Molecular diversity and genetic relationships in <Emphasis Type="Italic">Secale</Emphasis>

The objective of this study was to quantify the molecular diversity and to determine the genetic relationships among Secale spp. and among cultivars of Secale cereale using RAPDs, ISSRs and sequence analysis of six exons of ScMATE1 gene. Thirteen ryes (cultivated and wild) were genotyped using 21 RAPD and 16 ISSR primers. A total of 435 markers (242 RAPDs and 193 ISSRs) were obtained, with 293 being polymorphic (146 RAPDs and 147 ISSRs). Two RAPD and nine ISSR primers generated more than 80% of polymorphism. The ISSR markers were more polymorphic and informative than RAPDs. Further, 69% of the ISSR primers selected achieved at least 70% of DNA polymorphism. The study of six exons of the ScMATE1 gene also demonstrated a high genetic variability that subsists in Secale genus. One difference observed in exon 1 sequences from S. vavilovii seems to be correlated with Al sensitivity in this species. The genetic relationships obtained using RAPDs, ISSRs and exons of ScMATE1 gene were similar. S. ancestrale, S. kuprijanovii and S. cereale were grouped in the same cluster and S. segetale was in another cluster. S. vavilovii showed evidences of not being clearly an isolate species and having great intraspecific differences.     

Characterization,genetic diversity,phylogenetic relationships,and expression of the aluminum tolerance <Emphasis Type="Italic">MATE1</Emphasis> gene in <Emphasis Type="Italic">Secale</Emphasis> species

Aluminum (Al) is the main limiting factor for crop production in acidic soils. Efflux of organic acids is one of the mechanisms that determine Al-tolerance, and an Al-activated citrate transporter (multidrug and toxic compound extrusion) MATE1 gene is involved in different species. The contribution of the rye MATE1 gene (ScMATE1) depends on the rye (Secale cereale L.) cultivars and the crosses analyzed; there is no information about different rye species. The cDNA sequences, phylogenetic relationships, Al-tolerance, citrate exudation, and expression of the ScMATE1 gene were analyzed in several cultivars and wild species/subspecies of the Secale genus. Genotypes highly tolerant to Al were found within this genus. For the first time, sequences of the cDNA of the ScMATE1 gene were isolated and characterized in wild ryes. At least two copies of this gene were found likely to be related to Al-tolerance. The sequence comparison of 13 exons of ScMATE1 revealed variability between species, but also inter- and intra-cultivars. Variations were found in the Al-induced expression of ScMATE1 gene, as well as its contribution to Al-tolerance. The pattern of citrate exudation was inducible in most of the species/subspecies studied and constitutive in few. The phylogenetic analysis indicated that ScMATE1 is orthologue of two genes (HvMATE1 and TaMATE1) involved in the Al stress response in barley and wheat, respectively, but not orthologue of SbMATE, implicated in Al-tolerance in sorghum. ScMATE1 is involved in the response to Al stress in ryes, but its contribution to Al-tolerance is complex, and like in other species, there are tolerant and sensitive alleles in the different cultivars and species studied.     

Specific features in using SNP markers developed for allopolyploid wheat

In this work, we analyzed 54 domestic cultivars of hexaploid (common) wheat Triticum aestivum L. (AABBDD genome) and accessions of tetraploid wheats of the Timopheevi group (AAGG) and rye Secale cereale (RR) using 21 SNP markers for common wheat. It was demonstrated that application of the SNP markers developed and verified for particular common wheat cultivars in allele-specific PCR analysis of other cultivars with different geographic origins could lead to an incorrect estimation of the similarity between the genotypes tested. The studied SNP markers of common wheat are inappropriate for analyzing genomes of other cereal species, in particular, T. timopheevii wheats and rye S. cereale.     

Archaeobotanical analysis of radiocarbon-dated plant remains with special attention to <Emphasis Type="Italic">Secale cereale</Emphasis> (rye) cultivation at the medieval village of Mankby in Espoo (Finland)

Several urban medieval sites in Finland (ad 1000–1500) have been archaeobotanically investigated, but until now only a few rural medieval settlements have been studied. Therefore, many aspects of the crops and agricultural methods of medieval villages in Finland still remain unknown. At the 12th to mid-16th century medieval village of Mankby, Espoo, a systematic sampling for archaeobotanical material was carried out. The analysed samples derived from hearths, building contexts and medieval field layers etc. The archaeobotanical material was carbonised, and it consisted mostly of conifer needles, cereal grains and weed seeds. Secale cereale (rye) and Hordeum vulgare (barley) were the only crop species found, Secale being the most frequent. Seeds of Bromus secalinus (rye brome) and achenes of Centaurea cyanus (cornflower), which are associated with autumn sown winter cereal crops, were also present. The archaeobotanical material shows areas of activity linked to storing crops, as well as cultivation within the village boundaries. Based on radiocarbon dated grains, cultivation of the fields started in the 12th century and continued until the abandonment of the village in 1556. Archaeobotanical material from Mankby has been compared to other contemporary sites in Finland, and differences between the sites can be seen. Results from Mankby have added to our knowledge of medieval agriculture, past areas of activity and economic conditions within the village.     

Identification of LMW Glutenin-Like Genes from <Emphasis Type="Italic">Secale sylvestre</Emphasis> Host

Three low-molecular-weight (LMW) glutenin-like genes (designated as Ssy1, Ssy2, and Ssy3) from Secale sylvestre Host were isolated and characterized. The three genes consist of a predicted highly conservative signal peptide with 20 amino acids, a short N-terminal region with 13 amino acids, a highly variable repetitive domain and a less variable C-terminal domain. The deduced amino acid sequences of the three genes were the LMW-m type due to a methionine residue at the N-terminus. The phylogenetic analysis indicated that the prolamin genes could be perfectly clustered into five groups, including HMW-GS, LMW-GS, α/β-, γ-, and κ-prolamin. The LMW glutenin-like genes of S. sylvestre were more orthologous with the LMW-GS genes of wheat and B hordein genes of barley, which also had been confirmed by the homology analysis with the LMW-GS of wheat at Glu-A3, Glu-B3, and Glu-D3 loci. These results indicated that a chromosome locus (designated as Glu-R3) might be located on the R genome of S. sylvestre with the functions similar to the Glu-3 locus in wheat and its related species.     

The beginnings of rye (<Emphasis Type="Italic">Secale cereale</Emphasis>) cultivation in the East Baltics

In this paper we review the earliest Secale (rye) records, both pollen and macroremains, from the eastern Baltic region (northeast Poland, Lithuania, Latvia, Estonia and Finland) in order to understand the processes evident in the beginnings of rye cultivation. By taking note of the abundance of recovered Secale grains and pollen in relation to other cereals found in published archaeobotanical data, we try to understand when rye began to be used regionally as a staple food. The clarification of the timing of Secale in the East Baltic, that had social and economic implications, is of particular importance. In this publication we also present a radiocarbon date directly derived from dating a Secale grain from a Roman period hillfort in Lithuania. The date obtained constitutes the earliest record of Secale in the eastern Baltic region, showing that rye cultivation traditions and concomitant innovations in agricultural technology started there much earlier than previously suggested.     

Diversified chromosomal distribution of tandemly repeated sequences revealed evolutionary trends in Secale (Poaceae)

Genomic in situ hybridization (GISH) with Secale cereale cv. ‘Jingzhou rye’ DNA as a probe to chromosomes of hexaploid triticale line Fenzhi-1 revealed that not only were all chromosomes of rye strongly hybridized along the entire chromosome length, but there were also stronger signals in terminal or subtelomeric regions. This pattern of hybridization signals is referred to as GISH banding. After GISH banding, sequential fluorescene in situ hybridizaion (FISH) with tandem repeated sequence pSc200 and pSc250 as probes showed that the chromosomal distribution of pSc200 is highly coincident with the GISH banding pattern, suggesting that GISH banding revealed chromosomal distribution of pSc200 in rye. In addition, FISH using pSc200 and pSc250 as probes to chromosomes of 11 species of the genus Secale and two artificial amphiploids (Triticum aestivum-S. strictum subsp. africanum amphiploid and Aegilops tauschii-S. silvestre amphiploid) showed that (1) the chromosomal distribution of pSc200 and pSc250 differed greatly in Secale species, and the trend towards an increase in pSc200 and pSc250 binding sites from wild species to cultivated rye suggested that pSc200 and pSc250 sequences gradually accumulated during Secale evolution; (2) the chromosomal distribution of pSc200 and pSc250 presented polymorphism on homologous chromosomes, suggesting that the same species has two heterogeneous homologous chromosomes; (3) the intensity and number of hybridization signals varied differently on chromosomes between pSc200 and pSc250, suggesting that each repetitive family evolved independently.     

A multivariate morphometric delimitation of species boundaries in the South American genus <Emphasis Type="Italic">Nicoraepoa</Emphasis> (Poaceae: Pooideae: Poeae)

A multivariate morphometric study of the genus Nicoraepoa was carried out to examine patterns of morphological variation among the species and to identify additional characters to allow a clearer delimitation among species. Nicoraepoa is a taxonomically complex genus comprising seven species endemic to South America. Although most of the species are well delimited, two of them, N. andina and N. chonotica, are morphologically similar and very difficult to separate. The morphological variation among species, with overlapping morphological characters, pseudovivipary and possible hybridization make species boundaries unclear. In the present paper, sixty-seven characters were scored for a total of 216 specimens and analyzed using ordination, cluster and discriminant analyses. Based on multivariate results, we recognized species groups and morphological diagnostic characters that allow clearer species delimitation. As a result, N. chonotica has been transferred to N. andina as a subspecies that inhabit southern Patagonia. Other taxa could be recognized and delimited by diagnostic characters: N. erinacea, N. pugionifolia, N. stepparia, N. subenervis subsp. spegazziniana and N. subenervis subsp. subenervis. Moreover, we discuss the possibility that a new species from Bolivia, based on only one specimen, closely related to N. subenervis should be ascribed in Nicoraepoa.     

Assessment of Genetic Diversity in <Emphasis Type="Italic">Secale cereale</Emphasis> Based on SSR Markers

The primary aim of this study was to estimate genetic diversity among Secale cereale L. accessions using 22 previously published simple sequence repeat (SSR) markers. The plant material included 367 rye accessions comprising historical and contemporary cultivars, cultivated materials, landraces, and breeding strains from the Polish breeding company Danko. The studied accessions represented a wide geographical diversity. Several methods were employed to analyze genetic diversity among the Secale cereale L. accessions and to determine population structure: principal coordinate analysis (PCoA), neighbor-joining (NJ), and Bayesian clustering. We also defined a core collection of 25 rye accessions representing over 93 % of SSR alleles. The results of these analyses showed that accessions from the rye gene bank are clearly divergent in comparison with materials received directly from European breeding companies. Our findings suggest also that the genetic pool of current rye cultivars is becoming narrower during breeding processes. The selected panel of SSR markers performed well in detection of genetic diversity patterns and can be recommended for future germplasm characterization studies in rye.     

Molecular Analysis of the Triticale Lines with Different <Emphasis Type="Italic">Vrn</Emphasis> Gene Systems Using Microsatellite Markers and Hybridization In Situ

Hexaploid triticale (×Triticosecale Wittmack) lines were examined using molecular markers and the hybridization in situ technique. Triticale lines were generated based on wheat varieties differing by the Vrn gene systems and the earing times. Molecular analysis was performed using Xgwm and Xrms microsatellite markers with the known chromosomal localization in the common wheat Triticum aestivum, and rye Secale cereale genomes. Comparative molecular analysis of triticale lines and their parental forms showed that all lines contained A and B genomes of common wheat and also rye homoeologous chromosomes. In the three lines the presence of D genome markers, mapped to the chromosomes 2D and 7D, was demonstrated. This was probably the consequence of the translocations of homoeologous chromosomes from wheat genomes, which took part during the process of triticale formation. The data obtained by use of genomic in situ hybridization supported the data of molecular genetic analysis. In none of the lines wheat-rye translocations or recombinations were observed. These findings suggest that the change of the period between the seedling appearance and earing time in triticale lines compared to the initial wheat lines, resulted from the inhibitory effect of rye genome on wheat vernalization genes.     

Anatomical and micromorphological studies on <Emphasis Type="Italic">Teucrium</Emphasis> sect. <Emphasis Type="Italic">Isotriodon</Emphasis> (Lamiaceae) in Turkey with a taxonomic note

In this study, the anatomical features of the leaf and stem, besides the nutlet characteristics of some Teucrium sect. Isotriodon (Lamiaceae) taxa in Turkey, T. montbretii Betham subsp. montbretii, T. montbretii subsp. pamphylicum P. H. Davis, T. odontites Boiss. &; Bal., T. cavernarum P. H. Davis, T. antitauricum T. Ekim, along with an isolated population of T. montbretii (T. montbretii subsp.) were investigated. The anatomical studies revealed that the taxa share generally similar anatomical characters, such as thicker upper leaf cuticles and larger upper leaf epidermal cells compared to lower ones and diacytic to anomocytic stomata on the leaves. However, the portion of the mesophyll occupied by palisade parenchyma and the occurrence of mucilage cells in leaf epidermis shows difference among the taxa. Furthermore, the studied taxa have general stem characteristics of the Lamiaceae family, except for having poorly developed collenchyma at the corners. With the amphistomatic leaves and developed sclerenchymatic tissue in the leaf median vein, T. cavernarum is seperated from the other taxa. Trichome types on the vegetative organs and nutlet shape and sculpturing are generally the same or similar in the studied taxa, but trichomes on the nutlets are different among them. Based on nutlet characteristics and some morphological ones, it was revealed that the isolated population of T. montbretii represent a new subspecies, T. monbretii subsp. yildirimlii M.Dinç &; S.Do?u subsp. nov.     

New and little-known crickets of the subfamily phalangopsinae (Orthoptera,Gryllidae). 9. The african genus <Emphasis Type="Italic">Phaeophilacris</Emphasis>

The genus Phaeophilacris Walk. is divided into two subgenera: Phaeophilacris s. str. and Speluncacris Sjöst. The latter name, originally proposed as a generic one and synonymized with Phaeophilacris s. l., is restored as a subgeneric name. The former genera Opilionacris Sjöst. and Cavernacris Sjöst. previously synonymized with Phaeophilacris s. l. are considered as synonyms of the subgenus Speluncacris. Four new species (Ph. (S.) malawi sp. n., Ph. (S.) boldyrevi sp. n., Ph. (S.) dmitrievi sp. n., and Ph. (S.) gigantea sp. n.) and three new subspecies (Ph. (S.) bredoides mangochi subsp. n., Ph. (S.) bredoides mutinondo subsp. n., and Ph. (Ph.) townsendi aethiopica subsp. n.) of the genus Phaeophilacris are described.     

Phylogenetic relationships in Iranian <Emphasis Type="Italic">Scutellaria</Emphasis> (Lamiaceae) based on nuclear ribosomal ITS and chloroplast <Emphasis Type="Italic">trn</Emphasis>L-F DNA data

The genus Scutellaria (Lamiaceae, Scutellarioidae) includes taxa with a wide range of pharmacological traits, which make this genus economically important. Previous taxonomical studies on Scutellaria were mainly based on morphological and chromosomal characters. The infrageneric classification of the genus has been the subject of a long controversy among authors, and delimitation of taxa remains problematic. In this study, the phylogeny of the genus was evaluated using nrDNA ITS and trnL-F sequences, with a focus on the 42 Iranian taxa belonging to subgenera Apeltanthus and Scutellaria. In both ITS and trnL-F trees, there were two main clades within the genus corresponding to the two subgenera Scutellaria and Apeltanthus. In the subg. Scutellaria, the sect. Anaspis was monophyletic, but the monophyly of sect. Scutellaria was not supported. In this subgenus, S. galericulata was located away from other species in both trees, supported the isolation of this species from the sect. Scutellaria and inclusion in the sect. Galericularia as was previously considered by some authors. In subg. Apeltanthus, sect. Apeltanthus and sect. Lupulinaria were not monophyletic; furthermore, the monophyly of subsect. Lupulinaria was not supported. Based on the results of this study, it can be suggested that the sectional classification of both subgenera Apeltanthus and Scutellaria should be revised.     

Plant remains from the early modern garden of the manor of Kumpula,Helsinki, Finland: an alternative sampling method for macrofossil analysis

Garden history can be investigated through archaeobotanical research. This paper discusses the plant remains which were obtained from the soil of the historical garden of the manor of Kumpula in Helsinki, Finland. This study was an experiment to enable macrofossil analysis without archaeological excavations. The aim was to develop an alternative method for sampling for macrofossils also including radiocarbon dates, and to evaluate the usability, cost and functionality of this method. The character of the garden was also considered. The soil samples for macrofossil analysis were collected from the garden from three to eight different levels using an end-filling open-ended sampler. A total of 38 one litre soil samples from eight different pits yielded 2,036 identified macrofossils, mostly seeds. These comprised 63 different taxa, of which 26 were identified to species level with certainty. Taxa with more than 25 seeds found were Chelidonium majus, Chenopodium spp., Juncus spp., Rubus idaeus, Sambucus racemosa and Urtica dioica. Important species were Secale cereale and Hordeum vulgare. Nine AMS radiocarbon dates were obtained from macrofossil material from four different pits, giving results ranging from 1120–920 cal bc to cal ad 1680–1930 for charred wood, and from cal ad 1450–1640 to 1640–1930 for charred grains of Secale cereale and seeds of Chenopodium album. The sampling method proved to work reasonably well, considering the limitations of the sample size.     

Phylogenetic reconstruction of the South American genus <Emphasis Type="Italic">Leucheria</Emphasis> Lag. (Asteraceae,Nassauvieae) based on nuclear and chloroplast DNA sequences

The genus Leucheria Lag. (Asteraceae Bercht. and J. Presl, tribe Nassauvieae Cass.) comprises 45 species and three infraspecific taxa distributed in the Andean region from southern Chile and Argentina to Peru. Six species are annual herbs. The genus has had a long taxonomic history involving the transference of species described originally under many different genera. The main objectives of this paper were to determine the phylogenetic relationships of species of Leucheria, examine the hypothesis that the ancestor of Leucheria would have originated in a forested habitat and examine the validity of nine morphologically defined evolutionary lines recognized in earlier work on the genus. Additionally we investigated whether the annual species of Leucheria are derived. We extracted DNA from leaf material for 45 taxa (94%) of Leucheria. We used Bayesian inference and plastid and nuclear genes to construct a phylogenetic hypothesis. Results show that Leucheria is monophyletic and is comprised of two main clades. One clade comprises perennial acaulescent/subacaulescent species, all with a solitary capitulum. We recognized three lineages in the second clade comprised of caulescent species that exhibit multiple capitula. Optimization of life-form over the phylogeny showed that five of the six annual species studied are derived in our tree. We conclude that the appearance of the annual habit is associated with the colonization of arid conditions in the winter rainfall coastal desert of northern Chile. Our result shows that species of Leucheria from forested habitats are derived. Discrepancies with previously recognized morphologically defined evolutionary lines were detected.     

Characterization and expression analyses of the H<Superscript>+</Superscript>-pyrophosphatase gene in rye

The H⁺-pyrophosphatase (H ⁺-PPase) gene plays an important role in maintaining intracellular proton gradients. Here, we characterized the full-length complementary DNA (cDNA) and DNA of the H ⁺-PPase gene ScHP1 in rye (Secale cereale L. ‘Qinling’). We determined the subcellular localization of this gene and predicted the corresponding protein structure. We analysed the evolutionary relationship between ScHP1 and H ⁺?PPase genes in other species, and did real-time quantitative polymerase chain reaction to explore the expression patterns of ScHP1 in rye plants subjected to N, P and K deprivation and to cold, high-salt and drought stresses. ScHP1 cDNA included a 2289 bp open reading frame (ORF) encoding 762 amino acid residues with 14 transmembrane domains. The genomic ScHP1 DNA was 4354 bp and contained eight exons and seven introns. ScHP1 was highly homologous with other members of the H ⁺-PPase gene family. When the full-length ORF was inserted into the expression vector pA7-YFP, the fluorescent microscopy revealed that ScHP1-YFP fusion protein was located in the plasma membrane. Rye plants that were subjected to N deprivation, cold and high-salt stresses, ScHP1 expression was higher in the leaves than roots. Conversely, plants subjected to P and K deprivation and drought stress, ScHP1 expression was higher in the roots than leaves. Under all the investigated stress conditions, expression of ScHP1 was lower in the stem than in the leaves and roots. Our results imply that ScHP1 functions under abiotic stress response.     

The Antioxidant Activity of the Russian Far East Representatives of the <Emphasis Type="Italic">Spiraea</Emphasis> L. (Rosaceae Juss.) Genus

Biologically active substances and antioxidant activity of extracts from leaves and inflorescences of nine representatives of the genus Spiraea L. growing on the territory of the Far East of Russia were investigated. Widespread species of the genus Spiraea (S. salicifolia, S. media var. media, S. betulifolia and S. ussuriensis subsp. ussuriensis) have the highest levels of biologically active substances. The inflorescences of spiraeas there contain more flavonols (up to 3.9%), oxycinnamic acids (up to 1.2%), catechins (up to 5.7%) and saponins (up to 5.1%) compared to their leaves, and there are more tannins (up to 11.6%) in the leaves. Among the Far Eastern representatives of the genus Spiraea, S. betulifolia and S. beauverdiana (section Calospira), S. humilis and S. salicifolia (section Spiraria), S. pubescens and S. media var. media (section Chamaedryon) are promising antioxidants. Plants of the genus Spiraea probably contain water-soluble antioxidant compounds of phenolic type, because the antioxidant activity of aqueous extracts in the leaves and inflorescences of spiraeas is higher (0.16–2.79 mg/g) than that of water-alcoholic compounds (0.06–2.54 mg/g). The antioxidant activity in the leaves of spiraeas is generally higher than that in the inflorescence. A reliable positive correlation is observed between the antioxidant activity of aqueous extracts from the organs of spiraeas and a content of oxycinnamic acids.     

Unique configuration of genes of silicon transporter in the freshwater pennate diatom <Emphasis Type="Italic">Synedra acus</Emphasis> subsp. <Emphasis Type="Italic">radians</Emphasis>

The existence of the cluster of duplicated sit silicon transporter genes in the chromosome of the diatom Synedra acus subsp. radians was shown for the first time. Earlier, the localization of sit genes in the same chromosome and cluster formation caused by gene duplication was shown only for the marine raphid pennate diatom P. tricornutum. Only non-clustered sit genes were found in the genomes of other diatoms. It is reasonable to assume that sit tandem (sit-td) and sit triplet (sit-tri) genes of S. acus subsp. radians occurred as a result of gene duplication followed by divergence of gene copies.