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United States Department of Agriculture

Agricultural Research Service

Research Project: RESPONSE OF DIVERSE RICE GERMPLASM TO BIOTIC AND ABIOTIC STRESSES Title: Understanding rice heterosis using deep sequencing

Authors
item Venu, R-C -
item Jia, Yulin
item Liu, Guangjie -
item Jia, Melissa
item Nobuta, Kan -
item Sreerekha, M-V -
item Moldenhauer, Karen -
item Pellgrini, Matteo -
item Jacobsen, Steven -
item McClung, Anna
item McClung, Anna

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: December 3, 2011
Publication Date: February 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..

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.

Last Modified: 11/22/2014
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