Identification of a diverse mini‐core panel of Indian rice germplasm based on genotyping using microsatellite markers

Identification of a small core germplasm set representing the available genetic diversity is essential for its proper evaluation and subsequent utilization in rice improvement programmes. For constituting a small diverse mini‐core panel of Indian rice germplasm, a representative set of 6912 accessions drawn based on their geographic origin from the whole rice germplasm collection available in the National Gene Bank was genotyped using 36 microsatellite markers. Automated fragment analysis of amplicons yielded a total of 435 alleles, with an average 12.4 and range of 3–29 alleles per locus. Polymorphism information content (PIC) ranged from 0.08 (RGNMS190) to 0.86 (RM552) with an average of 0.528. Based on genotyping data, a mini‐core consisting of 98 genotypes was identified. Ninety‐four per cent of the alleles present in the core set were present in the mini‐core. The identified small but diverse panel will be useful for further intensive trait‐specific evaluation and utilization in allele mining.     

Evaluation of housekeeping genes as references for quantitative real-time PCR analysis of gene expression in the murrel <Emphasis Type="Italic">Channa striatus</Emphasis> under high-temperature stress

Quantitative real-time polymerase chain reaction is the most advanced method of quantifying gene expression studies; however, the significance of the obtained results strongly depends on the normalization of the data to compensate for differences between the samples. In the present study, expression analysis of six different constitutively expressed genes viz. 18S ribosomal RNA, glyceraldehyde-3-phosphate dehydrogenase (gapdh), beta actin (βactin), ribosomal binding protein L13, tubulin and TATA-box-binding protein (tbp) were carried out to test their efficacy as reference genes in three different tissues, namely liver, gill and muscle of murrel Channa striatus exposed to high temperature for variable time periods. The stability and suitability of the genes were determined by using bioinformatic tools: GeNorm, NormFinder and BestKeeper. Based on the results, tub/βactin could be used as the reference genes for liver and gill tissues and βactin/gapdh could be the reference genes for muscle tissues in Channa striatus under both short- and long-term thermal stress.     

Accelerated aerobic degradation of γ-hexachlorocyclohexane in suspensions of flooded and non-flooded soils pretreated with hexachlorocyclohexane

Summary A commercial wettable-powder formulation (50% a. i.) of hexachlorocyclohexane (HCH) was applied to unplanted and planted (to rice) soils under flooded and non-flooded conditions at 1 kg a. i. ha^–1 at 15-day intervals. A mineral salts medium supplemented with -HCH as a sole source of C was inoculated with suspensions from HCH-treated and untreated soils (unplanted or planted to rice) and incubated under aerobic conditions. -HCH disappeared completely within 10 days from the aerobically incubated medium inoculated with the suspension from the treated soil compared to less than 30% loss from the uninoculated medium or from the medium inoculated with the suspension from the untreated soil, during the corresponding period. Soil samples from HCH-treated flooded pots lost their capacity for accelerated degradation of -HCH after autoclaving. The addition of HCH clearly stimulated aerobic degradation of -HCH, even in predominantly anaerobic flooded soil. The factor responsible for the accelerated degradation of -HCH in pretreated soil was not detected in the deeper layers (>10 cm) of flooded soil and in fields that had dried following the rice harvest.     

Dietary supplementation of curcumin augments heat stress tolerance through upregulation of <Emphasis Type="Italic">nrf-2</Emphasis>-mediated antioxidative enzymes and <Emphasis Type="Italic">hsps</Emphasis> in <Emphasis Type="Italic">Puntius sophore</Emphasis>

Heat stress is one of the major environmental concerns in global warming regime and rising temperature has resulted in mass mortalities of animals including fishes. Therefore, strategies for high temperature stress tolerance and ameliorating the effects of heat stress are being looked for. In an earlier study, we reported that Nrf-2 (nuclear factor E2-related factor 2) mediated upregulation of antioxidative enzymes and heat shock proteins (Hsps) provide survivability to fish under heat stress. In this study, we have evaluated the ameliorative potential of dietary curcumin, a potential Nrf-2 inducer in heat stressed cyprinid Puntius sophore. Fishes were fed with diet supplemented with 0.5, 1.0, and 1.5% curcumin at the rate 2% of body weight daily in three separate groups (n = 40 in each group) for 60 days. Fishes fed with basal diet (without curcumin) served as the control (n = 40). Critical thermal maxima (CTmax) was determined for all the groups (n = 10, in duplicates) after the feeding trial. Significant increase in the CTmax was observed in the group fed with 1.5% curcumin- supplemented fishes whereas it remained similar in groups fed with 0.5%, and 1% curcumin-supplemented diet, as compared to control. To understand the molecular mechanism of elevated thermotolerance in the 1.5% curcumin supplemented group, fishes were given a sub-lethal heat shock treatment (36 °C) for 6 h and expression analysis of nrf-2, keap-1, sod, catalase, gpx, and hsp27, hsp60, hsp70, hsp90, and hsp110 was carried out using RT-PCR. In the gill, expression of nrf-2, sod, catalase, gpx, and hsp60, hsp70, hsp90, and hsp110 was found to be elevated in the 1.5% curcumin-fed heat-shocked group compared to control and the basal diet-fed, heat-shocked fishes. Similarly, in the liver, upregulation in expression of nrf-2, sod, catalase, and hsp70 and hsp110 was observed in 1.5% curcumin supplemented and heat shocked group. Thus, this study showed that supplementation of curcumin augments tolerance to high temperature stress in P. sophore that could be attributed to nrf-2-induced upregulation of antioxidative enzymes sod, catalase, gpx, and the hsps.     

Assessing the extent and causes of forest degradation in India: Where do we stand?

In India, conservation of biodiversity goes hand in hand with human welfare, as millions of people live adjacent or within protected areas and depend upon forests products. The high density and biomass requirements of these households could result in the degradation of forests and loss of biodiversity. We assessed the collection of forest products among households in five sites in the Western and Eastern Ghats of peninsular India: the Kogar region of the Central Western Ghats, the Bandipur and Sigur regions of the Nilgiri Biosphere Reserve, the Kalakad-Mundanthurai Tiger Reserve of the southern Western Ghats and Similipal Tiger Reserve of the northern Eastern Ghats, and tested whether extraction pressure on forests was associated with the proportion of agricultural households, wage labour and population density. We also examined whether data on loss of cover as stated by the State of the Forest Reports was supported by field data. The regions differed in land use: Kogar, KMTR and Similipal were primarily agricultural regions, whereas households engaged in wage labour or in running small businesses were predominant in Sigur and Bandipur. Fuel-wood was collected ubiquitously for household use in all sites, used mainly for domestic requirements and secondarily for generating income. Green leaves for making fertilizer and fodder were collected for household use and did not enter the market. Cattle manure for the global organic coffee industry was a major forest product in Bandipur and Sigur. Extraction pressure on forests was positively associated with the availability of wage labour and was negatively with the proportion of agricultural households. Data from official sources seem inadequate to measure forest degradation in protected forests. Accurate estimation of forest condition through field assessments and remote sensing, and understanding the socio-economic variables associated with forest loss and degradation are needed for the sustainable management of Indian protected areas.     

Conventional and contemporary approaches for drought tolerance rice breeding: Progress and prospects

Drought is becoming a major threat to rice farming across the globe owing to the depletion of water tables in rice-growing belts. Drought affects rice plants at multiple stages, causing damage at morphological and physio-biochemical levels, leading to severe losses that exceed losses from all other stresses. The amalgamation of conventional breeding methods with modern molecular biology tools and biometrical methods could help accelerate the genetic gain for drought tolerance in rice. Many drought-tolerance traits with genetic determinants have been identified and exploited for tolerance rice variety breeding. The integration of genome-wide association study and genomic selection tools with speed breeding shortened the breeding cycle and aided in rapid improvement of genetic gain. In this review, we emphasized the progress made through classical breeding as well as the limitations and usefulness of current genomic methods in improving drought tolerance. We briefly addressed methods for identifying genetic determinants for drought tolerance and deploying them through genomics-assisted breeding programmes to develop high-yielding drought-tolerant rice cultivars.     

Impact of seasonal thermal stress on physiological and blood biochemical parameters in pigs under different dietary energy levels

The present study was formulated to find out the status of important season related thermal stress biomarkers of pure-bred (Hampshire) and crossbred (50% Hampshire × 50% local) pigs under the agro-climatic condition of Assam State, India. The experiment was also aimed to study the role of different level of energy ration (110, 100, and 90% energy of NRC feeding standard for pig) in variation of physiological and biochemical parameters in two genetic groups of pigs in different seasons. The metabolizable energy value were 3260, 2936.5, and 3585.8 kcal/kg in grower ration and 3260.2, 2936.6, and 3587 kcal/kg in finisher ration for normal energy (NE), low energy (LE) and high energy (HE), respectively. Both the genetic group of animals were housed separately under intensive system of management. Each pen was measuring 10′ × 12′ along with an outer enclosure. Six weaned piglets (almost similar body weight of average 10.55 kg) of each group were kept in a separate pen. However, after attainment of 35 kg body weight, the animals of a group were divided in two pens of three animals each. The present experiment indicated that average ambient temperature during summer months (27.33–29.51 °C) was above the comfort zone for pigs (22 °C). The significantly (P?<?0.01) higher relative humidity (RH) (%) was recorded in outdoor environment (87.26–91.10%) and in the morning time (86.60–91.10%). The temperature humidity index (THI) during the study period was found to be indicative of thermal stress to the experimental animals during summer (79.55–82.56). Physiological parameters viz., respiration rate (RR) and rectal temperature (RT) were significantly (P?<?0.01) higher in summer season (43.75–72.12 breaths/min. and 102.29–103.23 °F) and non-significantly higher values were recorded in Hampshire pigs. It was also found that the significantly (P?<?0.01) lower RR as well as RT was recorded in the pigs fed with high energy (HE) ration during summer season. Serum triiodothyronine (T₃) and thyroxine (T₄) concentrations were significantly (P?<?0.01) lower during summer, while both the genetic groups showed significantly (P?<?0.01) higher concentration of serum cortisol during summer season. It was also observed that thyroid hormone and cortisol concentrations were maintained in groups of pig fed vegetable oil incorporated HE diet during summer. From the present study, it is found that the increasing the energy level of the ration might be helpful to minimize the effects of thermal stress during summer.     

Genetic Dissection of Grain Size Traits Through Genome-Wide Association Study Based on Genic Markers in Rice

Grain size plays a significant role in rice, starting from affecting yield to consumer preference, which is the driving force for deep investigation and improvement of grain size characters. Quantitative inheritance makes these traits complex to breed on account of several alleles contributing to the complete trait expression. We employed genome-wide association study in an association panel of 88 rice genotypes using 142 new candidate gene based SSR (cgSSR) markers, derived from yield-related candidate genes, with the efficient mixed-model association coupled mixed linear model for dissecting complete genetic control of grain size traits. A total of 10 significant associations were identified for four grain size-related characters (grain weight, grain length, grain width, and length-width ratio). Among the identified associations, seven marker trait associations explain more than 10% of the phenotypic variation, indicating major putative QTLs for respective traits. The allelic variations at genes OsBC1L4, SHO1 and OsD2 showed association between 1000-grain weight and grain width, 1000-grain weight and grain length, and grain width and length-width ratio, respectively. The cgSSR markers, associated with corresponding traits, can be utilized for direct allelic selection, while other significantly associated cgSSRs may be utilized for allelic accumulation in the breeding programs or grain size improvement. The new cgSSR markers associated with grain size related characters have a significant impact on practical plant breeding to increase the number of causative alleles for these traits through marker aided rice breeding programs.