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Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.)

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Abstract

Identification of genes for quantitative traits is difficult using any single approach due to complex inheritance of the traits and limited resolving power of the individual techniques. Here a combination of genetic mapping and bulked transcriptome profiling was used to narrow down the number of differentially expressed salt-responsive genes in rice in order to identify functional polymorphism of genes underlying the quantitative trait loci (QTL). A population of recombinant inbred lines (RILs) derived from cross between salt-tolerant variety CSR 27 and salt-sensitive variety MI 48 was used to map QTL for salt ion concentrations in different tissues and salt stress susceptibility index (SSI) for spikelet fertility, grain weight, and grain yield. Eight significant QTL intervals were mapped on chromosomes 1, 8, and 12 for the salt ion concentrations and a QTL controlling SSI for spikelet fertility was co-located in one of these intervals on chromosome 8. However, there were total 2,681 genes in these QTL intervals, making it difficult to pinpoint the genes responsible for the functional differences for the traits. Similarly, transcriptome profiling of the seedlings of tolerant and sensitive parents grown under control and salt-stress conditions showed 798 and 2,407 differentially expressed gene probes, respectively. By analyzing pools of RNA extracted from ten each of extremely tolerant and extremely sensitive RILs to normalize the background noise, the number of differentially expressed genes under salt stress was drastically reduced to 30 only. Two of these genes, an integral transmembrane protein DUF6 and a cation chloride cotransporter, were not only co-located in the QTL intervals but also showed the expected distortion of allele frequencies in the extreme tolerant and sensitive RILs, and therefore are suitable for future validation studies and development of functional markers for salt tolerance in rice to facilitate marker-assisted breeding.

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Acknowledgments

We are thankful to the Indian Council of Agricultural Research, New Delhi, for financial support of the NPTC project.

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Author notes

  1. Rakesh Singh

    Present address: DNA Fingerprinting, NBPGR, New Delhi, 110012, India

Authors and Affiliations

  1. Rice Genome Laboratory, National Research Centre on Plant Biotechnology, New Delhi, 110012, India

    Awadhesh Pandit, Vandna Rai, Subhashis Bal, Shikha Sinha, Rakesh Singh, Kishor Gaikwad, Tilak R. Sharma, Trilochan Mohapatra & Nagendra K. Singh

  2. University School of Biotechnology, GGSIP University, New Delhi, 110006, India

    Awadhesh Pandit & Prakash C. Sharma

  3. Central Soil Salinity Research Institute, Karnal, 132001, India

    Vinod Kumar, Mahesh Chauhan & Raj K. Gautam

  4. Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India

    Ashok K. Singh

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  1. Awadhesh Pandit
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Correspondence to Nagendra K. Singh.

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Communicated by R. Waugh.

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Pandit, A., Rai, V., Bal, S. et al. Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.). Mol Genet Genomics 284, 121–136 (2010). https://doi.org/10.1007/s00438-010-0551-6

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