Genetic diversity of potato varieties bred in Russia and near-abroad countries based on polymorphism of SSR-loci and markers associated with resistance R-genes

The genetic diversity of potato varieties from the VIR collection was analyzed based on microsatellite analysis. These varieties have been bred in Russia and near-abroad countries since the 1931. Application of 14 highly polymorphic nuclear microsatellites (SSR) enabled the complete discrimination of all 113 varieties. Additionally, we have studied these varieties for the distribution of 8 DNA markers associated with three R-genes involved in the control of resistance to two quarantine objects: the potato wart Synchytrium endobioticum and golden potato cyst nematode Globodera rostochiensis, which occur locally in some regions of the Russian Federation. All the analyzed varieties with resistance to S. endobioticum pathotype 1 revealed the diagnostic marker Nl-251400 of the Sen1 gene and a few susceptible cultivars lost this diagnostic fragment. The tested markers of the H1 and Gro1-4 genes, which confer resistance to G. rostochiensis pathotype Ro1 revealed different predictiveness. In the molecular screening of potato varieties, it is better to use several markers of these genes. Results of molecular screening using six markers of the H1 and Gro1-4 genes allowed us to detect 6 haplotypes in the tested subset. Five haplotypes include varieties with different combinations of the markers tested, the majority (87.9 %) of these varieties were highly resistant or moderately resistant to G. rostochiensis. The most numerous haplotype H1/0 included 76 varieties, which did not possess any marker; 96.1 % of these varieties were susceptible to G. rostochiensis. Predictive associations between haplotype content, wart and nematode resistance, pedigree and ‘variety age’ are discussed

MARKER-ASSOCIATED SELECTION OF RUSSIAN POTATO VARIETIES WITH USING MARKERS OF RESISTANCE GENES TO THE GOLDEN POTATO CYST NEMATODE (PATHOTYPE RO1)

The results of molecular screening of 103 Russian breeding varieties from the VIR potato collection are presented. These varieties were studied for the presence of diagnostic markers associated with the HI and Grol-4 genes conferring resistance to the golden potato cyst nematode - Globodera rostochiensis (Woll.) Behr. - pathotype Ro1. 25 varieties possessed the diagnostic markers of these genes. Among the nematode-resistant varieties, the frequency of genotypes with the diagnostic fragments of 57R and N195 markers of the Hl locus was 98%, and of marker Gro1-4-1 of the Grol-4 gene - 2%

Finding RB/Rpi-blb1/Rpi-sto1-like sequences in conventionally bred potato varieties

The main objectives in potato breeding are increasing yield abilities and improving resistance to numerous pathogens and pests. Among them, the late blight caused by the Phytophthora infestans oomycete is one of the most destructive potato diseases both in Russia and worldwide. Wild relatives of cultivated potato are traditionally used in breeding as the source of valuable R genes conferring resistance to pathogens. Of particular interest are Mexican wild species because Mexico is the centre of origin and diversity of P. infestans and at the same time, it is the centre of potato species diversity.  Mexican wild potato species S. bulbocastanum and S. stoloniferum are an important source of the R genes conferring broad-spec trum resistance against various isolates of P. infestans (Rpi-blb1,  Rpi-blb2, Rpi-sto1). Recently these genes have been transferred into cultivated potato gene pool using the cisgene  approach. At the same time there is a high probability of finding geno types with the Rpi-sto1 gene (functional homologues of  Rpi-blb1) among conventionally bred varieties because for about 40 years S. stoloniferum has been used in breeding as a source of the Rysto and Ry-fsto genes of the extreme resistance to the most important viral pathogen PVY. In this study 188 potato varieties bred in Russia and in near-abroad countries were screened for the presence of six gene-specific markers of the RB/Rpi-blb1 =  Rpi-sto1 and Rpi-blb2 genes conferring broad-spectrum resistance against P. infestans, and for the markers linked to the Rysto and Ry-fsto genes conferring extreme resistance to PVY. In addition, a marker for detecting male sterile mitochondrial DNA type gamma derived from S. stoloniferum was used. The genotypes selected through the molecular markers were divided into four groups: (A) 13 PVY resistant varieties carrying diagnostic markers of the Rysto, Ry-fsto genes and having sterile mt-type gamma; (B) four varieties possessing mt-type gamma and not having the markers of the R genes introgressed from S. stoloniferum; (C) eight genotypes carrying five gene-specific markers for the RB/Rpi-blb1/= Rpi-sto1; (D) the rest 166 (86.9 %) varieties not possessing any of the diagnostic markers associated with the S. stoloniferum genetic material. The sequences of the Rpi-sto1- and BLB1 F/R-amplicons were identical in all the genotypes of group ‘C’ and showed respective 99 % and 100 % similarity to the corresponding fragments of the Rpi-sto1 and Rpi-blb1 genes from the GenBank database. Among the genotypes of group ‘C’ various mt-types were detected, and some of them were male fertile

Baby MIND: A magnetised spectrometer for the WAGASCI experiment

The WAGASCI experiment being built at the J-PARC neutrino beam line will measure the difference in cross sections from neutrinos interacting with a water and scintillator targets, in order to constrain neutrino cross sections, essential for the T2K neutrino oscillation measurements. A prototype Magnetised Iron Neutrino Detector (MIND), called Baby MIND, is being constructed at CERN to act as a magnetic spectrometer behind the main WAGASCI target to be able to measure the charge and momentum of the outgoing muon from neutrino charged current interactions.Comment: Poster presented at NuPhys2016 (London, 12-14 December 2016). Title + 4 pages, LaTeX, 6 figure

Baby MIND Experiment Construction Status

Baby MIND is a magnetized iron neutrino detector, with novel design features, and is planned to serve as a downstream magnetized muon spectrometer for the WAGASCI experiment on the T2K neutrino beam line in Japan. One of the main goals of this experiment is to reduce systematic uncertainties relevant to CP-violation searches, by measuring the neutrino contamination in the anti-neutrino beam mode of T2K. Baby MIND is currently being constructed at CERN, and is planned to be operational in Japan in October 2017.Comment: Poster presented at NuPhys2016 (London, 12-14 December 2016). 4 pages, LaTeX, 7 figure

Synchronization of the Distributed Readout Frontend Electronics of the Baby MIND Detector

Baby MIND is a new downstream muon range detector for the WGASCI experiment. This article discusses the distributed readout system and its timing requirements. The paper presents the design of the synchronization subsystem and the results of its test

Baby MIND: A magnetized segmented neutrino detector for the WAGASCI experiment

T2K (Tokai-to-Kamioka) is a long-baseline neutrino experiment in Japan designed to study various parameters of neutrino oscillations. A near detector complex (ND280) is located 280~m downstream of the production target and measures neutrino beam parameters before any oscillations occur. ND280's measurements are used to predict the number and spectra of neutrinos in the Super-Kamiokande detector at the distance of 295~km. The difference in the target material between the far (water) and near (scintillator, hydrocarbon) detectors leads to the main non-cancelling systematic uncertainty for the oscillation analysis. In order to reduce this uncertainty a new WAter-Grid-And-SCintillator detector (WAGASCI) has been developed. A magnetized iron neutrino detector (Baby MIND) will be used to measure momentum and charge identification of the outgoing muons from charged current interactions. The Baby MIND modules are composed of magnetized iron plates and long plastic scintillator bars read out at the both ends with wavelength shifting fibers and silicon photomultipliers. The front-end electronics board has been developed to perform the readout and digitization of the signals from the scintillator bars. Detector elements were tested with cosmic rays and in the PS beam at CERN. The obtained results are presented in this paper.Comment: In new version: modified both plots of Fig.1 and added one sentence in the introduction part explaining Baby MIND role in WAGASCI experiment, added information for the affiliation

Ancient human mitochondrial genomes from Bronze Age Bulgaria: new insights into the genetic history of Thracians

Abstract One of the best documented Indo-European civilizations that inhabited Bulgaria is the Thracians, who lasted for more than five millennia and whose origin and relationships with other past and present-day populations are debated among researchers. Here we report 25 new complete mitochondrial genomes of ancient individuals coming from three necropolises located in different regions of Bulgaria – Shekerdja mogila, Gabrova mogila and Bereketska mogila – dated to II-III millennium BC. The identified mtDNA haplogroup composition reflects the mitochondrial variability of Western Eurasia. In particular, within the ancient Eurasian genetic landscape, Thracians locate in an intermediate position between Early Neolithic farmers and Late Neolithic-Bronze Age steppe pastoralists, supporting the scenario that the Balkan region has been a link between Eastern Europe and the Mediterranean since the prehistoric time. Spatial Principal Component Analysis (sPCA) performed on Thracian and modern mtDNA sequences, confirms the pattern highlighted on ancient populations, overall indicating that the maternal gene pool of Thracians reflects their central geographical position at the gateway of Europe

Cytoplasmic genetic diversity of potato varieties bred in Russia and FSU countries

Male sterility in potato is little studied since traditional breeding is based  on the vegetative reproduction of highly heterozygous tetraploid varieties. The rapid development of hybrid diploid breeding contributes to growing interest in studying the male sterility of this important crop. In this work, a set of 6 cytoplasmic markers was employed to describe cytoplasmic genetic diversity of 185 potato cultivars bred in Russia and FSU countries. Three cytoplasm types were identified, T (40.0 %), D (50.8 %) and W/γ (8.7 %), which according to literature  are associated with male sterility. With a single exception (0.5 %), cytoplasm types characteristic of male fertile forms (A, P) were not found in the subset  of 185 cultivars. A comparison of these results with previously published data suggested expanding the subset  to up to 277 cultivars, all developed in Russia or FSU countries;  however,  the resulting  differentiation into three cytoplasm  types (T, D and W/γ) was nearly the same. Fertility phenotyping helped identify both  male-sterile and male-fertile genotypes within the three groups  of varieties with T-, D- and W/γ-type cytoplasm. Fifteen genotypes differing in cytoplasm  type and male sterility/fertility traits were selected for direct sequencing of 8 mtDNA loci. Fragments of the  nad2, nad7, cox2, atp6 and  CcmFc genes  were identical  in all 15 selected genotypes. The polymorphism, detected in the rps3, atp9 and CcmFc loci, was not associated with male sterility. Two SNPs in the nad1/atp6 and nad2 loci differentiated 7 genotypes with W/γ-type cytoplasm into five genotypes with tetrad sterility, and two with fertile pollen. The results of an NGS analysis confirmed  the association of these  SNPs with tetrad sterility in a larger set of 28 genotypes of different origin, all with W/γ-type cytoplasm.  A heteroplasmy state  was observed both in male-sterile and in male-fertile genotypes