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Not AvailableRice is an important staple food crop and primary diet source for majority of the world’s population. However, biotic stress such as Sheath blight (ShB) is one of major disease which effects 50-60% yield loss. ShB disease is mainly caused by Rhizoctonia solani, however, no rice cultivar has been found to be completely tolerance. We developed the BPT5204 mutant lines through EMS method. The mutant lines (BPT5204) were screened through detached leaf method (Dath 1987) under standard glass house conditions and the protocol was standardized in ICAR-IIRR. After 72hrs of infection, the lesion length of each cut leaf was measured and according to tolerance we scored 0-9 scale. We observed that 13 out of 40 were showed tolerance against sheath blight. ShB-1, ShB-5, ShB-11, ShB-12, ShB-13 (score-0) lines were showed highly tolerance, ShB-2 and ShB-8 (score 1-8) were moderately tolerant, wild type (BPT5204) was complete susceptible (scores up to 9). Therefore, this standardized detached leaf assay can be used to assess against sheath blight disease.Council for scientific and industrial research, Government of India, New Delh

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Not AvailableSamba Mahsuri (BPT5204) is a medium slender rice variety highly popular among the farmers in South and Eastern India. It is one of the best Rice varieties with good cooking quality. The yield of BPT 5204 is 6-6.5 tons/ha, even though it is showing maximum susceptibility to many biotic stresses and exhibits incomplete panicle emergence, this make it an ideal genotype for identifying mutational changes in traits of agronomic importance. To obtain agronomical important traits mutation breeding plays an important role. Mutagenesis plays key role among these genetic resources, mutant stocks with discrete genetic lesions are essential to determining gene function and dissecting biochemical and metabolic pathways. Chemical mutagenesis has been routinely used to generate genetic variability for breeding research and genetic studies. In rice, there are several advantages of using chemical mutagenesis to produce mutant populations suitable for both forward and reverse genetics. First, mutant populations can be produced using any genotypes. Second, because of the high density of mutations, genome-wide saturation mutagenesis can be achieved using a relatively small mutant population [1, 2]. Third, it provides a large allelic series as a complement to the knockout mutants produced by insertional mutagenesis or transformation methods (over- and under-expression) [3-6]. Morphological variations including grain types, maturity and traits contributing to yield are observed in every generation. In present study, observed the agro-morphological variations in the BPT-5204 sheath blight tolerant mutants which developed through chemical mutagen EMS (Ethyl Methane Sulfonate) [7].o Council for scientific and industrial research, Government of India, New Delh

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Not AvailableAims: The aim of the present work was to generate complete panicle emergence mutants of Samba Mahsuri (BPT-5204), using the chemical mutagen, ethyl methane sulphonate (EMS) Place and Duration of Study: The field evaluation was carried out repeatedly in two locations at Indian Institute of Rice Research, Rajendranagar and at ICRISAT Patancheru Hyderabad. The duration of the study was three successive seasons in triplicates namely, june-2014, january-2015 and june-2015.Methodology: Seedlings of 28-30 days old were transplanted in 5 lines (each line containing 20 plants) into the field. The plant spacing was 20cm by 15cm with density of one hill. The field was irrigated throughout the experiment with average of 10cm water above the soil level. Regular hand weeding was embarked upon to free the plant of inter specific competition. The phenotypic data was recorded for CPE mutants through visual assessment. The characteristics that required measurements weredone according to the usual procedure. The Distinctness, Uniformity and stability of the CPE mutant lines have been recorded following (DUS) test guidelines by UPOV guidelines for rice (38) & Yoshida S (44).Results:The identified stabilized thirteen complete panicle emergence (CPE) mutants showed superior agro morphological characters, compared with wild type (BPT-5204). The mutants CPE-2 and CPE-3 took 100 days to flowering and CPE-4 and CPE-7 mutants showed superiority for panicle length, and CPE-5 exhibited good performance for grain yield.In correlation analysis CPE trait had a significantly positive correlation with PH and TGW and negative correlation with 50%DFF. The CPE mutants used in the present study exhibited variability for most of the studied traits. Significant variation was detected in the identified stabilized CPE mutants for plant height, panicle length, flag leaf length and width, 50% flowering, different grain types and 1000 grain weight.Conclusion:The present study discovered adequate genetic divergence in the thirteen stabilized CPE mutants for various qualitative and quantitative traits. The promising mutants identified during the current study have the potential to be used in future breeding programs for getting productive and quality results.Council for Scientific and Industrial Research (CSIR), Government of Indi

Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci

Background Genetic variation can alter transcriptional regulatory activity contributing to variation in complex traits and risk of disease, but identifying individual variants that affect regulatory activity has been challenging. Quantitative sequence-based experiments such as ChIP-seq and DNase-seq can detect sites of allelic imbalance where alleles contribute disproportionately to the overall signal suggesting allelic differences in regulatory activity. Methods We created an allelic imbalance detection pipeline, AA-ALIGNER, to remove reference mapping biases influencing allelic imbalance detection and evaluate accuracy of allelic imbalance predictions in the absence of complete genotype data. Using the sequence aligner, GSNAP, and varying amounts of genotype information to remove mapping biases we investigated the accuracy of allelic imbalance detection (binomial test) in CREB1 ChIP-seq reads from the GM12878 cell line. Additionally we thoroughly evaluated the influence of experimental and analytical parameters on imbalance detection. Results Compared to imbalances identified using complete genotypes, using imputed partial sample genotypes, AA-ALIGNER detected >95 % of imbalances with >90 % accuracy. AA-ALIGNER performed nearly as well using common variants when genotypes were unknown. In contrast, predicting additional heterozygous sites and imbalances using the sequence data led to >50 % false positive rates. We evaluated effects of experimental data characteristics and key analytical parameter settings on imbalance detection. Overall, total base coverage and signal dispersion across the genome most affected our ability to detect imbalances, while parameters such as imbalance significance, imputation quality thresholds, and alignment mismatches had little effect. To assess the biological relevance of imbalance predictions, we used electrophoretic mobility shift assays to functionally test for predicted allelic differences in CREB1 binding in the GM12878 lymphoblast cell line. Six of nine tested variants exhibited allelic differences in binding. Two of these variants, rs2382818 and rs713875, are located within inflammatory bowel disease-associated loci. Conclusions AA-ALIGNER accurately detects allelic imbalance in quantitative sequence data using partial genotypes or common variants filling a critical methodological gap in these analyses, as full genotypes are rarely available. Importantly, we demonstrate how experimental and analytical features impact imbalance detection providing guidance for similar future studies