Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/17/2014
Publication Date: 4/17/2014
Publication URL: http://handle.nal.usda.gov/10113/60689
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 positive and negative heterosis in rice. PLoS One. 9(4):e95178. Interpretive Summary: Heterosis is a biological phenomenon that allows the offspring to have superior traits compared to the inbred parents. Heterosis can be positive, offspring with enhanced traits for breeding, or negative, with unwanted traits enhanced for breeding. We used massively parallel signature sequencing (MPSS) libraries of two parents, ‘Nipponbare’ and ’93-11’, and their F1 hybrid population to identify positive and negative heterosis related genes. We found several differentially expressed genes in the F1 hybrid population. The location of these genes was determined by yield related quantitative trait loci (QTL) regions. These candidate genes will allow for future work to clarify molecular basis of heterosis in rice.
Technical Abstract: Heterosis is a complex biological phenomenon in which the offspring show superior performance compared to the inbred parents. Heterosis can be positive or negative. To identify the genes related to positive and negative heterosis, 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. From the MPSS libraries, 1-3 million signatures were obtained. Using cluster analysis, commonly and specifically expressed genes in the parents and their F1 hybrid were identified. To understand positive and negative heterosis for the yield related traits in the F1 hybrid, the differentially expressed genes in the F1 hybrid were mapped to 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. Quantitative trait loci were identified for yield related traits including days to heading, plant height, plant type, number of tillers, main panicle length, number of primary branches per main panicle, number of kernels per main panicle, total kernel weight per main panicle, 1000 grain weight and total grain yield per plant. Seventy one QTLs related to the mentioned yield traits were mapped, of which 3 QTLs were novel. Many highly expressed chromatin-related genes in the F1 hybrid encoding histone demethylases, histone deacetylases, argonaute-like proteins and polycomb proteins were located in these yield QTL regions. A total of 336 highly expressed transcription factor (TF) genes belonging to 50 TF families were identified in the yield QTL intervals. We identified many differentially expressed genes in the F1 hybrid and determined their location in the yield related QTL regions. Identification of these candidate genes provided the starting genomic materials to elucidate the molecular basis of heterosis in rice.