Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic

BACKGROUND: X chromosome inactivation is a spectacular example of epigenetic silencing. In order to deduce how this complex system evolved, we examined X inactivation in a model marsupial, the tammar wallaby (Macropus eugenii). In marsupials, X inactivation is known to be paternal, incomplete and tissue-specific, and occurs in the absence of an XIST orthologue. RESULTS: We examined expression of X-borne genes using quantitative PCR, revealing a range of dosage compensation for different loci. To assess the frequency of 1X- or 2X-active fibroblasts, we investigated expression of 32 X-borne genes at the cellular level using RNA-FISH. In female fibroblasts, two-color RNA-FISH showed that genes were coordinately expressed from the same X (active X) in nuclei in which both loci were inactivated. However, loci on the other X escape inactivation independently, with each locus showing a characteristic frequency of 1X-active and 2X-active nuclei, equivalent to stochastic escape. We constructed an activity map of the tammar wallaby inactive X chromosome, which identified no relationship between gene location and extent of inactivation, nor any correlation with the presence or absence of a Y-borne paralog. CONCLUSIONS: In the tammar wallaby, one X (presumed to be maternal) is expressed in all cells, but genes on the other (paternal) X escape inactivation independently and at characteristic frequencies. The paternal and incomplete X chromosome inactivation in marsupials, with stochastic escape, appears to be quite distinct from the X chromosome inactivation process in eutherians. We find no evidence for a polar spread of inactivation from an X inactivation center.This project was funded by grants to JAMG and PDW from the Australian Research Council

Bioactivity of Locally Available Plants on Cotton Whitefly, Bemisia tabaci and the fungus isolated from cotton

Aqueous, diethyl ether, chloroform, petroleum ether, N-hexane and benzene extracts of locally available plant species were tested for phytochemical and insecticidal bioactivity against cotton whitefly, Bemisia tabaci, under controlled conditions. This study is within bioprospection context, for utilizing local plant species as alternative in sustainable agriculture development. The leaf and stem extract was used. The whole plant extract of T.procumbens followed by N.oleander and V.rosea showed repellent and toxic effect against adult and second nymphal instars. Leaf extract of all three plants showed high inhibition activity against nymphal instars. In case of flower extract less inhibition activity was shown respectively. Fungi which grow on the cotton plant was screened, characterized and checked for antifungal activity against the extracts of the plant material. Phytochemical analysis was also carried out by standard protocols

Studies on soil fertility status of coffee growing regions in Wayanad district

Top soil in Wayanad region is prone to disturbance and erosion, as the coffee growers’ practice scraping, scuffling and cover digging. It isnecessary to conserve the inherent fertility of top soil by minimum disturbance during farming operations. Otherwise soil deterioration can become one of the major constraints for crop production in the present day exploitative cultivation of plantation crops. It is well known that nutrient availability is influenced by their distribution in the soil as well as other soil characteristics. Soil fertility is the key to meet the nutrient requirement of the crops. Soil test based nutrient management will increase the crop productivity there by helping to save the fertility. The study, carried out to understand the fertility status of the coffee soils, revealed a higher acidity (98%) with deficiencies of calcium (32%), magnesium (96%) and boron (31%) limiting the coffee productivity in the district. The coffee area in the district is strongly acidic (69%) due to lack of liming and continuous use of acid producing fertilizers. Fifty per cent of soil sampleswere high in phosphorus which in turn impair the nutrient balance and affects micronutrient absorption by plants. Deficiency of calcium and magnesium affects uptake of other nutrients which upsets cellular functions. In coffee, boron deficiency will reduce the productivity by affecting flowering and fruit set. Amelioration of soil acidity and optimal use of major, secondary and micronutrients are must to enhance coffee productivity in the district. Application of manures and fertilizers based on soil test values will save the fertilizers and also sustain the soil health. Integrated management of plant nutrients is essential to achieve sustainable coffee crop production

Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes.

Cancer Informatics for Cancer Centers (CI4CC) is a grassroots, nonprofit 501c3 organization intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world but with a special emphasis on the 70 National Cancer Institute-funded cancer centers. Although each of the participating cancer centers is structured differently, and leaders' titles vary, we know firsthand there are similarities in both the issues we face and the solutions we achieve. As a consortium, we have initiated a dedicated listserv, an open-initiatives program, and targeted biannual face-to-face meetings. These meetings are a place to review our priorities and initiatives, providing a forum for discussion of the strategic and pragmatic issues we, as informatics leaders, individually face at our respective institutions and cancer centers. Here we provide a brief history of the CI4CC organization and meeting highlights from the latest CI4CC meeting that took place in Napa, California from October 14-16, 2019. The focus of this meeting was "intersections between informatics, data science, and population science." We conclude with a discussion on "hot topics" on the horizon for cancer informatics

Detection of a Cis eQTL Controlling BMCO1 Gene Expression Leads to the Identification of a QTG for Chicken Breast Meat Color

Classical quantitative trait loci (QTL) analysis and gene expression QTL (eQTL) were combined to identify the causal gene (or QTG) underlying a highly significant QTL controlling the variation of breast meat color in a F2 cross between divergent high-growth (HG) and low-growth (LG) chicken lines. Within this meat quality QTL, BCMO1 (Accession number GenBank: AJ271386), encoding the β-carotene 15, 15′-monooxygenase, a key enzyme in the conversion of β-carotene into colorless retinal, was a good functional candidate. Analysis of the abundance of BCMO1 mRNA in breast muscle of the HG x LG F2 population allowed for the identification of a strong cis eQTL. Moreover, reevaluation of the color QTL taking BCMO1 mRNA levels as a covariate indicated that BCMO1 mRNA levels entirely explained the variations in meat color. Two fully-linked single nucleotide polymorphisms (SNP) located within the proximal promoter of BCMO1 gene were identified. Haplotype substitution resulted in a marked difference in BCMO1 promoter activity in vitro. The association study in the F2 population revealed a three-fold difference in BCMO1 expression leading to a difference of 1 standard deviation in yellow color between the homozygous birds at this haplotype. This difference in meat yellow color was fully consistent with the difference in carotenoid content (i.e. lutein and zeaxanthin) evidenced between the two alternative haplotypes. A significant association between the haplotype, the level of BCMO1 expression and the yellow color of the meat was also recovered in an unrelated commercial broiler population. The mutation could be of economic importance for poultry production by making possible a gene-assisted selection for color, a determining aspect of meat quality. Moreover, this natural genetic diversity constitutes a new model for the study of β-carotene metabolism which may act upon diverse biological processes as precursor of the vitamin A

Backcross breeding in groundnut (Arachis hypogaea L.)

Rust caused by Puccinia arachidis Speg. is the most serious disease of groundnut and causes substantial yield loss and reduces the fodder and seed quality. Recombinant inbred lines (F6) were generated by SSD method from cross GPBD-5 x GPBD-4 and the rust resistant plants were backcrossed to the recurrent parent (GPBD-5) to develop a backcross population (BC1F4). The objective ofthis experiment was to study the possibilities of linkage break-down between yield component traits and rust resistance in groundnut. Analysis of data revealed that there was a shift in correlation from negative (F6) to positive significant direction (BC1F4) between pod yield per plant with plant height and between plant height with number of primary branches. Similarly there was linkage break-down between negative significant to positive significant association of number of primary branches with number of pods per plant, kernel yield per plant and shelling percent at both genotypic and phenotypic levels. Altogether a desirable shift in association and the proof of broken repulsion phase linkage and release of concealed variability, which is useful in plant breeding, provides a lot of scope for selection. Unchanged negative association between pod yield per plant with reaction to rust and shelling percent in both phenotypic and genotypic level in both the populations, indicated the operation of strong linkage blocks and which requires an intensive selection to combine disease resistance with yield. Otherwise inter-mating of highly extreme segregants in the populations also would cause breakage of these stubborn linkages. Thus, for yield component traits, backcrossing of selected plants is more rewarding than the single cross and advance by single seed decent method of breeding in groundnut

Genetic variability and marker detection for rust resistance in recombinant inbred lines and backcross inbred lines of groundnut (Arachis hypogaea l.)

A F6 mapping population and backcross populations (BC1F4 and BC2F3 BC3F2) were developed from the cross between the susceptible parent GPBD-5 and resistant parents ICGV 86699 and ICGV 99005 to dissect the genetic variation and SSR markers linked to the rust resistance in groundnut. Genetic variability revealed that there were highly significant differences among recombinants for rust reaction. Less differences were observed between PCV and GCV for rust reaction in both crosses, which indicated a greater role of genetic components. High values of heritability (>80%) genetic advance and-genetic advance as percent mean was observed for rust reaction in F6 and backcross populations. Bulk segregant analysis in the segregating populations of both crosses (GPBD-5 x ICGV 86699 and GPBD-5 x ICGV 99005) indicated Tc4g10 marker was putatively linked to the rust resistant gene. The association of the putative marker identified based on DNA pooling from the selected segregants was established by single marker analysis (SMA). In the F6 population of both crosses GPBD-5 x ICGV 86699 and GPBD-5 x ICGV 99005, the Tc4glO marker accounted for 72.40% and 50.60% total variation, respectively. Tc4g10 marker accounted for 67.10%,38.40% and 61.30% total variation in the cross GPBD-5 x ICGV 86699, and the same marker accounted for 73.8%, 54.7% and 84.4% total variation in the cross GPBD-5 x ICGV 99005 in BC1F4, BC2F3 and BC3F2, respectively. This marker can be used in marker assisted selection for rust resistance in groundnut improvement programs

G × E interactions in QTL introgression lines of Spanish-type groundnut (Arachis hypogaea L.)

Multi-environment testing at five locations for rust and late leaf spot (LLS) resistance with 41 introgressed lines (ILs) bred using marker-assisted backcross breeding in the genetic background Spanish- type groundnut varieties identified significant genotype, and genotype 9 environment interactions (GEI) for LLS disease resistance and yield parameters. Significant GEI effects suggest the need to identify location specific breeding lines to achieve gains in pod yield and LLS resistance. The observed variable LLS disease reaction among the ILs in part suggests influence of background genotype on the level of resistance. A breeding scheme with early generation selection using molecular markers followed by phenotyping for LLS, and multi-location testing of fixed breeding lines was optimized to enhance selection intensity and accuracy in groundnut breeding. The ILs, ICGVs 14431, 14436 and 14438 with pooled LLS score at 90 DAS of 3.5–3.7 were superior to respective recurrent parent for pod yield, with early maturing similar to recurrent parents. The pod yield advantage in ILs is attributed by more number of pods, besides resistance to LLS that contributes to better filling