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Microsatellite based linkage disequilibrium analyses reveal Saltol haplotype fragmentation and identify novel QTLs for seedling stage salinity tolerance in rice (Oryza sativa L.)

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Abstract

A set of 84 diverse rice genotypes were assessed for seedling stage salt tolerance and their genetic diversity using 41 polymorphic SSR markers comprising of 19 Saltol QTL linked and 22 random markers. Phenotypic screening under hydroponics identified three indica landraces (Badami, Shah Pasand and Pechi Badam), two Oryza rufipogon accessions (NKSWR2 and NKSWR17) and one each of Basmati rice (Seond Basmati) and japonica cultivars (Tompha Khau) as salt tolerant, having similar tolerance as of Pokkali and FL478. Among the salt tolerant genotypes, biomass showed positive correlation with shoot fresh weight and negative association with root and shoot Na+ content. The results indicated repression of Na+ loading within the tolerant plants. Linkage disequilibrium (LD) of the Saltol linked markers was weak, suggestive of high fragmentation of Pokkali haplotype, a result of evolutionary active recombination events. Poor haplotype structure of the Saltol region, may reduce its usefulness in marker assisted breeding programmes, if the target foreground markers chosen are wide apart. LD mapping identified eight robust marker-trait associations (QTLs), of which RM10927 was found linked to root and shoot Na+ content and RM10871 with shoot Na+/K+ ratio. RM271 on chromosome 10, an extra Saltol marker, was found associated to root Na+/K+ ratio. This marker showed a distinct allele among O. rufipogon accessions. There were also other novel loci detected on chromosomes 2, 5 and 10 influencing salt tolerance in the tested germplasm. Although Saltol remained as the key locus, the role of other genomic regions cannot be neglected in tailoring seedling stage salt tolerance in rice.

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Abbreviations

SSR:

Microsatellite

LD:

Linkage disequilibrium

QTL:

Quantitative trait locus

MST:

Mean salt tolerance score

PIC:

Polymorphism information content

PCA:

Principal component analysis

MLM:

Mixed linear model

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Acknowledgements

NNB acknowledges Department of Science and Technology, Government of India (GoI) for awarding the DST-INSPIRE Fellowship for his doctoral programme at the ICAR-Indian Agricultural Research Institute, New Delhi of which this study formed a part. The experiments conducted in this study were carried with the financial support to AKS under the accelerated crop improvement programme on development of abiotic stress tolerant rice (BT/PR11694/AGR/02/642/2008) from Department of Biotechnology, GoI.

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Authors and Affiliations

  1. Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    N. Naresh Babu, S. Gopala Krishnan, Ashutosh Yadav, P. K. Bhowmick, K. V. Prabhu & A. K. Singh

  2. Rice Breeding and Genetics Research Centre, ICAR-Indian Agricultural Research Institute, Aduthurai, Tamil Nadu, 612101, India

    K. K. Vinod & M. Nagarajan

  3. ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India

    S. L. Krishnamurthy

  4. ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India

    N. K. Singh

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  1. N. Naresh Babu
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Babu, N.N., Vinod, K.K., Krishnamurthy, S.L. et al. Microsatellite based linkage disequilibrium analyses reveal Saltol haplotype fragmentation and identify novel QTLs for seedling stage salinity tolerance in rice (Oryza sativa L.). J. Plant Biochem. Biotechnol. 26, 310–320 (2017). https://doi.org/10.1007/s13562-016-0393-3

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