A hierarchical analysis of minisatellite DNA diversity in Gambel oak (Quercus gambelii Nutt.; Fagaceae)

Gambel oak is a short shrub to medium-sized tree of southwest North America for which the potential to grow in large clonal stands has been proposed. Here we use three different multilocus VNTR DNA probes (synthesized via PCR) to demonstrate that clones growing together can be identified, but individual clones exceeding 50 m in diameter do not commonly occur in the study population of Quercus gambelii . Further, using a hierarchical sampling scheme (three circular transects with diameters of 9, 1100, and 28 000 m), we estimate that for nonclonal individuals: (i) mean number of bands analysed per individual = 22.92; (ii) mean similarity (band sharing) between individuals = 0.322; (iii) mean probability that two randomly chosen individuals share all bands = 4.93 × 10^–11; and (iv) mean estimated heterozygosity = 0.796. F _ST calculated for the two nonclonal levels of the sampling hierarchy was 0.023, indicating that little genetic differentiation exists between them. These results support previous findings that, due to life-history traits of the genus and this species (out-crossing, wind-pollinated, animal-dispersed, long-lived woody perennials), gene flow is high and genetic subdivision of populations is low in oaks. At this study site, the clonal nature demonstrated for Gambel oak appears to have little detectable effect on these population genetic characteristics.     

Mutational landscape of the human Y chromosome-linked genes and loci in patients with hypogonadism

Sex chromosome-related anomalies engender plethora of conditions leading to male infertility. Hypogonadotropic hypogonadism (HH) is a rare but well-known cause of male infertility. Present study was conducted to ascertain possible consensus on the alterations of the Y-linked genes and loci in males representing hypogonadism (H), which in turn culminate in reproductive dysfunction. A total of nineteen 46, XY males, clinically diagnosed with H (11 representative HH adults and eight prepubertal boys suspected of having HH) were included in the study. Sequence-tagged site screening, SRY gene sequencing, fluorescence in situ hybridization mapping (FISH), copy number and relative expression studies by real-time PCR were conducted to uncover the altered status of the Y chromosome in the patients. The result showed random microdeletions within the AZFa (73%)/b (78%) and c(26%) regions. Sequencing of the SRY gene showed nucleotide variations within and outside of the HMG box in four males (21%). FISH uncovered mosaicism for SRY, AMELY, DAZ genes and DYZ1 arrays, structural rearrangement for AMELY (31%) and duplication of DAZ (57%) genes. Copy number variation for seven Y-linked genes (2–8 rounds of duplication), DYZ1 arrays (495–6201copies) and differential expression of SRY, UTY and VCY in the patients’ blood were observed. Present work demonstrates the organizational vulnerability of several Y-linked genes in H males. These results are envisaged to be useful during routine diagnosis of H patients.     

Agroclimatic conditions in Europe under climate change

To date, projections of European crop yields under climate change have been based almost entirely on the outputs of crop‐growth models. While this strategy can provide good estimates of the effects of climatic factors, soil conditions and management on crop yield, these models usually do not capture all of the important aspects related to crop management, or the relevant environmental factors. Moreover, crop‐simulation studies often have severe limitations with respect to the number of crops covered or the spatial extent. The present study, based on agroclimatic indices, provides a general picture of agroclimatic conditions in western and central Europe (study area lays between 8.5°W–27°E and 37–63.5°N), which allows for a more general assessment of climate‐change impacts. The results obtained from the analysis of data from 86 different sites were clustered according to an environmental stratification of Europe. The analysis was carried for the baseline (1971–2000) and future climate conditions (time horizons of 2030, 2050 and with a global temperature increase of 5 °C) based on outputs of three global circulation models. For many environmental zones, there were clear signs of deteriorating agroclimatic condition in terms of increased drought stress and shortening of the active growing season, which in some regions become increasingly squeezed between a cold winter and a hot summer. For most zones the projections show a marked need for adaptive measures to either increase soil water availability or drought resistance of crops. This study concludes that rainfed agriculture is likely to face more climate‐related risks, although the analyzed agroclimatic indicators will probably remain at a level that should permit rainfed production. However, results suggests that there is a risk of increasing number of extremely unfavorable years in many climate zones, which might result in higher interannual yield variability and constitute a challenge for proper crop management.     

Characterization of variation and quantitative trait loci related to terpenoid indole alkaloid yield in a recombinant inbred line mapping population of <Emphasis Type="Italic">Catharanthus roseus</Emphasis>

Improved Catharanthus roseus cultivars are required for high yields of vinblastine, vindoline and catharanthine and/or serpentine and ajmalicine, the pharmaceutical terpenoid indole alkaloids. An approach to derive them is to map QTL for terpenoid indole alkaloids yields, identify DNA markers tightly linked to the QTL and apply marker assisted selection. Towards the end, 197 recombinant inbred lines from a cross were grown over two seasons to characterize variability for seven biomass and 23 terpenoid indole alkaloids content-traits and yield-traits. The recombinant inbred lines were genotyped for 178 DNA markers which formed a framework genetic map of eight linkage groups (LG), spanning 1786.5 cM, with 10.0 cM average intermarker distance. Estimates of correlations between traits allowed selection of seven relatively more important traits for terpenoid indole alkaloids yields. QTL analysis was performed on them using single marker (regression) analysis, simple interval mapping and composite interval mapping procedures. A total of 20 QTL were detected on five of eight LG, 10 for five traits on LG1, five for four traits on LG2, three for one trait on LG3 and one each for different traits on LG three and four. QTL for the same or different traits were found clustered on three LG. Co-location of two QTL for biomass traits was in accord of correlation between them. The QTL were validated for use in marker assisted selection by the recombinant inbred line which transgressively expressed 16 traits contributory to the yield vinblastine, vindoline and catharanthine from leaves and roots that possessed favourable alleles of 13 relevant QTL.     

Development and characterization of genic SSR markers from low depth genome sequence of <Emphasis Type="Italic">Clarias batrachus</Emphasis> (magur)

Indian magur (Clarias batrachus) is an important freshwater catfish, which is listed as endangered under A3cde + 4acde ver. 3.1 categories by the IUCN (2015) due to decreasing population trend. Microsatellites or short sequence repeats (SSRs) tagged to genes have been utilized as gene marker. In the present study, 31,814 SSRs of C. batrachus (magur) were identified using microsatellite identification tool programme from the next generation sequencing data generated on Roche 454 and Ion Torrent platforms. A bioinformatics pipeline, with stringent criteria resulted in selection of 1672 microsatellite loci falling in the genic region. Initially, a total of 30 loci were selected for primer development; and of these 14 were successfully amplified and five were found to be polymorphic in 30 individuals of C. batrachus (magur). The observed as well as expected heterozygosity ranged from 0.038 to 0.526 and 0.434 to 0.784, respectively, and the number of observed alleles ranged from three to five. The study reported the application of next generation sequencing technologies for rapid development of microsatellite loci in Indian catfish species, C. batrachus (magur).     

Isolation and Characterization of Sodium Chloride-Resistant Callus Culture of Vigna radiata (L.) Wilczek var. radiata

Callus cultures were initiated from seedling root segments ofmungbean (Vigna radiata (L.) Wilczek var. radiata) cv. K 851on modified PC-L2 basal medium. Growing cells were exposed toincreasing concentrations of NaCl in the medium. A concentrationof 300 mol m^–3 NaCl proved completely inhibitory to growthof the calli. On incubation for 25 d, cells which could toleratethis concentration of NaCl grew to form cell clones. Selectedclones were characterized with regard to their growth behaviour,K⁺, Na⁺ and free proline content when grown under stress aswell as on normal media and were compared with the normal sensitivecallus. The selected callus was capable of growing on mediumcontaining NaCl at the inhibitory concentration. The K⁺ contentof the selected callus was lower in the case of the NaCl mediumthan for the normal medium. However, the selected clones maintainedhigher K⁺ and Na⁺ levels, with increased salinization comparedwith the wild-type cells. Salt-selected cells accumulated higherlevels of free proline under NaCl stress compared to wild-typecells. Under normal conditions, however, the amounts of freeproline in selected and non-selected calli were comparable. Key words: Vigna radiata, callus culture, NaCl stress