Soile Jokipii-Lukkari

• PhD
• Academy Research Fellow at University of Oulu

Bilberry ( Vaccinium myrtillus L.) is a wild berry species that is prevalent in northern Europe. It is renowned and well‐documented for its nutritional and bioactive properties, especially due to its anthocyanin content. However, an overview of biological systems governing changes in other crucial quality traits, such as size, firmness, and flavour...

Background Stone wool is commonly used as a plant substrate in soilless cultivation and discarded after one growing season. Stone wool waste is difficult to recycle, and thus it is typically landfilled. Alkali-activation of stone wool (i.e., milling and mixing with an alkaline solution) has been shown to be a feasible way to upcycle this waste frac...

Vaccinium is a large genus of shrubs that includes a handful of economically important berry crops. Given the numerous hybridizations and polyploidization events, the taxonomy of this genus has remained the subject of long debate. In addition, berries and berry-based products are liable to adulteration, either fraudulent or unintentional due to mis...

Plant respiratory burst oxidase homologs (RBOHs) are plasma membrane-localized NADPH oxidases that generate superoxide anion radicals, which then dismutate to H2O2, into the apoplast using cytoplasmic NADPH as an electron donor. PaRBOH1 is the most highly expressed RBOH gene in developing xylem as well as in a lignin-forming cell culture of Norway...

Background Vaccinium is an economically important genus of berry crops in the family Ericaceae. Given the numerous hybridizations and polyploidization events among Vaccinium species, the taxonomy of this genus has remained uncertain and the subject of long debate. Therefore, the availability of more genomic resources for Vaccinium can provide usefu...

In this study, cuticular wax load, its chemical composition, and biosynthesis, was studied during development of wild type (WT) bilberry fruit and its natural glossy type (GT) mutant. GT fruit cuticular wax load was comparable with WT fruits. In both, the proportion of triterpenoids decreased during fruit development concomitant with increasing pro...

Cuticular wax plays an important role in fruits in protection against environmental stresses and desiccation. In this study, biosynthesis and chemical composition of cuticular wax in wild type (WT) bilberry fruit was studied during development and compared with its natural glossy type (GT) mutant. The cuticular wax load in GT fruit was comparable t...

Plants have evolved a suite of photoreceptors to perceive information from the surrounding light conditions. The aim of this study was to examine photomorphogenic effects of light quality on the growth of Scots pine (Pinus sylvestris L.)seedlings representing southern (60 °N)and northern (68 °N)origins in Finland. We measured the growth characteris...

A cryopreservation method was developed for a Norway spruce (Picea abies L. Karst.) cell line characterised by highly vacuolated cells and ability to produce natural-like extracellular lignin in a cell suspension culture. Spruce callus cultured in a photoperiod of 16 h light, 8 h dark contained two types of callus morphologies. Soft callus was comp...

Thickening of tree stems is the result of secondary growth, accomplished by the meristematic activity of the vascular cambium. Secondary growth of the stem entails developmental cascades resulting in the formation of secondary phloem outwards and secondary xylem (i.e., wood) inwards of the stem. Signaling and transcriptional reprogramming by the ph...

Protein alignment of CTR1 isoform(s) of A. thaliana (At), P. trichocarpa (Potri), P. abies (MA), Salix purpurea (Sapur). Kinase domain is labeled according to Huang et al. (2003).

Primers used in this study.

Phylogenetic analysis of genes involved in ethylene biosynthesis (A–C), perception and signaling (D,E), transcriptional reprogramming (F,G) and regulation (H) in A. thaliana (At; brown) and the two woody species P. trichocarpa (Pt; black) and P. abies (Pa; gray). Exact gene identities can be extracted from Supplementary Table S1.

Gene identities and abbreviations used for phylogenetic analysis of gene families in the ethylene pathway.

Expression values for genes in the ethylene pathway during secondary growth.

Structure and assembly of ERF co-expression networks.

TF hubs from the AspWood network. Centrality parameters of TF hubs (BTW, Cl and degree, listed in Supplementary Table S4). Colors indicate TF family. The plant TF database (v4.0) was used to identify TF families. Families that are not present in top 20% genes are: ARR-B, BBR-BPC, BES1, CAMTA, E2F, FAR1, GeBP, HB-PHD, HB-others, HRT-like, LFY, LSD,...

Transgene expression levels in 35S::PtEIN3D/ein3-1 and 35S::PtEIN3F/ein3-1. Each bar represents the mean of three pools of seedlings ± SD, with each pool consisting of five seedlings per tested line.

Expression values of ethylene pathway and ethylene-responsive genes upon ACC treatment.

Identified hubs from “AspWood” co-expression network.

Structure and assembly of EIN3 co-expression networks.

Structure and assembly of co-expression networks from ethylene-responsive TFs.

Expression pattern of analysis of genes involved in ethylene biosynthesis (A–C), perception and signaling (D,E), transcriptional reprogramming (F,G) and regulation (H) during secondary growth in P. trichocarpa. Gene expression data was extracted from the AspWood database (Sundell et al., 2017). Each data point represents expression values in cryose...

Complementation of ein3-1 mutants by PtEIN3D.

Seasonal cues influence several aspects of the secondary growth of tree stems, including cambial activity, wood chemistry, and transition to latewood formation. We investigated seasonal changes in cambial activity, secondary cell wall formation, and tracheid cell death in woody tissues of Norway spruce (Picea abies) throughout one seasonal cycle. R...

Metacaspases (MCs) are cysteine proteases that are implicated in programmed cell death of plants. AtMC9 ( Arabidopsis thaliana Metacaspase9) is a member of the Arabidopsis MC family that controls the rapid autolysis of the xylem vessel elements, but its downstream targets in xylem remain uncharacterized. PttMC13 and PttMC14 were identified as AtMC9...

Fig. S1 Principal component analysis plot of normalised expression values. Fig. S2 Gene expression heatmap indicating sample and gene clustering. Fig. S3 Midpoint rooted phylogenetic tree of Picea abies, Arabidopsis thaliana and Populus trichocarpa cellulose synthase (CesA) and CesA‐like (CSL) subfamilies B, D, E and G. Fig. S4 Co‐expression amo...

Table S2 Gene expression and sequence data quality

Table S3 Hierarchical clustering of genes

Table S4 Gene ontology enrichment of hierarchical clusters

Table S5 Gene ontology enrichment per sample

Table S1 Section pooling and cell profiling

Table S6 Network statistics

Table S8 Secondary cell wall cellulose synthase A gene network neighbourhoods

Table S7 Transcription factor network neighbours of the secondary cell wall cellulose synthase genes in Picea abies

The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high‐spatial‐resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA‐sequencing data from replica...

Previous reports have connected non-symbiotic and truncated hemoglobins (Hbs) to metabolism of nitric oxide (NO), an important signalling molecule involved in wood formation. We have studied the capability of poplar (Populus tremula × tremuloides) Hbs PttHb1 and PttTrHb proteins alone or with a flavin-protein reductase to relieve NO cytotoxicity in...

Thus far, research on plant hemoglobins (Hbs) has mainly concentrated on symbiotic and non-symbiotic Hbs, and information on truncated Hbs (TrHbs) is scarce. The aim of this study was to examine the origin, structure and localization of the truncated Hb (PttTrHb) of hybrid aspen (Populus tremula L. × tremuloides Michx.), the model system of tree bi...

The responses of transcriptome and phenolic compounds were determined with Populus tremula L. × Populus tremuloides Michx. expressing the hemoglobin (Hb) of Vitreoscilla (VHb) and non-transformant (wt) line. After 24-h exposure of leaves to Conistra vaccinii L., the transcript levels of endogenous non-symbiotic class 1 Hb (PttHb1) and truncated Hb...

Extensive studies have revealed that large-scale, high-cell density bioreactor cultivations have significant impact on metabolic networks of oxygen-requiring production organisms. Oxygen transfer problems associated with fluid dynamics and inefficient mixing efficiencies result in oxygen gradients, which lead to reduced performance of the bioproces...

To date, haemoglobins (Hbs) have been shown to exist in all kingdoms of life. The least studied and understood groups are plant non-symbiotic haemoglobins (nsHbs) and the recently found plant truncated Hbs (trHbs). From a biotechnological point of view, the best characterized and almost exclusively applied Hb is the bacterial Vitreoscilla haemoglob...

Present knowledge on plant non-symbiotic class-1 (Hb1) and truncated (TrHb) haemoglobin genes is almost entirely based on herbaceous species while the corresponding tree haemoglobin genes are not well known. The function of these genes has recently been linked with endosymbioses between plants and microbes. In this work, the coding sequences of hyb...

The Food and Agriculture Organization of the United Nations’ (FAO’s) international definition of a forest, as presented in the Global Forest Resources Assessment 2000 (GFRA-2000), sets the canopy cover requirement of 10% as the threshold value between forest and other types of land. According to the latest preliminary information of GFRA published...

An automated nucleic acid extraction procedure with magnetic particles originally designed for isolation of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from animal tissues was tested for plant material. We isolated genomic DNA and total RNA from taxonomically diverse plant species representing conifers (Scots pine), broad-leaved trees (s...

The aim of the present study was to develop an effective cryopreservationmethod for hybrid aspen (PopulustremulaL.×PopulustremuloidesMichx.), an economically important woody plant and widely used model system of forest scientists. Specific attention was paid to geneticfidelity of cryopreserved materials and transgene stability after retrieval. Thre...

We describe the first ever expression of Vitreoscilla haemoglobin (VHb) in an economically important boreal woody plant hybrid aspen (Populus tremula x tremuloides). VHb has mainly been expressed in biotechnologically important unicellular organisms of both prokaryotic and eukaryotic origin. VHb expression, in this study, was analysed under differe...