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Molecular Plant Advance Access originally published online on August 5, 2008
Molecular Plant 2008 1(5):720-731; doi:10.1093/mp/ssn022
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© The Author 2008. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPP and IPPE, SIBS, CAS.

A Genome-Wide Transcription Analysis Reveals a Close Correlation of Promoter INDEL Polymorphism and Heterotic Gene Expression in Rice Hybrids

Hui-Yong Zhanga,2, Hang Hea,b,2, Liang-Bi Chenc, Lei Lid,e, Man-Zhong Liangc, Xiang-Feng Wanga,e, Xi-Gang Liua, Guang-Ming Hea, Run-Sheng Chenb, Li-Geng Maa and Xing Wang Denga,d,e,1

a National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
b Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
c Department of Botany, College of Life Sciences, Hunan Normal University, Changsha 410081, China
d Peking–Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
e Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA

1 To whom correspondence should be addressed. E-mail xingwang.deng{at}yale.edu, fax 1-203-432-5726, tel. 1-203-432-8908.

Heterosis, or hybrid vigor, refers to the phenomenon in which hybrid progeny of two inbred varieties exhibits enhanced growth or agronomic performance. Although a century-long history of research has generated several hypotheses regarding the genetic basis of heterosis, the molecular mechanisms underlying heterosis and heterotic gene expression remain elusive. Here, we report a genome-wide gene expression analysis of two heterotic crosses in rice, taking advantage of its fully sequenced genomes. Approximately 7–9% of the genes were differentially expressed in the seedling shoots from two sets of heterotic crosses, including many transcription factor genes, and exhibited multiple modes of gene action. Comparison of the putative promoter regions of the ortholog genes between inbred parents revealed extensive sequence variation, particularly small insertions/deletions (INDELs), many of which result in the formation/disruption of putative cis-regulatory elements. Together, these results suggest that a combinatorial interplay between expression of transcription factors and polymorphic promoter cis-regulatory elements in the hybrids is one plausible molecular mechanism underlying heterotic gene action and thus heterosis in rice.

2 These authors contributed equally to this work.


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