Mapping QTLs using a novel source of salinity tolerance from Hasawi and their interaction with environments in rice

Background

Salinity is one of the most severe and widespread abiotic stresses that affect rice production. The identification of major-effect quantitative trait loci (QTLs) for traits related to salinity tolerance and understanding of QTL × environment interactions (QEIs) can help in more precise and faster development of salinity-tolerant rice varieties through marker-assisted breeding. Recombinant inbred lines (RILs) derived from IR29/Hasawi (a novel source of salinity) were screened for salinity tolerance in the IRRI phytotron in the Philippines (E1) and in two other diverse environments in Senegal (E2) and Tanzania (E3). QTLs were mapped for traits related to salinity tolerance at the seedling stage.

Results

The RILs were genotyped using 194 polymorphic SNPs (single nucleotide polymorphisms). After removing segregation distortion markers (SDM), a total of 145 and 135 SNPs were used to construct a genetic linkage map with a length of 1655 and 1662 cM, with an average marker density of 11.4 cM in E1 and 12.3 cM in E2 and E3, respectively. A total of 34 QTLs were identified on 10 chromosomes for five traits using ICIM-ADD and segregation distortion locus (SDL) mapping (IM-ADD) under salinity stress across environments. Eight major genomic regions on chromosome 1 between 170 and 175 cM (qSES1.3, qSES1.4, qSL1.2, qSL1.3, qRL1.1, qRL1.2, qFWsht1.2, qDWsht1.2), chromosome 4 at 32 cM (qSES4.1, qFWsht4.2, qDWsht4.2), chromosome 6 at 115 cM (qFWsht6.1, qDWsht6.1), chromosome 8 at 105 cM (qFWsht8.1, qDWsht8.1), and chromosome 12 at 78 cM (qFWsht12.1, qDWsht12.1) have co-localized QTLs for the multiple traits that might be governing seedling stage salinity tolerance through multiple traits in different phenotyping environments, thus suggesting these as hot spots for tolerance of salinity. Forty-nine and 30 significant pair-wise epistatic interactions were detected between QTL-linked and QTL-unlinked regions using single-environment and multi-environment analyses.

Conclusions

The identification of genomic regions for salinity tolerance in the RILs showed that Hasawi possesses alleles that are novel for salinity tolerance. The common regions for the multiple QTLs across environments as co-localized regions on chromosomes 1, 4, 6, 8, and 12 could be due to linkage or pleiotropic effect, which might be helpful for multiple QTL introgression for marker-assisted breeding programs to improve the salinity tolerance of adaptive and popular but otherwise salinity-sensitive rice varieties.

     

An inactivated vaccine for the control of bluetongue virus serotype 16 infection in sheep in Italy

Because no suitable products are at the moment available to safely control the spread of BTV-16 in Europe, an inactivated vaccine was produced from the reference field isolate of bluetongue virus serotype 16. One group of six sheep was vaccinated subcutaneously with the inactivated vaccine twice, on days 0 and 28, whereas a second group of eight sheep was inoculated with saline solution and used as mock-vaccinated control animals. Seventy-eight days after the first vaccination, all sheep were inoculated subcutaneously with a suspension containing 10(6.3) TCID(50) of a virulent reference BTV-16 isolate. Apart from a transient inflammatory reaction at the injection site, no adverse effects were reported following vaccination. All vaccinated animals developed high titres (7.3-9.3log(2)(ED50%/50 microl)) of virus-specific neutralising antibodies and were resistant to challenge with BTV-16. Conversely, following challenge, control animals developed hyperthermia and long lasting high-titre viraemia.     

Emamectin,a novel insecticide for controlling field crop pests

Emamectin is a macrocyclic lactone insecticide with low toxicity to non-target organisms and the environment, and is considered an important component in pest-management programmes for controlling field crop pests. It is a powerful compound for controlling the cotton bollworm Helicoverpa armigera (Hübner). A spray concentration of 25 mg AI litre-1 in a cotton field resulted in over 90% suppression of H armigera larvae up to day 28 after treatment, while similar mortality of the Egyptian cotton leafworm Spodoptera littoralis Boisduval, under the same conditions, was maintained for 3 days only. Emamectin is a potent compound for controlling the western flower thrips Frankliniella occidentalis (Pergande) under both laboratory and field conditions and its activity on adults was over 10-fold greater than that of abamectin. Spray concentrations of 10 and 50 mg AI litre-1 in Ageratum houstonianum Mill flowers resulted in total suppression of adults up to day 11 and of larvae up to day 20 after treatment. Under standard laboratory conditions, emamectin exhibits a considerable activity on the whitefly Bemisia tabaci (Gennadius) and the leafminer Liriomyza huidobrensis (Blanchard). Further studies are required to evaluate its potential activity on the latter pests under field conditions.     

Assessment of the response of carrot somaclones to Pythium violae, causal agent of cavity spot

Cavity spot is a major disease of carrots, causing cavities on the surface of the root. Available commercial varieties show a range of susceptibility but no significant resistance. Seed progeny from 46 tissue culture-derived carrot ( Daucus carota ) somaclones were screened for viability, then 19 selected somaclone families were sown under glasshouse conditions, along with commercial cultivars (Bertan, Nandor, Bolero and Vita Longa) as controls. Mature roots were exposed to Pythium violae in a cavity spot bioassay to determine their response as measured by disease incidence and severity. Some somaclones formed fewer lesions than the least susceptible control cultivar, Vita Longa. Seven somaclonal families that showed a range of susceptibility were sown under field conditions and the assessment was repeated. Although there was little relationship between glasshouse and field-trial results, under field conditions one of the somaclones had a mean incidence of disease, as estimated by transformed data, of 1·9 compared with 37·9 for the most susceptible somaclone and 3·5 for Bolero, the most resistant commercial cultivar. The results indicated that significant genetic variation in susceptibility to cavity spot disease was present in the somaclones.     

Temporal changes in soil carbon and nitrogen in west African multistrata agroforestry systems: a chronosequence of pools and fluxes

The conversion of forests to agroecosystems or agroforests comes with many changes in biological and chemical processes. Agroforestry, a tree based agroecosystem, has shown promise with respect to enhanced system nutrient accumulation after land conversion as compared to sole cropping systems. Previous research on tropical agroforestry systems has revealed increases in soil organic matter and total organic nitrogen in the short term. However, research is lacking on long-term system level sustainability of nutrient cycles and storage, specifically in traditional multi-strata agroforestry systems, as data on both the scope and duration of nutrient instability are inconclusive and often conflicting. This study, conducted in Ghana, West Africa, focused on carbon and nitrogen dynamics in a twenty-five year chronosequence of cacao (Theobroma cacao Linn.) plantations. Three treatments were selected as on-farm research sites: 2, 15 and 25-year-old plantations. Soil carbon (C, to a depth of 15 cm) varied between treatments (2 years: 22.6 Mg C ha⁻¹; 15 years: 17.6 Mg C ha⁻¹; 25 years: 18.2 Mg C ha⁻¹) with a significant difference between the 2- and 15- and the 2- and 25-year-old treatments (p < 0.05). Total soil nitrogen in the top 15 cm varied between 1.09 and 1.25 Mg N ha⁻¹ but no significant differences were noted between treatments. Soil nitrification rates and litter fall increased significantly with treatment age. However, photosynthetically active radiation (PAR) and soil temperature showed a significant decrease with age. No difference was found between decay rates of litter at each treatment age. By 25 years, system carbon sequestration rates were 3 Mg C ha⁻¹ y⁻¹, although results suggest that even by 15 years, system-level attributes were progressing towards those of a natural system.     

Litter dynamics of six multipurpose trees in a homegarden in Southern Kerala, India

Multipurpose trees, the integral components of homegardens, contribute significantly to the closed nutrient cycling processes and sustainability of the ecosystem. Although, the litter production and probable nutrient returns via litter in homegardens have been documented, quantification and characterization of the decomposition and bioelement release from the litter have received relatively little scientific attention. The objective of the present study is to explore the litter dynamics of six locally important multipurpose trees (Mangifera indica L., Artocarpus heterophyllus Lamk., Anacardium occidentale L., Ailanthus triphysa Dennst., Artocarpus hirsutus L. and Swietenia macrophylla L.), in an agroforestry homegarden in Southern Kerala, India. Litterfall and nutrient additions in the six species ranged from 383 to 868 g m⁻² yr⁻¹, nitrogen, 6.4 to 8.8, phosphorus, 0.17 to 0.42 and potassium, 1.1 to 2.8 g m⁻² yr⁻¹. The annual litter output in the homegarden was 425 kg with A. hirsutus, M. indica, A. heterophyllus and A. occidentale recording significantly higher litter and nutrient additions. Leaf litter decay studies revealed A. heterophyllus and A. occidentale to be the most labile litter species and S. macrophylla the most recalcitrant. The decay rate coefficients varied significantly among the species. Foliage decomposition rates related to the initial chemical composition of the litter revealed best correlation with lignin. NPK release was almost complete by the end of decay in all species inspite of the initial phases of accumulation observed for nitrogen and phosphorus. Two-way analysis of variance test revealed significant differences in the contents of the three elements as a function of species and time elapsed. Macronutrients were released in the order K>N/P. The higher rates of decay and nutrient turnover in M. indica, A. heterophyllus and A. occidentale foliage indicated the potential of using these species’ litter as nutrient inputs in agriculture while A. triphysa, A. hirsutus and S. macrophylla perform better as organic mulches taking a longer time for decay and hence nutrient release.     

Estimating coarse root biomass with ground penetrating radar in a tree-based intercropping system

Conventional measurements of tree root biomass in tree-based intercropping (TBI) systems can be inadequate in capturing the heterogeneity of rooting patterns or can be highly destructive and non-repeatable. In this study, we estimated coarse root biomass using ground penetrating radar (GPR) of 25-year-old trees inclusive of five species (Populus deltoides × nigra clone DN-177, Juglans nigra L., Quercus rubra L., Picea abies L. Karst, and Thuja occidentalis L.) at a TBI site in Southern Ontario, Canada. Subsurface images generated by GPR were collected in grids (4.5 × 4.5 m) centred on tree stems. The predictive relationship developed between GPR signal response and root biomass was corrected for species effects prior to tree-scale estimates of belowground biomass. Accuracy of the tree-scale estimates was assessed by comparing coarse root biomass measured from complete excavations of the corresponding tree. The mean coarse root biomass estimated from GPR analysis was 54.1 ± 8.7 kg tree^?1 (mean ± S.E.; n = 12), within 1 % of the mean coarse root biomass measured from excavation. Overall there was a root mean square error of 14.4 kg between measured and estimated biomass with no detectable bias despite variable conditions within the in-field and multi-species study. Root system C storage by species, calculated with species-specific root carbon concentrations, is estimated at 5.4 ± 0.7–34.8 ± 6.9 kg C tree^?1 at this site. GPR is an effective tool for non-destructively predicting coarse root biomass in multi-species environments such as temperate TBI systems.