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Bulked line analysis: a useful tool to identify microsatellite markers linked to drought tolerance in rice

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Abstract

Eighty rice germplasm collections were used to study the variation in root traits and water use efficiency (WUE based on ∆13C value) for two seasons. Deep and shallow root genotypes were selected on the basis of phenotypic data. Similarly based upon ∆13C values, high and low WUE plant types were selected. Basis of selection for BLA being, the genotype with extreme values on either side of the grand mean is given as either positive (+) negative (−) sign for each trait studied. The genotypes which has scored nearer value to either side of the grand mean is omitted and were not considered for bulking in order to have two very distinct bulks amongst the genotypes. Varieties identified for deep and thick roots were Chuvanna modan (Ptb 30), Ptb1 (Aryan), Ptb2 (Ponnaryan), Ptb 6 (Athikkiraya) and Ptb15 (Kavunginpoothala). Varieties identified for high WUE (based on ∆13C value) were Ptb5 (Veluthari kayama), Ptb7 (Parambuvattan), Ptb9 (Thavalakannan), Ptb10 (Thekkancheera) and Ptb19 (Athikiraya). Selected genotypes were used for molecular characterization using microsatellite markers. A total of 216 microsatellite markers representing 12 different chromosomes were selected for genotyping. DNA from each group were bulked together for bulked line analysis of root traits and WUE. RM 202 showed polymorphism between deep root and shallow root bulked DNA. For WUE, RM313 is polymorphic between the high and low WUE genotypes. Although the BLA method cannot be used directly to localize genes, it is useful for the identification of DNA markers that are associated with the target gene. Through such markers, the linked trait can be precisely localized if the markers used have been previously mapped.

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Acknowledgements

Financial support from Kerala State Council for Science, Technology and Environment, Young Investigator’s Programme in Biotechnology is gratefully acknowledged.

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Authors and Affiliations

  1. Regional Agricultural Research Station, Pattambi, Kerala Agricultural University, Palakkad, Kerala, 679 306, India

    R. Beena, V. P. Praveenkumar, Veena Vighneswaran & M. C. Narayankutty

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  1. R. Beena
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  2. V. P. Praveenkumar
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  3. Veena Vighneswaran
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  4. M. C. Narayankutty
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Correspondence to R. Beena.

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Beena, R., Praveenkumar, V.P., Vighneswaran, V. et al. Bulked line analysis: a useful tool to identify microsatellite markers linked to drought tolerance in rice. Ind J Plant Physiol. 23, 7–15 (2018). https://doi.org/10.1007/s40502-017-0321-0

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  • DOI: https://doi.org/10.1007/s40502-017-0321-0

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