leading to different lignification patterns. Co-optation of this developmental network is a mean to facilitate adaptation to stress by promoting functional adaptation. Supporting this hypothesis, a growing number of transcription factors known to be involved in the regulation of secondary cell wall, were shown to integrate both developmental and environmental signals leading to an increased tolerance to abiotic stresses, such as drought or salinity. On the other hand, some transcription factors known to be involved in stress response were shown to impact lignin biosynthesis as part of the functional adaptation performed by plants to cope with natural constraints. In this review, we focus on the most recent findings on the cross-talk between stress-signaling pathways and regulation of lignin biosynthesis in response to abiotic stress and to a lesser extent to biotic stresses. We consider the transcriptional regulation level which has received much attention and the emerging roles of posttranscriptional and posttranslational regulations in the control of lignin biosynthesis in response to stresses. We end discussing future outlines and challenges to fill gaps in this emerging and exciting research field. [ABSTRACT FROM AUTHOR]

Competing Interests: The authors declare that they have no conflicts of interest regarding the publication of this article.

While potassium fertilization increases growth yield in Brazilian eucalyptus plantations, it could also increase water requirements, making trees more vulnerable to drought. Sodium fertilization, which has been shown to promote eucalyptus growth compared to K-deficient trees, could partially mitigate this adverse effect of potassium. However, little is known about the influence of K and Na fertilization on the tree metabolic response to water deficit. The aim of the present study was thus to analyze the transcriptome of leaves sampled from Eucalyptus grandis trees subjected to 37% rainfall reduction, and fertilized with potassium (K), sodium (Na), compared to control trees (C). The multifactorial experiment was set up in a field with a throughfall exclusion system. Transcriptomic analysis was performed on leaves from two-year-old trees, and data analyzed using multifactorial statistical analysis and weighted gene co-expression network analysis (WGCNA). Significant sets of genes were seen to respond to rainfall reduction, in interaction with K or Na fertilization, or to fertilization only (regardless of the water supply regime). The genes were involved in stress signaling, primary and secondary metabolism, secondary cell wall formation and photosynthetic activity. Our focus on key genes related to cation transporters and aquaporins highlighted specific regulation of ion homeostasis, and plant adjustment to water deficit. While water availability significantly affects the transcriptomic response of eucalyptus species, this study points out that the transcriptomic response is highly dependent on the fertilization regime. Our study is based on the first large-scale field trial in a tropical region, specifically designed to study the interaction between water availability and nutrition in eucalyptus. To our knowledge, this is the first global transcriptomic analysis to compare the influence of K and Na fertilization on tree adaptive traits in water deficit conditions., Competing Interests: The authors have declared that no competing interests exist.