Development and validation of class I SSR markers targeting (GATA) n repeat motifs in rice

SSR markers targeting (GATA) _n motifs are known to be highly polymorphic and useful in many organisms. (GATA) _n motif specific SSR markers covering the whole rice genome are not available. The present study was carried out with an objective to identify class I rice microsatellites in the rice genome with (GATA)_n motifs, in-silico, and validate their potential as molecular markers. A total of 243 such motifs were identified; 65 of these were present in the genic region, 59 were in the upstream region and the remaining motifs were found in the intergenic regions. Many of the (GATA) _n motifs were found within and/or upstream of genes associated with biotic or abiotic stress tolerance. A total of 230 PCR-based markers targeting all the class I (GATA) _n microsatellites were developed and 35 of these markers spread across the rice genome were validated in a set of 24 representative rice varieties belonging to five distinct cultivar groups. All the markers were polymorphic, with average polymorphism information content (PIC) value of 0.61, and the rice cultivars could be uniquely distinguished into different cultivar groups based on marker analysis. These informative markers targeting (GATA) _n motifs representing a new set of markers in rice will be highly useful for genetic studies and marker-assisted selection. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Passoupathy Rajendrakumar, Akshaya Kumar Biswal and Kannabiran Sakthivel contributed equally.     

Improving hybrid rice parental lines for blast resistance by introgression of broad-spectrum resistance genes Pi54 and Pi9 by marker-assisted selection

Hybrid rice technology offers a great promise to produce 15% to 20% more yield than pure line varieties. The success of hybrid rice hinges on developing superior parental lines. To improve the blast resistance of hybrid rice parental line RP5933-1-19-2R, crosses were made with donors of two major blast resistance genes namely, Pi54 (Tetep) and Pi9 (IR71033–121-15) and the resulting F₁s were confirmed for their hybridity by using Pi54MAS and NMSMPi9-1 genic markers. The confirmed F₁s were intercrossed to obtain ICF₁s and selected positive plants by markers were backcrossed to the recurrent parent, as well as selfed for advancing further to BC₁F₃ and ICF₄ generations. The segregating plants were phenotyped for blast resistance at Uniform Blast Nursery. The identified complete restorers namely, RP 6619-1, RP 6616-26, RP 6619-3 and RP 6619-11 with Pi9 and Pi54 genes would serve as donors for broad spectrum blast resistance. This could ultimately lead to the development of new rice hybrids with improved resistance to blast disease, which is crucial for sustainable rice production and food security.     

Accelerating gene discovery in climate-resilient and nutrient-rich major and minor millets through genome-wide association studies: Progress and prospects

Millets are known for their resilience and nutritional benefits and hence believed to have a promising role in ensuring food and nutritional security under changing climatic conditions. Research on millets has intensified in recent years, especially in dissecting the genetic components of yield, stress tolerance and nutritional quality traits. Recent advances in next-generation sequencing, bioinformatics and associated statistical procedures for genome-wide association studies (GWAS) have provided wide opportunities to resolve the genetic complexity of polygenic traits by measuring historical and evolutionary recombination events in the natural population(s). During the past decade, GWAS has been successfully employed to identify key genes controlling growth, development, stress tolerance, nutrient use efficiency and nutritional quality traits in sorghum, pearl millet, foxtail millet and finger millet. However, progress in other minor millets is still in its infancy. Genetic dissection of these complex traits in millets may pave the way for genetic alteration of climate resilience, photosynthesis and nutrient accumulation in rice and wheat. In this review, progress in GWAS analysis in detecting QTLs underlying complex traits in sorghum and other millets is highlighted.     

Effect of N,P and K fertilizers on their availability in soil in relation to the Stevia plant (Stevia rebaudiana Bert.)

Abstract

A greenhouse experiment was conducted at the Indian Institute of Horticultural Research (IIHR), Bangalore, to study the effect of combined applications of nitrogen (N), phosphorous (P) and potassium (K) fertilizers on their availability in soils in relation to their contents in the Stevia plant. The results show that the amount of available N, P and K in soil has been found to be increased initially up to 45 days and thereafter, the amount of the same content decreased with the progress of plant growth up to 60 days irrespective of treatments. However, the magnitudes of such increases in N, P and K contents both in soils and plants have also been enhanced with the simultaneous application of N, P and K (40:20:30) kg/ha over that of their corresponding individual applications.     

Microsatellite marker-based identification of mother plants for the reliable propagation of olive (Olea europaea L.) cultivars in Australia

Summary

Olive production in Australia has continued to increase in recent years, however there remains a high degree of confusion on the genetic identities of the cultivars being grown. In the present study, seven microsatellite (simple sequence repeat; SSR) loci were used to identify a set of 53 olive tree samples from different sources. The microsatellite DNA profiles of all 53 tree samples, including seven unknown trees, were compared with the SSR profiles of 14 reference olive cultivars. A total of 60 fragments (alleles), averaging 8.57 alleles per microsatellite locus, were amplified. High average values were found for the observed heterozygosity, the expected heterozygosity, and the polymorphic information content (0.73, 0.74, and 0.72, respectively). While all seven microsatellite markers proved useful for characterisation and identification purposes, a combination of three SSR primer pairs (DCA9, DCA18, and EM030) was sufficient to distinguish all 53 olive samples. The microsatellite allelic profiles allowed the 53 tree samples to be grouped into 23 genotypes. The allelic profiles of 14 of these genotypes matched with their reference cultivars, while the genetic identities of the remaining nine genotypes could not be confirmed. Some of these unknown genotypes may have been derived from feral olive trees, or were due to mislabelling and/or planting errors among Australian olive cultivars. Our results confirm the usefulness of microsatellite markers as a tool for cultivar differentiation and identification, and indicate the need for reliable identification of mother plants for commercial propagation.     

Anti-oxidative and immuno-hematological status of Tilapia (Oreochromis mossambicus) during acute toxicity test of endosulfan

Endosulfan is an organochlorine pesticide widely used in agriculture and hence finds its way into natural water bodies, thus affecting aquatic life. The purpose of this study was to determine LC₅₀ of endosulfan (99%; α:β ratio of 7:3) in Tilapia, Oreochromis mossambicus and study its effect on anti-oxidative enzymes (superoxide dismutase, glutathione-S-transferase and catalase), immuno-hematological profile (RBC, WBC, Hb, serum protein, albumin-A, globulin-G, A/G ratio, phygocytic activity as indicated by nitroblue tetrazolium reduction, serum cortisol and serum lipid peroxidation) and neurotransmitter acetylcholine esterase enzyme activity. The LC₅₀ value at 96 h and 95% confidence limit for tilapia (46.78 g) was estimated as 3.6 μg/L. Activities of anti-oxidative enzymes, immuno-hematological profile, blood glucose and neurotransmitter activity was significantly influenced (P < 0.01) in dose dependent manner. This was reflected in the behavior of fish that was altered from normal during acute toxicity.     

Investigations on C-glycosyl flavonoids from Rhynchosia capitata,its antimicrobial and dyeing properties

Natural dyes extracted from a novel source Rhynchosia capitata (R. capitata) Heyne ex roth were applied to cotton fabric by applying traditional and pad dyeing processes using pre-, post- and simultaneous-mordanting techniques. Both dyeing processes were carried out in the presence of natural mordants: Myrobalan, Pomegranate rind, Rhizhophora mucronata fruits, Manjistha, and eco-friendly metallic mordants such as tannic acid, stannous chloride (SnCl₂), ferrous sulfate (FeSO₄), and copper sulfate (CuSO₄). The range of color developed on dyed materials was evaluated in terms of (L*, a*, b*, C*) CIELAB coordinates and dye absorption concentration on textile materials was studied by using K/S values. Natural mordant Rhizhopora mucronata fruits exhibited good absorption value. It was found that metallic mordants FeSO₄ and CuSO₄ exhibited higher K/S values than SnCl₂. For other mordants except FeSO₄ shade developed on cotton fabric varied from pale yellow to brown. The fastness properties ranged from good to excellent. High pressure thin layer chromatographic analysis for solvents of varying polarity has been investigated and maximum yield was obtained from 80 % aqueous ethanol fraction. Antimicrobial activity was carried out with the aid of two human pathogenic strains, Staphylococcus aureus and Klebsiella pneumonia and the cotton fabric dyed with plain extract of R. capitata shows good activity.