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.

     

Effects of feeding a blend of grains naturally contaminated with Fusarium mycotoxins on swine performance,brain regional neurochemistry,and serum chemistry and the efficacy of a polymeric glucomannan mycotoxin adsorbent

The co-occurrence of Fusarium mycotoxins in contaminated swine diets has been shown to result in synergistic toxicity beyond that observed for individual toxins. An experiment was conducted, therefore, to investigate the effects of feeding a blend of grains naturally contaminated with Fusarium mycotoxins on growth, brain regional neurochemistry, serum immunoglobulin (Ig) concentrations, serum chemistry, hematology, and organ weights of starter pigs. Three levels of glucomannan polymer (GM polymer, extract of yeast cell wall, Alltech Inc.) were also tested for its efficacy to overcome Fusarium mycotoxicoses. A total of 175 starter pigs (initial weight of 10 +/- 1.1 kg) were fed five diets (seven pens of five pigs per diet) for 21 d. Diets included (1) control, (2) blend of contaminated grains, (3) contaminated grains + 0.05% GM polymer (4) contaminated grains + 0.10% GM polymer and (5) contaminated grains + 0.20% GM polymer. Diets containing contaminated grains averaged 5.5 ppm deoxynivalenol, 0.5 ppm 15-acetyldeoxynivalenol, 26.8 ppm fuuric acid, and 0.4 ppm zearalenone. Feed intake and weight gain of all pigs fed contaminated grains was significantly reduced compared to controls throughout the experiment. The weights of liver and kidney, expressed as a percentage of body weight, were lower in pigs fed the contaminated diet than in those fed the control diet. The feeding of contaminated grains significantly reduced concentrations of dopamine in the hypothalamus and pons and concentrations of dihydroxyphenylacetic acid and norepinephrine in the pons. The ratios of 5-hydroxyindoleacetic acid to serotonin, however, were elevated in the hypothalamus and pons. The feeding of contaminated grains increased serum IgM and IgA concentrations, while serum IgG concentrations were not altered. The supplementation of GM polymer prevented some of the mycotoxin-induced alterations in brain neurotransmitter and serum Ig concentrations. In summary, the feeding of grains naturally contaminated with Fusarium mycotoxins reduced growth, altered brain neurochemistry, increased serum Ig concentrations, and decreased organ weights in starter pigs. Some of the Fusarium mycotoxin-induced changes in neurochemistry and serum Ig concentrations can be prevented by the feeding of yeast cell wall polymer at appropriate concentrations, although this was not reflected in increased growth rate under these experimental conditions.     

Evaluation of Populus deltoides clones under nursery,field and agrisilviculture system in subhumid tropics of Central India

Populus deltoides Bartr., a native of North America, is generally grown in India above latitude 28 °N. One hundred and six clones were evaluated for four years at Raipur situated at 21°12N latitude and 81°36E longitude. These were grown on vertisol soil. Based on growth and survival performance in the nursery for two successive years, nineteen clones were selected for field evaluation. The best five clones (G3, G48, 65/27, D121 and S7C1) were planted in an agrisilviculture system at a spacing of 4 × 4 m with soybean grown as an intercrop. After 4 years these clones had an increment of DBH by 66.5 to 77.5% and of height by 42.2 to 78.6% within one year when compared to that observed at 3 years of age. In rank order of growth the best five clones were 65/27 > G3 > D121 > G48 > S7C1. Total biomass varied between 20.9 to 35.8 Mg ha^–1 in different clones. Among the tree components, stemwood accounted for 52–61% of the total biomass, followed by branches (20–25%), bark (9–13%) and leaves (7–10%). No significant variation between net primary productivity and photosynthetic efficiency was found in different clones. Soybean productivity decreased as the trees aged, reaching 40.5 to 58.1% in 4-year-old trees.     

Purification and partial characterization of acetic acid esterase from malted finger millet (Eleusine coracana, Indaf-15)

Acetic acid esterase (EC 3.1.1.6) cleaves the acetyl groups substituted at O-2/O-3 of the xylan backbone of arabinoxylans and is known to modulate their functional properties. To date, this enzyme from cereals has not received much attention. In the present study, acetic acid esterase from 72 h ragi malt was isolated and purified to apparent homogeneity by a four-step purification, i.e., ammonium sulfate precipitation, DEAE-cellulose, Sephacryl S-200, and phenyl-Sepharose column chromatography, with a recovery of 0.36% and a fold purification of 34. The products liberated from alpha-NA and PNPA by the action of purified ragi acetic acid esterase were authenticated by ESI-MS and 1H NMR. The pH and temperature optima of the enzyme were found to be 7.5 and 45 degrees C, respectively. The enzyme is stable in the pH range of 6.0-9.0 and temperature range of 30-40 degrees C. The activation energy of the enzymatic reaction was found to be 7.29 kJ mol-1. The apparent Km and Vmax of the purified acetic acid esterase for alpha-NA were 0.04 microM and 0.175 microM min-1 mL-1, respectively. The molecular weight of the native enzyme was found to be 79.4 kDa by GPC whereas the denatured enzyme was found to be 19.7 kDa on SDS, indicating it to be a tetramer. EDTA, citric acid, and metal ions such as Fe+3 and Cu+2 increased the activity while Ni+2, Ca+2, Co+2, Ba+2, Mg+2, Mn+2, Zn+2, and Al+3 reduced the activity. Group-specific reagents such as eserine and PCMB at 25 mM concentration completely inhibited the enzyme while iodoacetamide did not have any effect. Eserine was found to be a competitive inhibitor.     

Misidentification of Macrotyloma sar-garhwalensis R.D.Gaur & L.R.Dangwal and its implication in horsegram germplasm management

Genetic Resources and Crop Evolution - Correcting taxonomic misidentifications is crucial to ensuring the conservation and use of wild relatives in crop breeding programmes. Macrotyloma...     

Village seed systems and the biological diversity of millet crops in marginal environments of India

The study relates village seed systems to biological diversity of millet crops grown by farmers in the semi-arid lands of Andhra Pradesh and Karnataka, India. In these subsistence-oriented, semi-arid production systems the environment is marginal for crop growth and often there is no substitute for millet crops. Across communities, farmers grow 13 different combinations of pearl millet, sorghum, finger millet, little millet, and foxtail millet varieties, but individual farmers grow an average of only 2–3 millet varieties per season. The “village seed system” in this study refers to all channels through which farmers acquire genetic materials, separate from or in interaction with the commercial seed industry, observed at the local level. Data are compiled through household surveys and interviews with traders and dealers in village and district markets. Based on the concept of the seed lot, several seed system parameters are defined and measured by millet crop. Most seed transactions, including gifts of seed, appear to be monetized. Seed supply channels differ by improvement status of the genetic material. Regression results confirm that seed system parameters are statistically significant determinants of the spatial diversity of millet crops measured at the village level. Furthermore, both the trade through weekly village markets (shandies) and through the formal seed supply channel contribute positively to the breadth of genetic materials in these communities. Ways should be found to strengthen and improve the overall efficiency of the seed system, including both formal and informal channels, in order to reduce the costs to farmers of procuring and managing diverse crop varieties.     

Chemical composition, iron bioavailability, and antioxidant activity of Kappaphycus alvarezzi (Doty)

Kappaphycus alvarezzi, an edible seaweed from the west coast of India, was analyzed for its chemical composition. It was found that K. alvarezzi is rich in protein (16.24% w/w) and contains a high amount of fiber (29.40% w/w) and carbohydrates (27.4% w/w). K. alvarezzi showed vitamin A activity of 865 mug retinal equivalents/100 g of sample. It contained a higher quantity of unsaturated fatty acids (44.50% of the total), in which relative percentage of oleic acid was 11%, cis-heptadecanoic acid 13.50%, and linoleic acid 2.3% and 37.0% of saturated fatty acids (mainly heptadecanoic acid). K. alvarezziwas also found to be good source of minerals, viz 0.16% of calcium, 0.033% of iron, and 0.016% of zinc, which are essential for various vital biological activities. Bioavailability of iron by in vitro methods showed a higher efficiency in intestinal conditions than in stomach conditions. Ascorbic acid influenced higher bioavailability of iron. Successive extracts of n-hexane, acetone, ethyl acetate, ethanol, and direct extractables of chloroform/methanol (1:1 and 2:1) were screened for antioxidant activity using a beta-carotene linoleic acid model system (B-CLAMS), DPPH (alpha,alpha-diphenyl-beta-picrylhydrazyl) model system and hydroxyl radical scavenging activity. The chloroform/methanol (2:1) extract has shown 82.5% scavenging activity at 1000 ppm. Acetone fraction extracts at the 1000 ppm level showed 63.31% antioxidant activity in beta-carotene linoleic acid system. The acetone extract showed 46.04% scavenging activity at 1000 ppm concentration. In the case of hydroxyl radical scavenging activity, all the extracts showed better activity at the concentrations of 25 and 50 ppm, where at the 50 ppm level ethyl acetate extract showed 76.0%, acetone 75.12%, and hexane 71.15% activity, respectively. Results of this study suggest the utility of K. alvarezzi (Eucheuma) for various nutritional products, including antioxidant for use as health food or nutraceutical supplement.     

Effects of feeding blends of grains naturally contaminated with Fusarium mycotoxins on brain regional neurochemistry of starter pigs and broiler chickens

Two experiments were conducted to compare the effects of feeding a blend of grains naturally contaminated with Fusarium mycotoxins on brain regional neurochemistry of starter pigs and broiler chickens. A polymeric glucomannan mycotoxin adsorbent (GM polymer) was also tested for its efficacy in preventing Fusarium mycotoxicoses. In Exp. 1, a total of 150 starter pigs (initial weight = 9.3+/-1.1 kg) were fed five diets (six pens of five pigs per diet) for 21 d. Diets (as-fed basis) included control, 17% contaminated grains, 24.5% contaminated grains, 24.5% contaminated grains + 0.2% GM polymer, and a pair-fed control for comparison with pigs receiving 24.5% contaminated grains. In Exp. 2,360 1-d-old male broiler chicks were fed for 56 d one of four diets containing the same source of contaminated grains as was fed to pigs. The diets included control, 37% contaminated grains, 58% contaminated grains, and 58% contaminated grains + 0.2% GM polymer (as fed). Neurotransmitter concentrations in the cortex, hypothalamus, and pons were analyzed by HPLC. The following brain neurotransmitter alterations (P < or = 0.05) were observed. In pigs, inclusion of contaminated grains in the diet 1) linearly increased cortex 5-hydroxytryptamine (5HT, serotonin) concentrations, while linearly decreasing hypothalamic tryptophan concentrations; 2) quadratically increased hypothalamic and pons 5-hydroxyindoleacetic acid (5HIAA):5HT ratios, whereas the ratio decreased linearly in the cortex; and 3) linearly increased the ratio of hypothalamic 3,4-dihydroxyphenylacetic acid:dopamine (DA) concentrations, whereas hypothalamic norepinephrine (NRE) and pons DA and homovanillic acid (HVA) concentrations linearly decreased. In broiler chickens, inclusion of contaminated grains in the diet 1) linearly increased concentrations of 5HT and 5HIAA in the pons and 5HT concentrations in the cortex; 2) linearly decreased 5HIAA:5HT ratio; and 3) linearly increased pons NRE, 3-methoxy-4-hydroxyphenylethylene glycol, DA, and HVA concentrations. Supplementation of GM polymer to the contaminated diet decreased (P < 0.05) 5HT and 5HIAA concentrations in the cortex of pigs. It was concluded that the differences in alterations of brain neurochemistry might explain the species differences in the severity of Fusarium mycotoxin-induced feed refusal.     

Assessment of biomass and net primary productivity of a dry tropical forest using geospatial technology

This study quantifies biomass, aboveground and belowground net productivity, along with additional environmental factors over a 2-3 year period in Barnawapara Sanctuary of Chhattisgarh, India through satellite remotesensing and GIS techniques. Ten sampling quadrates20×20, 5×5 and 1×1 m were randomly laid for overstorey (OS), understorey (US) and ground vegetation(GS), respectively. Girth of trees was measured at breast height and collar diameters of shrubs and herbs at 0.1 m height. Biomass was estimated using allometric regression equations and herb biomass by harvesting. Net primary productivity (NPP) was determined by Ssumming biomass increment and litter crop values. Aspect and slope influenced the vegetation types, biomass and NPP in different forests. Standing biomass and NPP varied from 18.6 to101.5 Mg ha^-1 and 5.3 to 12.7 Mg ha^-1 a^-1, respectively,in different forest types. The highest biomass was found in dense mixed forest, while net production recoded in Teak forests. Both were lowest in degraded mixed forests of different forest types. OS, US and GS contributed 90.4, 8.7and 0.7%, respectively, for the total mean standing biomass in different forests. This study developed spectral models for the estimation of biomass and NPP using Normalized Difference Vegetation Index and other vegetation indices.The study demonstrated the potential of geospatial tools for estimation of biomass and net productivity of dry tropical forest ecosystem.     

Yield Traits and Associated Marker Segregation in Elite Introgression Lines Derived from O. sativa × O. nivara

Introgression lines (ILs) derived from interspecific crosses are a source of new genetic variability. A total of 55 ILs derived from two crosses Swarna × O. nivara IRGC81848 (population A) and Swarna × O. nivara IRGC81832 (population B) were characterized for yield and yield-related traits/QTLs. Segregation of 103 simple sequence repeat (SSR) markers associated with yield-related QTLs was studied. Population A showed an average of 12.6% homozygous O. nivara alleles and population B showed 10.6%. Interestingly, three SSR markers, RM223, RM128 and RM517, showed conspicuous pattern of segregation. The distribution of parental alleles at three loci RM223, RM128 and RM517 linked to yield-related traits was unique. These markers flanked to several yield-related QTLs. RM223, flanking to qyld8.3, was heterozygous in almost all the 55 ILs except in IL10-3S and IL131S. RM128 on chromosome 1 and RM517 on chromosome 3 were mutually exclusive in 46 out of 55 ILs. These 46 ILs showed either of the marker allele RM128 or RM517 from O. nivara but not both. IL166S had both RM128 and RM517 from O. nivara and the other ILs showed homozygous Swarna allele at RM517 except IL65S. Population structure assigned the 55 ILs to three sub-populations based on their genomic diversity. IL65S, IL166S, IL248S, IL7K and IL250K showed high yields in multi-location trials, and IL248S was released for cultivation as DRRDhan 40.