Worldwide gene pool of fiber flax at VIR, and breeding of rust-resistant varieties

Background. There are strict requirements for a modern flax cultivar. It must have a whole set of valuable characters, including rust resistance.Materials and methods. The flax collection of 2485 accessions held by VIR was evaluated using artificial provocative infection.Results. Almost all domestic and foreign accessions and varieties collected before 1957 were highly or extremely susceptible to rust. Five Russian kryazhs and cv. ‘GDS-3’ developed at VIR were found to retain rust resistance up to the present moment. Lines derived from them and from three foreign varieties, with an identified number of the original effective R genes, were submitted to breeders. Nineteen donors with a set of economically useful traits, analogous to cvs. ‘Orshansky 2’ and ‘Prizyv 81’ and carrying the same genes, were produced and distributed to breeders. The VIR collection holds 10 donors of rust resistance with high fiber content developed at the All-Russian Research Institute of Flax. Some donors of resistance to other diseases released by the same Institute also possess high rust resistance, thus forming a rich stock of source material. The first cultivar relatively resistant to rust (‘L-1120’) was released in 1951. Possessing polygenic resistance, it was also resistant to Fusarium wilt and lodging, so it was widely used for breeding other cultivars with similar characteristics. As their cultivation expanded, the harvest losses caused by rust dropped. The first rust-resistant cultivar with oligogenic resistance (‘Tomsky 16’) appeared in 1990. By now, many cultivars protected by R genes of rust resistance have been developed. They combine this trait with resistance to Fusarium and lodging, high yield, and high fiber content. Flax rust incidence is not a problem anymore.Conclusion. Plant breeders have at their disposal a rich stock of source material preserved in the VIR collection to produce resistant flax cultivars. The use of rust resistance donors in hybridization cannot disrupt the most important properties of a cultivar

Localization of rust resistance genes in old local Russian flaxes by methods of classical genetics

Flax rust, a disease  that  destroyed a significant portion  of the yield before  the creation  of resistant varieties, is currently defeated, but it can cause new outbreaks as identical resistance genes  are used in breeding. Since only one of the allelic genes  can be introduced into a variety, the aim of this work is to identify genes  for resistance to the disease  in lines selected during  the evaluation of old Russian flaxes from the VIR collection. The original accessions  were  added to  the  collection  in 1922, that  is, before  the  release  of breeding varieties,  so  their genes  are of natural  origin. The analysis was performed on an artificial infectious  background by methods of classical genetics,  including the test for allelism. Nine monogenic lines with the original R genes  were crossed to tester  varieties for six loci: K, L, M, N, P, and Q. F2 hybrids in the phase  of cotyledon leaves were inoculated with monopustule clones  of the  fungus,  not  virulent  to any of evaluated genes.  Gene allelism was checked  by the absence of the segregation. It was exactly proven  that  R genes  of the k-716 line from the Pskov kryazh (gc-32) and  the  k-780 accession  from the  Minsk oblast  (gc-33) were located  in the  P locus, the  gene  of the  k-846 line from the Ivanovo-Voznesensk oblast (gc-39) was in the M locus, and the gene of the k-834 line from the Vladimir oblast (gc-38) probably belonged to the K locus. The segregation in the crosses of all testers to the k-630 line from the Simbirsk oblast (gc-25) showed that  its gene  was not allelic to any of the known loci. Probably, there  was a formerly unknown locus. The location of the other genes  failed to be identified due to the linkage between loci N and P and the presence of several resistance genes  in some lines. The gene in gc-9 was in either M or K locus; and the genes  of gc-34, gc-40, and gc-46 were located in P or K. Since all the evaluated genes  were original, the genes of these lines were different alleles of the identified loci

Prospective study of serum 25(OH)-vitamin D concentration and risk of oesophageal and gastric cancers

We prospectively examined the relation between pretrial serum vitamin D status and risk of oesophageal and gastric cancers among subjects who developed cancer over 5.25 years of follow-up, including 545 oesophageal squamous cell carcinomas (ESCC), 353 gastric cardia adenocarcinomas, 81 gastric noncardia adenocarcinomas, and an age- and sex-stratified random sample of 1105 subjects. The distribution of serum 25(OH)D was calculated using the known sampling weights. For the cohort as a whole, the 25th, 50th, and 75th percentile concentrations of 25(OH)-vitamin D were 19.6, 31.9, and 48.7 nmol l−1, respectively, and we found that higher serum 25(OH)D concentrations were associated with monotonically increasing risk of ESCC in men, but not in women. Comparing men in the fourth quartile of serum 25(OH)D concentrations to those in the first, we found a hazard ratio (HR) (95% confidence interval (CI)) of 1.77 (1.16–2.70), P trend=0.0033. The same comparison in women had a HR (95% CI) of 1.06 (0.71–1.59), P trend=0.70. We found no associations for gastric cardia or noncardia adenocarcinoma. Among subjects with low vitamin D status, higher serum 25(OH)D concentrations were associated with significantly increased risk of ESCC in men, but not in women. Further refinements of the analysis did not suggest any factors, which could explain this unexpected result

Toll-like receptor 4 and high-mobility group box-1 are involved in ictogenesis and can be targeted to reduce seizures

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Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats

<p>Abstract</p> <p>Background</p> <p>Identification of approximate tandem repeats is an important task of broad significance and still remains a challenging problem of computational genomics. Often there is no single best approach to periodicity detection and a combination of different methods may improve the prediction accuracy. Discrete Fourier transform (DFT) has been extensively used to study primary periodicities in DNA sequences. Here we investigate the application of DFT method to identify and study alphoid higher order repeats.</p> <p>Results</p> <p>We used method based on DFT with mapping of symbolic into numerical sequence to identify and study alphoid higher order repeats (HOR). For HORs the power spectrum shows equidistant frequency pattern, with characteristic two-level hierarchical organization as signature of HOR. Our case study was the 16 mer HOR tandem in AC017075.8 from human chromosome 7. Very long array of equidistant peaks at multiple frequencies (more than a thousand higher harmonics) is based on fundamental frequency of 16 mer HOR. Pronounced subset of equidistant peaks is based on multiples of the fundamental HOR frequency (multiplication factor <it>n </it>for <it>n</it>mer) and higher harmonics. In general, <it>n</it>mer HOR-pattern contains equidistant secondary periodicity peaks, having a pronounced subset of equidistant primary periodicity peaks. This hierarchical pattern as signature for HOR detection is robust with respect to monomer insertions and deletions, random sequence insertions etc. For a monomeric alphoid sequence only primary periodicity peaks are present. The 1/<it>f</it>^{<it>β </it>}– noise and periodicity three pattern are missing from power spectra in alphoid regions, in accordance with expectations.</p> <p>Conclusion</p> <p>DFT provides a robust detection method for higher order periodicity. Easily recognizable HOR power spectrum is characterized by hierarchical two-level equidistant pattern: higher harmonics of the fundamental HOR-frequency (secondary periodicity) and a subset of pronounced peaks corresponding to constituent monomers (primary periodicity). The number of lower frequency peaks (secondary periodicity) below the frequency of the first primary periodicity peak reveals the size of <it>n</it>mer HOR, i.e., the number <it>n </it>of monomers contained in consensus HOR.</p

The Genetic Signatures of Noncoding RNAs

The majority of the genome in animals and plants is transcribed in a developmentally regulated manner to produce large numbers of non–protein-coding RNAs (ncRNAs), whose incidence increases with developmental complexity. There is growing evidence that these transcripts are functional, particularly in the regulation of epigenetic processes, leading to the suggestion that they compose a hitherto hidden layer of genomic programming in humans and other complex organisms. However, to date, very few have been identified in genetic screens. Here I show that this is explicable by an historic emphasis, both phenotypically and technically, on mutations in protein-coding sequences, and by presumptions about the nature of regulatory mutations. Most variations in regulatory sequences produce relatively subtle phenotypic changes, in contrast to mutations in protein-coding sequences that frequently cause catastrophic component failure. Until recently, most mapping projects have focused on protein-coding sequences, and the limited number of identified regulatory mutations have been interpreted as affecting conventional cis-acting promoter and enhancer elements, although these regions are often themselves transcribed. Moreover, ncRNA-directed regulatory circuits underpin most, if not all, complex genetic phenomena in eukaryotes, including RNA interference-related processes such as transcriptional and post-transcriptional gene silencing, position effect variegation, hybrid dysgenesis, chromosome dosage compensation, parental imprinting and allelic exclusion, paramutation, and possibly transvection and transinduction. The next frontier is the identification and functional characterization of the myriad sequence variations that influence quantitative traits, disease susceptibility, and other complex characteristics, which are being shown by genome-wide association studies to lie mostly in noncoding, presumably regulatory, regions. There is every possibility that many of these variations will alter the interactions between regulatory RNAs and their targets, a prospect that should be borne in mind in future functional analyses

Burials with Beads from Anatkasy Burial Ground

The paper features the materials of burials with beads from the Anatkasy burial ground corresponding to the medieval Mari culture. The site is located on the B. Tsivil river, right tributary of the Volga river. A total of 33 burials, 2 sacrificial complexes and 2 pits with traces of ritual activities were revealed during excavations. The total number of discovered beads is 340 items, which were located in following six burials with beads: No. 2, 3, 5, 22, 24, 31. The article contains a classification of beads on the basis of Yu.L. Shchapova's work “Ancient glass. Morphology, technology, chemical composition” (Shchapova, 1989). On the basis of numerous counterparts, the authors conducted dating of the bead material representing an important chronological indicator of the site. This is the first introduction of the material from these burial complexes with beads into scientific discourse

FIBRE FLAX ACCESSIONS OF CHINESE BREEDING AS SOURCES OF VALUABLE AGRONOMIC CHARACTERS

Evaluated in the environments of the North-West of Russia were 75 accessions of fibre flax varieties bred in China. They were planted for 2-3 years during the period from 2006 to 2012. As a result of the study, new sources of valuable agronomic characters were identified