Abstract
The genomes of two rice cultivars, Nipponbare and 93-11, have been well studied. However, there is little available genetic information about nutraceutical rice cultivars. To remedy this situation, the present study aimed to provide a basic genetic landscape of nutraceutical rice. The genome of Black-1, a black pericarp rice containing higher levels of anthocyanins, flavonoids, and a more potent antioxidant capacity, was sequenced at ≥30 × coverage using Solexa sequencing technology. The complete sequences of Black-1 genome shared more consensus sequences with indica cultivar 93-11 than with Nipponbare. With reference to the 93-11 genome, Black-1 contained 675,207 single-nucleotide polymorphisms, 43,130 insertions and deletions (1–5 bp), 1,770 copy number variations, and 10,911 presence/absence variations. These variations were observed to reside preferentially in Myb domains, NB-ARC domains and kinase domains, providing clues to the diversity of biological functions or secondary metabolisms in this cultivar. Intriguingly, 496 unique genes were identified by comparing it with the genomes of these two rice varieties; among the genes, 119 genes participate in the biosynthesis of secondary metabolites. Furthermore, several unique genes were predicted to be involved in the anthocyanins synthesis pathway. The genome-wide landscape of Black-1 uncovered by this study represents a valuable resource for further studies and for breeding nutraceutical rice varieties.
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Acknowledgments
This research was supported financially by the National Key Technology R&D Program (2013BAD01B05), the 948 Project of the Ministry of Agriculture (2011-Z59 and 2012-Z30), the Key Project of Science and Technology Cooperation of Fujian Province (2010I0001), the Science and Technology Project of the Education Department of Fujian Province (K8012053A), and the Major Science and Technology Projects of Fujian Province (2013NZ0002-2) in China. We thank BGI-Shenzhen for their help with the sequencing and annotation.
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Communicated by B. Yang.
J. Lin and Z. Cheng contributed equally to this work.
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Lin, J., Cheng, Z., Xu, M. et al. Genome re-sequencing and bioinformatics analysis of a nutraceutical rice. Mol Genet Genomics 290, 955–967 (2015). https://doi.org/10.1007/s00438-014-0964-8
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DOI: https://doi.org/10.1007/s00438-014-0964-8