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Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice

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Abstract

Chromosomal segments from wild rice species Oryza rufipogon, introgressed into an elite indica rice restorer line (KMR3) using molecular markers, resulted in significant increase in yield. Here we report the transcriptome analysis of flag leaves and fully emerged young panicles of one of the high yielding introgression lines IL50-7 in comparison to KMR3. A 66-fold upregulated gene Os11Gsk, which showed no transcript in KMR3 was highly expressed in O. rufipogon and IL50-7. A 5-kb genomic region including Os11Gsk and its flanking regions could be PCR amplified only from IL50-7, O. rufipogon, japonica varieties of rice-Nipponbare and Kitaake but not from the indica varieties, KMR3 and Taichung Native-1. Three sister lines of IL50-7 yielding higher than KMR3 showed presence of Os11Gsk, whereas the gene was absent in three other ILs from the same cross having lower yield than KMR3, indicating an association of the presence of Os11Gsk with high yield. Southern analysis showed additional bands in the genomic DNA of O. rufipogon and IL50-7 with Os11Gsk probe. Genomic sequence analysis of ten highly co-expressed differentially regulated genes revealed that two upregulated genes in IL50-7 were derived from O. rufipogon and most of the downregulated genes were either from KMR3 or common to KMR3, IL50-7, and O. rufipogon. Thus, we show that Os11Gsk is a wild rice-derived gene introduced in KMR3 background and increases yield either by regulating expression of functional genes sharing homology with it or by causing epigenetic modifications in the introgression line.

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Acknowledgments

This work and ST were supported by a DBT grant to NS [DBT No.BT/AD/FG-2(PH-II)2009]. AKB was funded by Indian Council for Agricultural Research project 3019 (NPTC/FG/05/2672/33). We acknowledge the contributions of A Prasad Babu, C Surendhar Reddy, and BP Mallikarjuna Swamy in earlier work on developing and evaluating introgression lines and marker aided selection. We thank Project Director, DRR for the encouragement. We thank G. Haritha and N. Naga Deepthi for help in identifying polymorphic markers. The authors are thankful to the Sequencing laboratory CCMB, India for providing the sequencing facility used for this study.

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  1. Biotechnology Unit, Directorate of Rice Research, Rajendranagar, Hyderabad, 500 030, India

    Sudhakar Thalapati, Anil K. Batchu & Sarla Neelamraju

  2. Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 009, Andhra Pradesh, India

    Rajeshwari Ramanan

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  1. Sudhakar Thalapati
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Correspondence to Rajeshwari Ramanan.

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The microarray data have been submitted to the GEO repository and assigned GEO accession number. GSE30487. It was released on the 31st of December 2011.

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Thalapati, S., Batchu, A.K., Neelamraju, S. et al. Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice. Funct Integr Genomics 12, 277–289 (2012). https://doi.org/10.1007/s10142-012-0265-4

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