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Alterations in inheritance pattern and level of cytosine DNA methylation, and their relationship with heterosis in rice

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Abstract

Novel hybrid-specific/heterotic gene expression patterns observed from expression studies suggest the need to characterize the underlying regulatory mechanism(s) to reveal the biological basis of heterosis in crop plants. To gain an insight into the molecular basis of heterosis in rice, we investigated the inheritance pattern and level of cytosine methylation, a major epigenetic regulatory mechanism, in the leaf tissue of an elite Indian rice hybrid KRH2 and its parents at three stages (15 day-old, 35 day-old seedling and flag leaf) and their correlation with heterosis using methylation-sensitive amplification polymorphism (MSAP) technique. In contrast to parents, the level of methylation was high during initial growth stages and reduced as the hybrid grew. Even though, a majority of cytosine methylation profiles were transmitted to hybrid at all stages, a considerable level (25.4%) of cytosine methylation pattern was observed to be novel in hybrid and some of these altered loci were identified to code for known/hypothetical proteins. It was also observed that demethylation events occurred more predominantly during early stages than hypermethylation while the frequency of demethylation events decreased in flag leaf with a remarkable increase in hypermethylation in the hybrid. These bi-directional events in methylation in KRH2 were validated in six hybrids with different levels of grain yield heterosis and the level of cytosine methylation in the hybrid was observed to be significantly correlated with heterosis.

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Acknowledgments

The fellowship and facilities provided to K.S. by Barwale foundation are gratefully acknowledged. The authors thank Dr Amalraj John Joel for useful discussion and Mahyco Life Science Research Center, Jalna for sequencing facility. Seed material supplied by IRRI, Philippines and DRR, Hyderabad is thankfully acknowledged. We also thank R. M. Sundaram and P. Rajendrakumar for their useful suggestions which helped to improve the manuscript.

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  1. G. Ramkumar

    Present address: Directorate of Rice Research, Rajendranagar, Hyderabad, India

  2. K. Girishkumar

    Present address: Nunhems Seeds Pvt. Ltd., Bangalore, India

Authors and Affiliations

  1. Research and Training Center, Barwale Foundation, A.G. Heights, Road No.12, Banjara Hills, Hyderabad, 500 034, India

    K. Sakthivel, K. Girishkumar, G. Ramkumar & V. V. Shenoy

  2. Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, 580005, India

    S. T. Kajjidoni & P. M. Salimath

  3. Directorate of Rice Research, Rajendranagar, Hyderabad, India

    K. Sakthivel

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Sakthivel, K., Girishkumar, K., Ramkumar, G. et al. Alterations in inheritance pattern and level of cytosine DNA methylation, and their relationship with heterosis in rice. Euphytica 175, 303–314 (2010). https://doi.org/10.1007/s10681-010-0167-2

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