Genome-based trait prediction in multi- environment breeding trials in groundnut

Genomic selection (GS) can be an efficient and cost-effective breeding approach which captures both small- and large-effect genetic factors and therefore promises to achieve higher genetic gains for complex traits such as yield and oil content in groundnut. A training population was constituted with 340 elite lines followed by genotyping with 58 K ‘Axiom_Arachis’ SNP array and phenotyping for key agronomic traits at three locations in India. Four GS models were tested using three different random cross-validation schemes (CV0, CV1 and CV2). These models are: (1) model 1 (M1 = E + L) which includes the main effects of environment (E) and line (L); (2) model 2 (M2 = E + L + G) which includes the main effects of markers (G) in addition to E and L; (3) model 3 (M3 = E + L + G + GE), a naïve interaction model; and (4) model 4 (E + L + G + LE + GE), a naïve and informed interaction model. Prediction accuracy estimated for four models indicated clear advantage of the inclusion of marker information which was reflected in better prediction accuracy achieved with models M2, M3 and M4 as compared to M1 model. High prediction accuracies (> 0.600) were observed for days to 50% flowering, days to maturity, hundred seed weight, oleic acid, rust@90 days, rust@105 days and late leaf spot@90 days, while medium prediction accuracies (0.400–0.600) were obtained for pods/plant, shelling %, and total yield/plant. Assessment of comparative prediction accuracy for different GS models to perform selection for untested genotypes, and unobserved and unevaluated environments provided greater insights on potential application of GS breeding in groundnut

A922 Sequential measurement of 1 hour creatinine clearance (1-CRCL) in critically ill patients at risk of acute kidney injury (AKI)

Meeting abstrac

Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species

Background Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary. Results Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis’ strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes. Conclusions Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds

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Not AvailableImpact of different quality irrigation water viz., normal tap water (NTW, EC 0.7 dS m-1), dilute saline water (DSW, EC 5.0 dS m-1; SAR 5.0 mmol½ L-½), concentrated saline water (CSW, EC 10.0 dS m-1; SAR 5.0 mmol½ L-½), dilute alkali water (DAW, RSC 2.5 me L-1) and concentrated alkali water (CAW, RSC 10.0 me L-1) was evaluated on the physical properties of normal (pHs 7.5, ECe 1.0 dS m-1), saline (pHs 7.7, ECe 10.6 dS m-1) and alkali (pHs 9.15, ECe 2.9 dS m-1) sandy loam soils in the micro-lysimeters during growth of wheat (cv. KRL 213) and rice (cv. CSR 36). Initial saturated hydraulic conductivity (Ks) for normal, saline and alkali soil was 0.16, 0.23 and 0.005 cm h-1, respectively. Ks was reduced significantly to one fifth of initial value under CAW while DSW and CSW caused 20 and 50% increase, respectively as compared to normal soil. In alkali soil, Ks decreased significantly i.e. > 50% under DAW from its initial value of 0.005 cm h-1 and reduced to about onefifth (0.001), under CAW. While Ks increased significantly to 0.07 and 0.21 cm h-1 on the application of DSW and CSW, respectively. In post wheat samples, Ks increased by 10 to 15-times in normal soil while, 5 to 9-times in saline soil and 15 to 30-times in alkali soil under both DSW and CSW. But in comparison to post-rice soil, no effect was observed in alkali soil in post-wheat soil on alkali water application but Ks increased 5 to 10-times in normal and saline soil under saline water irrigations. Dispersion index (DI) and Ks found inversely proportional to each other in all water treatments in all three soils. Under DAW (31.3) and CAW (39.9), DI was increased significantly by 5 and 33%, respectively as compared to the initial soil. DI increased by 12 and 30% under dilute and concentrated alkali water application, respectively in saline soil. DI increased significantly with application of CAW (65.3) and decreased when irrigation was applied with DSW (37.0) and CSW (34.2), respectively. Under different quality water irrigation, soil water retention was the highest in alkali soil followed by normal and saline soils at all matric suctions. Under the application of saline water in all three soils, water retention either decreased or remains unchanged with increase in TEC of irrigation water as compared to normal tap water. Whereas under the application of alkali water, it increased in all the three soils with increase in TEC of irrigation water as compared to normal tap water application,.Not Availabl

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Not AvailableA field experiment was conducted to study the impact of different nitrogen (N) management options on the nutrient uptake, biomass carbon sequestration and yield of maize-wheat system in reclaimed sodic soil of the Trans-Gangetic Plains of India. Seven N management treatments – T1 [100% recommended dose of N (RDN) + 10 t ha−1 farm yard manure (FYM)]; T2 (100% RDN); T3 (75% RDN + 25% N through FYM); T4 (50% RDN + 50% N through FYM), T5 (25% N through FYM); T6 (50% N through FYM) and T7 (control; No N) were tested. Maximum nutrient uptake, biomass carbon sequestration and yield of maize-wheat system were reported in 100% RDN + FYM treatment. Total biomass carbon sequestration and yield were significantly higher by 47.8% and 30.4%, respectively in 100% RDN + FYM as compared to control treatment. However, 100% RDN + FYM was statistically at par with the 100% RDN, 75% RDN + 25% N through FYM, and 50% RDN + 50% N through FYM treatments for both these variables. Nutrient uptake, total carbon sequestration and yield in 50% N through FYM and 25% N through FYM were insignificantly higher as compared to control, but significantly lower than the 100% RDN treatment. Results indicated that the addition of FYM with RDN increased the nutrient uptake, biomass carbon sequestration and yield of maize-wheat system. Higher biomass carbon sequestration and sustainability to maize and wheat cropping system is need of the hour in the study area.Not Availabl

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Not Available• Data base on salt affected soils and poor quality waters in the country needs to be updated on priority taking the help of modern tools such as GIS, remote sensing and GPS based surveys. Policy decision is required on this issue to enhance allocation of funds and infrastructural support to delineate the areas affected by salinity/ alkalinity for developing appropriate technologies for their reclamation. • Research on low-cost amendments (alternatives to gypsum) for alkaline /vertisol soils should be expedited and new generation problems related to soil fertility, salinity should be diagnosed and effective remedial measures should be explored. • New refinements in research technologies related to sub-surface drainage and integrated approach involving fast-growing plantation based technologies (biodrainage) should be investigated both for inland and coastal conditions. • Second generation problems of resodification as well as decline in productivity from the reclaimed alkali soils needs to be addressed on priority. Research on laser land levelling, zero tillage planting or turbo seeding needs to be accelerated in different crop rotations. • Research efforts should be advanced on management of dry-land salinity and coastal salinity in the scenario of climate change. • More research efforts are needed to develop multiple stress tolerance cultivars with the help of genetic engineering and use of salt tolerant genes. Priority may be given on identification and selection of potential halophytic crops for domestication in highly saline and waterlogged areas. • Application of new research tools such as nano-technology and use of microbiology in reclamation of salty soils, micro irrigation, smart agriculture technologies etc. for increasing productivity, improving crops and phytoremediation processes must get priority. • During reclamation of alkali soils, addition of salt tolerant bacteria in the form of a commercial culture ‘CSR Bio’ to the soil enhances performance of banana and some other crops also. Policy support in the form of appropriate subsidy etc. could help reclaim large areas through these horticultural interventions, in the form of a tie-up with developmental schemes like National Horticulture Mission. • New integrated farming systems involving agroforestry technologies must be developed for increasing farm productivity in salty waterlogged areas. Several land shaping technologies have been developed, in inland alkaline waterlogged as well as coastal saline waterlogged conditions to reduce salinity build-up. Policy decisions needs to be undertaken to provide appropriate subsidy for implementing these land shaping technologies to the resource poor farming communities of the region. • Decision support systems needs to be developed to enhance productivity of salt affected areas, both under inland and coastal conditions. • Research efforts may also be made on value addition and quality of produce under saline agriculture and other stress conditions. • Social, economic, policy and political dimensions related to saline agriculture may be explored in recent scenarios.Not Availabl

ENSO, IOD and Indian Summer Monsoon in NCEP climate forecast system

El Niño-Southern Oscillation (ENSO), Indian Ocean Dipole (IOD) and Indian Summer Monsoon rainfall features are explored statistically and dynamically using National Centers for Environment Prediction (NCEP) Climate Forecast System (CFSv1) freerun in relation to observations. The 100 years of freerun provides a sufficiently long homogeneous data set to find out the mean state, periodicity, coherence among these climatic events and also the influence of ENSO and IOD on the Indian monsoon. Differences in the occurrence of seasonal precipitation between the observations and CFS freerun are examined as a coupled ocean-atmosphere system. CFS simulated ENSO and IOD patterns and their associated tropical Walker and regional Hadley circulation in pure ENSO (PEN), pure IOD (PIO) and coexisting ENSO-IOD (PEI) events have some similarity to the observations. PEN composites are much closer to the observation as compared to PIO and PEI composites, which suggest a better ENSO prediction and its associated teleconnections as compared to IOD and combined phenomenon. Similar to the observation, the model simulation also show that the decrease in the Indian summer monsoon rainfall during ENSO phases is associated with a descending motion of anomalous Walker circulation and the increase in the Indian summer monsoon rainfall during IOD phase is associated with the ascending branch of anomalous regional Hadley circulation. During co-existing ENSO and IOD years, however, the fate of Indian summer monsoon is dictated by the combined influence of both of them. The shift in the anomalous descending and ascending branches of the Walker and Hadley circulation may be somewhat attributed to the cold (warm) bias over eastern (western) equatorial Indian Ocean basin, respectively in the model. This study will be useful for identifying some of the limitations of the CFS model and consequently it will be helpful in improving the model to unravel the realistic coupled ocean-atmosphere interactions for the better prediction of Indian Summer Monsoon

Model biases in long coupled runs of NCEP CFS in the context of Indian summer monsoon

This study examines the performance of National Centers for Environmental Prediction (NCEP) Climate Forecast System (CFS) over the Indian monsoon region in 100 years long coupled run, in terms of biases of sea surface temperature (SST), rainfall and circulation. The study further explores the role of the feedback processes in maintaining these biases. The model simulates reasonable monsoon climatology during JJAS (June-September). It shows dry (wet) rainfall bias concomitant with cold (warm) SST bias over east (west) equatorial Indian Ocean. These biases of SST and rainfall affect both lower- and upper-level circulations in a feedback process, which in turn regulates the SST and rainfall biases by maintaining a coupled feedback process. A dry (wet) rainfall bias over east (west) Indian Ocean induces anomalous low level easterlies over tropical Indian Ocean and causes cold SST bias over east Indian Ocean by triggering evaporation and warm SST bias over west Indian Ocean through advection of warm waters. The persistent SST bias retains the zonal asymmetric heating and meridional temperature gradient resulting in a circum-global subtropical westerly jet core, which in turn magnifies the mid-latitude disturbances and decreases the Mascarene high. The decreased Mascarene high diminishes the strength of monsoon cross-equatorial flow and results in less upwelling as compared to that in the observation. It further increases the SST bias over the West Indian Ocean. The coupled interaction among SST, rainfall and circulation works in tandem through a closed feedback loop to maintain the model biases over tropical Indian Ocean