J Integr Plant Biol. ›› 2010, Vol. 52 ›› Issue (11): 971-980.DOI: 10.1111/j.1744-7909.2010.00985.x

Special Issue: Rice Genomics and Agriculture

• Metabolism and Biochemistry • Previous Articles     Next Articles

Expression Analysis of miRNAs and Highly-expressed Small RNAs in Two Rice Subspecies and Their Reciprocal Hybrids

Fangfang Chen1,2, Guangming He2,3,4, Hang He4, Wei Chen 4, Xiaopeng Zhu 5, Manzhong Liang6, Liangbi Chen6 and Xing-Wang Deng3,4*   

  1. 1Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
    2National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
    3Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    4Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
    5Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
    6Department of Botany, College of Life Sciences, Hunan Normal University, Changsha 410081, China
  • Received:2010-05-03 Accepted:2010-07-06 Published:2010-11-01
  • About author:*Author for correspondence Tel: +1 203 432 8908; Fax: +1 203 432 5726; E-mail: xingwang.deng@yale.edu

Abstract:

Heterosis, or hybrid vigor, is the phenomenon whereby progeny of two inbred lines exhibit superior agronomic performance compared with either parent. We analyzed the expression of miRNAs and highly expressed small RNAs (defined according to Solexa sequencing results) in two rice (Oryza sativa) subspecies (japonica cv. Nipponbare and indica cv. 93-11) and their reciprocal hybrids using microarrays. We found that of all the 1141 small RNAs tested, 140 (12%, 140 of 1141) and 157 (13%, 157 of 1141) were identified being significantly differentially expressed in two reciprocal hybrids, respectively. All possible modes of action, including additive, high- and low- parent, above high- and below low-parent modes were exhibited. Both F1 hybrids showed non-additive expression patterns, with downregulation predominating. Interestingly, 15 miRNAs displayed stark opposite expression trends relative to mid-parent in reciprocal hybrids. Computational prediction of targets of differentially expressed miRNAs showed that they participated in multifaceted developmental pathways, and were not distinguishable from the targets of non-differentially expressed miRNAs. Together, our findings reveal that small RNAs play roles in heterosis and add a new layer in the understanding and exploitation of molecular mechanisms of heterosis.

Chen F, He G, He H, Chen W, Zhu X, Liang M, Chen L, Deng XW (2010) Expression analysis of miRNAs and highly-expressed small RNAs in two rice subspecies and their reciprocal hybrids. J. Integr. Plant Biol. 52(11), 971–980.

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