Salt tolerance is an important complex trait in rice which helps the plant to survive under salt stress condition. The complexity of salt tolerance is governed by many genes which could be identified ...efficiently by genome wide association study (GWAS). In the present study, we evaluated 180 diverse rice accessions for salinity tolerance at reproductive stage and successfully genotyped them using simple sequence repeats markers covering all 12 chromosomes. Eleven physiological parameters which include Na
+
, K
+
, Ca
2+
, Mg
2+
content in stem and leaves and two important morphological traits grain yield and salt injury score were measured under control and saline conditions at reproductive stage. Population structure analysis revealed four subgroups and admixture level ranged from 0.70 to 57.2%. Association study using mixed linear model controlling both structure and kinship, identified 28 significant marker-trait associations and out of which 19 associations were identified for Na
+
, K
+
, Na
+
/K
+
uptake in stem and leaves. The phenotypic variance for these associations ranged from 5.12 to 13.37%. The position of several associated markers was found close to candidate genes like transcription factors, membrane transporters, signal transducers which have previously shown to play active roles of salinity tolerance in rice. The present GWAS was successful in unravelling genomic regions that regulate ionic homoeostasis in rice. Furthermore, the salinity tolerant accessions identified during the screening could become important resource for breeding programs.
We study the photon emission by bremsstrahlung and nonlinear Compton scattering from interaction of ultra-intense laser pulses with cone target and flat foil using particle-in-cell simulations. The ...simulations are performed for laser pulses interacting with Al and Au targets. The strength of the two mechanisms of photon emission from bremsstrahlung and nonlinear Compton scattering are compared. When an ultra-intense (I>10^{22}W/cm^{2}) laser interacts with a cone and a foil target, photon emission by bremsstrahlung is found to be comparable to that from nonlinear Compton scattering. The obtained electron energy as well as the energy and number of photons emitted were found to be higher in case of cone shaped target compared with that of a foil target. The enhanced photon emission from cone shaped target is attributed to the guiding or collimation of hot electrons towards the cone tip from the self-generated magnetic field and electrostatic field along the cone surface which pushes the hot electrons towards the tip.
Rice is the staple food and provides livelihood for smallholder farmers in the coastal delta regions of South and Southeast Asia. However, its productivity is often low because of several abiotic ...stresses including high soil salinity and waterlogging during the wet (monsoon) season and high soil and water salinity during the dry season. Development and dissemination of suitable rice varieties tolerant of these multiple stresses encountered in coastal zones are of prime importance for increasing and stabilizing rice productivity, however adoption of new varieties has been slow in this region. Here we implemented participatory varietal selection (PVS) processes to identify and understand smallholder farmers’ criteria for selection and adoption of new rice varieties in coastal zones. New breeding lines together with released rice varieties were evaluated in on-station and on-farm trials (researcher-managed) during the wet and dry seasons of 2008–2014 in the Indian Sundarbans region. Significant correlations between preferences of male and female farmers in most trials indicated that both groups have similar criteria for selection of rice varieties. However, farmers’ preference criteria were different from researchers’ criteria. Grain yield was important, but not the sole reason for variety selection by farmers. Several other factors also governed preferences and were strikingly different when compared across wet and dry seasons. For the wet season, farmers preferred tall (140–170cm), long duration (160–170 d), lodging resistant and high yielding rice varieties because these traits are required in lowlands where water stagnates in the field for about four months (July to October). For the dry season, farmers’ preferences were for high yielding, salt tolerant, early maturing (115–130 d) varieties with long slender grains and good quality for better market value. Pest and disease resistance was important in both seasons but did not rank high. When farmers ranked the two most preferred varieties, the ranking order was sometimes variable between locations and years, but when the top four varieties that consistently ranked high were considered, the variability was low. This indicates that at least 3–4 of the best-performing entries should be considered in succeeding multi-location and multi-year trials, thereby increasing the chances that the most stable varieties are selected. These findings will help improve breeding programs by providing information on critical traits. Selected varieties through PVS are also more likely to be adopted by farmers and will ensure higher and more stable productivity in the salt- and flood-affected coastal deltas of South and Southeast Asia.
We have extended the recently developed approach that employs first-principles Hamiltonian, tight-binding Hamiltonian, and Green’s function methods to study native point defect states in ...InAs/InAs0.7Sb0.3 strained layer superlattices (SLS) latticed matched to GaSb. Our calculations predict a defect level at 250 meV below the GaSb valance band edge, in agreement with values deduced recently from lifetime measurements and analysis Aytac et al. Phys. Rev. Appl., 5, 054016 (2016). In addition, we identify the defect level to be arising from an In-vacancy in the InAsSb region of the superlattice. The formation energy calculations further indicate that In-vacancies are easier to form in both regions of the superlattice than in bulk InAs or in InAsSb alloy. Our results suggest that In-vacancy is the most damaging native defect that limits lifetimes InAs/InAs0.7Sb0.3.
We studied the γ-ray emission from laser interactions with structured targets of Al and Au. Bremsstrahlung and Non-linear Compton Scattering (NCS) emission are considered for the γ-ray emission using ...the open source 2-D PIC code EPOCH. Different shapes of the target generated additional hot electrons, which helps to enhance the photon energy in individual cases. The enhancement of photon energy is due to the target's shape and the hot electrons. Hot electron generation and their dynamics, like refluxing behavior, are crucial phenomena in thin targets. This study uses four different shapes of Al and Au targets. The relative strength of emissions from both bremsstrahlung and NCS are compared. The shape of the target enhances the γ-ray energy, electron energy, and emitted photon number and improves the electron beam divergence. The effect of each target shape on hot electrons refluxing behavior and the role of the electric and magnetic fields are discussed in detail.
Pusa Basmati 1121 (PB1121), an elite Basmati rice cultivar is vulnerable to salinity at seedling stage. A study was undertaken to impart seedling-stage salt tolerance into PB1121 by transferring a ...quantitative trait locus (QTL),
, using FL478 as donor, through marker assisted backcrossing. Sequence tagged microsatellite site (STMS) marker RM 3412, tightly linked to
was used for foreground selection. Background recovery was estimated using 90 genome-wide STMS markers. Systematic phenotypic selection helped in accelerated recovery of recurrent parent phenome (RPP). A set of 51 BC
F
lines homozygous for
were advanced to develop four improved near isogenic lines (NILs) of PB1121 with seedling stage salt tolerance. The background genome recovery in the NILs ranged from 93.3 to 99.4%. The improved NILs were either similar or better than the recurrent parent PB1121 for yield, grain and cooking quality and duration. Biochemical analyses revealed significant variation in shoot and root Na
and K
concentrations. Correlation between shoot and root Na
concentration was stronger than that between root and shoot K
concentration. The effect of QTL integration into the NILs was studied through expression profiling of
, one of the genes present in the
region. The NILs had significantly higher
expression than the recurrent parent PB1121, but lower than FL478 on salt exposure validating the successful introgression of
in the NILs. This was also confirmed under agronomic evaluation, wherein the NILs showed greater salt tolerance at seedling stage. One of the NILs, Pusa1734-8-3-3 (NIL3) showed comparable yield and cooking quality to the recurrent parent PB1121, with high field level seedling stage salinity tolerance and shorter duration. This is the first report of successful introgression of
into a Basmati rice cultivar.
Inflammatory breast cancer (IBC) is an aggressive disease. To date, no molecular feature reliably predicts either the response to chemotherapy (CT) or the survival. Using DNA microarrays, we searched ...for multigene predictors.
The World IBC Consortium generated whole-genome expression profiles of 137 IBC and 252 non-IBC (nIBC) samples. We searched for transcriptional profiles associated with pathological complete response (pCR) to neoadjuvant anthracycline-based CT and distant metastasis-free survival (DMFS) in respective subsets of 87 and 106 informative IBC samples. Correlations were investigated with predictive and prognostic gene expression signatures published in nIBC (nIBC-GES). Supervised analyses tested genes and activation signatures of 19 biological pathways and 234 transcription factors.
Three of five tested prognostic nIBC-GES and the two tested predictive nIBC-GES discriminated between IBC with and without pCR, as well as two interferon activation signatures. We identified a 107-gene signature enriched for immunity-related genes that distinguished between responders and nonresponders in IBC. Its robustness was demonstrated by external validation in three independent sets including two IBC sets and one nIBC set, with independent significant predictive value in IBC and nIBC validation sets in multivariate analysis. We found no robust signature associated with DMFS in patients with IBC, and neither of the tested prognostic GES, nor the molecular subtypes were informative, whereas they were in our nIBC series (220 stage I–III informative samples).
Despite the relatively small sample size, we show that response to neoadjuvant CT in IBC is, as in nIBC, associated with immunity-related processes, suggesting that similar mechanisms responsible for pCR exist. Analysis of a larger IBC series is warranted regarding the correlation of gene expression profiles and DMFS.
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