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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #301032
Title: Identification of candidate genes associated with heterosis in rice

Author
item VENU, R - University Of Arkansas
item MA, JIANBING - University Of Arkansas
item Jia, Yulin
item LIU, GUANGJIE - University Of Arkansas
item Jia, Melissa
item NOBUTA, KAN - Delaware Biotechnology Institute
item SREEREKHA, MYSORE - University Of Arkansas
item MOLDENHAUER, KAREN - University Of Arkansas
item McClung, Anna
item MEYERS, BLAKE - Delaware Biotechnology Institute
item WANG, GUO-LIANG - The Ohio State University

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 2/18/2014
Publication Date: 12/15/2014
Citation: Venu, R.C., Ma, J., Jia, Y., Liu, G., Jia, M.H., Nobuta, K., Sreerekha, M.V., Moldenhauer, K., McClung, A.M., Meyers, B.C., Wang, G. 2014. Identification of candidate genes associated with heterosis in rice. Proc. 35th Rice Tech. Work. Group Meet., New Orleans, LA, p.53. Feb 18-21, 2014. CDROM.

Interpretive Summary:

Technical Abstract: Hybrid rice due to heterosis has played an important role for ensuring stable rice production in the USA and globally. Heterosis is a complex biological phenomenon in which the offspring show superior performance compared to their inbred parents. The heterosis can be positive or negative based on breeding objectives and parental traits. In the present study, massively parallel signature sequencing (MPSS) libraries were constructed from leaves, roots, and meristem tissues from the two parents, Nipponbare and 93-11, and their F1 hybrid to identify differentially expressed genes. A total of 1-3 million signatures were obtained from the MPSS libraries. Using cluster analysis, commonly and specifically expressed genes in the parents and their F1 hybrid were identified in all three tissues. The differentially expressed genes identified in F1 hybrids were mapped onto yield related quantitative trait loci (QTL) regions using a linkage map constructed from 131 polymorphic Simple Sequence Repeat markers with 259 recombinant inbred lines derived from a cross between Nipponbare and 93-11. The average of each yield component from replicated field plot experiments from three years and two locations was used for QTL mapping. QTLs were identified for yield related traits including days to heading, plant height, plant type, tiller number, panicle length, number of primary branches per panicle, number of seeds per panicle, total kernel weight per panicle, 1000 grain weight, and total grain yield per plant. Thus far, 71 QTLs related to the previously mentioned yield traits were mapped; three of which were novel. Many highly expressed chromatin-related genes in F1 hybrids encoding histone demethylases, histone deacetylases, argonaute-like proteins, and polycomb proteins were located in these yield QTL regions suggesting potential epigenetic regulation for rice yield. Additionally, a total of 336 highly expressed transcription factor (TF) genes belonging to 50 TF families were identified in the yield QTL intervals. Differentially expressed genes belonging to biochemical pathways including carbohydrate metabolism, energy metabolism, and metabolism of cofactors and vitamins were highly represented in leaves, roots, and meristem tissues suggesting these may be related to hybrid vigor. This study represents a comprehensive analysis of transcriptomes of F1 hybrids to identify the genes related to positive and negative heterosis of yield related traits in rice. Identification of these candidate genes provides the starting genomic materials to elucidate the molecular basis of heterosis in rice.