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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #276662

Title: Understanding rice heterosis using deep sequencing

item VENU, R-C - University Of Arkansas
item Jia, Yulin
item LIU, GUANGJIE - University Of Arkansas
item Jia, Melissa
item NOBUTA, KAN - University Of Delaware
item SREEREKHA, M-V - The Ohio State University
item MOLDENHAUER, KAREN - University Of Arkansas
item PELLGRINI, MATTEO - University Of California
item JACOBSEN, STEVEN - University Of California
item McClung, Anna

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/3/2011
Publication Date: 2/27/2012
Citation: Venu, R., Jia, Y., Liu, G., Jia, M.H., Nobuta, K., Sreerekha, M., Moldenhauer, K.A., Pellgrini, M., Jacobsen, S.E., Mcclung, A.M. 2012. Understanding rice heterosis using deep sequencing. Rice Technical Working Group Meeting Proceedings. Feb. 27 - Mar. 1, 2012. Hot Springs, AR. pg. 46-47..

Interpretive Summary:

Technical Abstract: Heterosis is a complex biological phenomenon where the offspring show better performance compared to the inbred parents. Although rice breeders have used heterosis in hybrid rice production for nearly 40 years, the genetic and molecular mechanism underlying the heterosis in rice is still poorly understood. Large scale transcriptome profiling has been used for heterosis studies in many crop plants and identified numerous candidate genes that are associated with the trait. In this study, we used Illumina’s massively parallel signature sequencing (MPSS) technique to deeply analyze the transcriptome of rice F1 hybrid derived from a cross between the sequenced japonica rice Nipponbare and indica rice 93-11. MPSS libraries were constructed using RNA isolated from leaves, roots and meristem tissues harvested from parents and their F1 hybrid. About 1 to 3 million signatures were obtained from each library. The gene expression level of unique signatures in the F1 hybrids was compared to their parents. The identified genes in the F1 hybrid were classified into five major categories based on their expression level: above the high parent level, high parent level, mid parent level, low parent level and below the low parent level. Using cluster analysis, the commonly and specifically expressed genes in Nipponbare, 93-11 and F1 hybrid were identified in all three tissues. Functional classification of these genes was carried out using Kyoto Encyclopedia of Genes and Genomes (KEGG), Gramene and MSU Rice Genome Annotation Project databases. Identification of these genes in the japonica/indica hybrid has provided new insights into the molecular basis of heterosis in rice.