Publications by authors named "Tuomas Toivainen"

8 Publications

  • Page 1 of 1

Allelic Variation of Is the Major Force Controlling Natural Variation in Skin and Flesh Color in Strawberry ( spp.) Fruit.

Plant Cell 2020 12 30;32(12):3723-3749. Epub 2020 Sep 30.

Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain

The fruits of diploid and octoploid strawberry ( spp) show substantial natural variation in color due to distinct anthocyanin accumulation and distribution patterns. Anthocyanin biosynthesis is controlled by a clade of R2R3 MYB transcription factors, among which MYB10 is the main activator in strawberry fruit. Here, we show that mutations in cause most of the variation in anthocyanin accumulation and distribution observed in diploid woodland strawberry () and octoploid cultivated strawberry ( ×). Using a mapping-by-sequencing approach, we identified a -transposon in that truncates the protein and knocks out anthocyanin biosynthesis in a white-fruited ecotype. Two additional loss-of-function mutations in were identified among geographically diverse white-fruited ecotypes. Genetic and transcriptomic analyses of octoploid spp revealed that , one of three homoeologs identified, regulates anthocyanin biosynthesis in developing fruit. Furthermore, independent mutations in are the underlying cause of natural variation in fruit skin and flesh color in octoploid strawberry. We identified a CACTA-like transposon () insertion in the promoter of red-fleshed accessions that was associated with enhanced expression. Our findings suggest that cis-regulatory elements in are responsible for enhanced expression and anthocyanin biosynthesis in strawberry fruit flesh.
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http://dx.doi.org/10.1105/tpc.20.00474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7721342PMC
December 2020

Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication.

Mol Biol Evol 2020 12;37(12):3507-3524

Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA.

Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered SVs across a population sample of 347 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read data set, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among data sets revealed different features of genome variability. For example, genome alignment identified a large (∼4.3 Mb) inversion in indica rice varieties relative to japonica varieties, and long-read analyses suggest that ∼9% of genes from the outgroup (O. longistaminata) are hemizygous. We focused, however, on the resequencing sample to investigate the population genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type-which included inversions, duplications, deletions, translocations, and mobile element insertions-was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs may be predominantly deleterious. Among transposable elements, SINE and mariner insertions were found at especially low frequency. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ∼25% more derived SVs and mobile element insertions than O. rufipogon, indicating that SVs contribute to the cost of domestication in rice. Peaks of SV divergence were enriched for known domestication genes, but we also detected hundreds of genes gained and lost during domestication, some of which were enriched for traits of agronomic interest.
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http://dx.doi.org/10.1093/molbev/msaa185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7743901PMC
December 2020

Population genetic analysis of a global collection of Fragaria vesca using microsatellite markers.

PLoS One 2017 30;12(8):e0183384. Epub 2017 Aug 30.

Faculty of Agricultural and Environmental Sciences, Agricultural University of Iceland, Keldnaholt, Reykjavik, Iceland.

The woodland strawberry, Fragaria vesca, holds great promise as a model organism. It not only represents the important Rosaceae family that includes economically important species such as apples, pears, peaches and roses, but it also complements the well-known model organism Arabidopsis thaliana in key areas such as perennial life cycle and the development of fleshy fruit. Analysis of wild populations of A. thaliana has shed light on several important developmental pathways controlling, for example, flowering time and plant growth, suggesting that a similar approach using F. vesca might add to our understanding on the development of rosaceous species and perennials in general. As a first step, 298 F. vesca plants were analyzed using microsatellite markers with the primary aim of analyzing population structure and distribution of genetic diversity. Of the 68 markers tested, 56 were polymorphic, with an average of 4.46 alleles per locus. Our analysis partly confirms previous classification of F. vesca subspecies in North America and suggests two groups within the subsp. bracteata. In addition, F. vesca subsp. vesca forms a single global population with evidence that the Icelandic group is a separate cluster from the main Eurasian population.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183384PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5576660PMC
October 2017

Altered regulation of TERMINAL FLOWER 1 causes the unique vernalisation response in an arctic woodland strawberry accession.

New Phytol 2017 Nov 16;216(3):841-853. Epub 2017 Aug 16.

Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014, Helsinki, Finland.

Vernalisation requirement is an agriculturally important trait that postpones the development of cold-sensitive floral organs until the spring. The family Rosaceae includes many agriculturally important fruit and berry crops that suffer from crop losses caused by frost injury to overwintering flower buds. Recently, a vernalisation-requiring accession of the Rosaceae model woodland strawberry (Fragaria vesca) has been identified in northern Norway. Understanding the molecular basis of the vernalisation requirement in this accession would advance the development of strawberry cultivars better adapted to temperate climate. We use gene silencing, gene expression analysis, genetic mapping and population genomics to study the genetic basis of the vernalisation requirement in woodland strawberry. Our results indicate that the woodland strawberry vernalisation requirement is endemic to northern Norwegian population, and mapping data suggest the orthologue of TERMINAL FLOWER1 (FvTFL1) as the causal floral repressor. We demonstrate that exceptionally low temperatures are needed to downregulate FvTFL1 and to make these plants competent to induce flowering at low postvernalisation temperatures in the spring. We show that altered regulation of FvTFL1 in the northern Norwegian woodland strawberry accession postpones flower induction until the spring, allowing plants to avoid winter injuries of flower buds that commonly occur in temperate regions.
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http://dx.doi.org/10.1111/nph.14734DOI Listing
November 2017

Additive QTLs on three chromosomes control flowering time in woodland strawberry ( L.).

Hortic Res 2017 24;4:17020. Epub 2017 May 24.

Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland.

Flowering time is an important trait that affects survival, reproduction and yield in both wild and cultivated plants. Therefore, many studies have focused on the identification of flowering time quantitative trait locus (QTLs) in different crops, and molecular control of this trait has been extensively investigated in model species. Here we report the mapping of QTLs for flowering time and vegetative traits in a large woodland strawberry mapping population that was phenotyped both under field conditions and in a greenhouse after flower induction in the field. The greenhouse experiment revealed additive QTLs in three linkage groups (LG), two on both LG4 and LG7, and one on LG6 that explain about half of the flowering time variance in the population. Three of the QTLs were newly identified in this study, and one co-localized with the previously characterized gene. An additional strong QTL corresponding to previously mapped was detected in both field and greenhouse experiments indicating that gene(s) in this locus can control the timing of flowering in different environments in addition to the duration of flowering and axillary bud differentiation to runners and branch crowns. Several putative flowering time genes were identified in these QTL regions that await functional validation. Our results indicate that a few major QTLs may control flowering time and axillary bud differentiation in strawberries. We suggest that the identification of causal genes in the diploid strawberry may enable fine tuning of flowering time and vegetative growth in the closely related octoploid cultivated strawberry.
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http://dx.doi.org/10.1038/hortres.2017.20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442962PMC
May 2017

Selection for population-specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post-glacial colonization.

Mol Ecol 2016 01 18;25(2):581-97. Epub 2016 Jan 18.

Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland.

Spatially varying selection can lead to population-specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location-specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population-specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population-specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.
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http://dx.doi.org/10.1111/mec.13489DOI Listing
January 2016

A recent local sweep at the PHYA locus in the Northern European Spiterstulen population of Arabidopsis lyrata.

Mol Ecol 2014 Mar 19;23(5):1040-52. Epub 2014 Feb 19.

Department of Biology, University of Oulu, Oulu, 90014, Finland; Biocenter Oulu, University of Oulu, Oulu, 90014, Finland.

Northern and central European Arabidopsis lyrata ssp. petraea populations are locally adapted to prevailing climatic conditions through differences in timing of life history events. The timing of flowering and, in perennials, the timing of growth cessation influence fitness. Phytochrome A may have an important role in regulating these life history traits as it perceives changes in daylength. We asked whether PHYA has contributed to local adaptation to the northern conditions in A. l. petraea. To search for signals of directional selection at the PHYA locus, we resequenced PHYA and 9 short fragments around PHYA from a 57-kb region from a German (Plech) and a Norwegian (Spiterstulen) population and compared patterns of differentiation and diversity to a set of 19 reference loci around the genome. First, we found that the populations were highly differentiated: there were three nonsynonymous fixed differences at the PHYA locus, which was in stark contrast with the total four fixed differences in the 19 reference loci. Compatible with a sweep hypothesis, variation was almost completely removed from the 9.4-kb region around PHYA in the northern Spiterstulen population. The overall level of linkage disequilibrium (LD) was higher in Spiterstulen, but there was no LD across the PHYA locus in the population, which is also a known consequence of a selective sweep. The sweep has likely occurred after the last glacial maximum, which suggests that it has contributed to adaptation to the northern conditions.
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http://dx.doi.org/10.1111/mec.12682DOI Listing
March 2014

Role of vernalization and of duplicated FLOWERING LOCUS C in the perennial Arabidopsis lyrata.

New Phytol 2013 Jan 26;197(1):323-335. Epub 2012 Oct 26.

Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland.

FLOWERING LOCUS C (FLC) is one of the main genes influencing the vernalization requirement and natural flowering time variation in the annual Arabidopsis thaliana. Here we studied the effects of vernalization on flowering and its genetic basis in the perennial Arabidopsis lyrata. Two tandemly duplicated FLC genes (FLC1 and FLC2) were compared with respect to expression and DNA sequence. The effect of vernalization on flowering and on the expression of FLC1 was studied in three European populations. The genetic basis of the FLC1 expression difference between two of the populations was further studied by expression quantitative trait locus (eQTL) mapping and sequence analysis. FLC1 was shown to have a likely role in the vernalization requirement for flowering in A. lyrata. Vernalization decreased its expression and the northern study populations showed higher FLC1 expression than the southern one. eQTL mapping between two of the populations revealed one eQTL affecting FLC1 expression in the genomic region containing the FLC genes. Most FLC1 sequence differences between the study populations were found in the promoter region and in the first intron. Variation in the FLC1 sequence may cause differences in FLC1 expression between late- and early-flowering A. lyrata populations.
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http://dx.doi.org/10.1111/j.1469-8137.2012.04378.xDOI Listing
January 2013
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