Abstract
Common wild rice (Oryza rufipogon Griff.) is an important germplasm for rice breeding, which contains many resistance genes. Re-sequencing provides an unprecedented opportunity to explore the abundant useful genes at whole genome level. Here, we identified the nucleotide-binding site leucine-rich repeat (NBS-LRR) encoding genes by re-sequencing of two wild rice lines (i.e. Huaye 1 and Huaye 2) that were developed from common wild rice. We obtained 128 to 147 million reads with approximately 32.5-fold coverage depth, and uniquely covered more than 89.6% (> = 1 fold) of reference genomes. Two wild rice lines showed high SNP (single-nucleotide polymorphisms) variation rate in 12 chromosomes against the reference genomes of Nipponbare (japonica cultivar) and 93–11 (indica cultivar). InDels (insertion/deletion polymorphisms) count-length distribution exhibited normal distribution in the two lines, and most of the InDels were ranged from -5 to 5 bp. With reference to the Nipponbare genome sequence, we detected a total of 1,209,308 SNPs, 161,117 InDels and 4,192 SVs (structural variations) in Huaye 1, and 1,387,959 SNPs, 180,226 InDels and 5,305 SVs in Huaye 2. A total of 44.9% and 46.9% genes exhibited sequence variations in two wild rice lines compared to the Nipponbare and 93–11 reference genomes, respectively. Analysis of NBS-LRR mutant candidate genes showed that they were mainly distributed on chromosome 11, and NBS domain was more conserved than LRR domain in both wild rice lines. NBS genes depicted higher levels of genetic diversity in Huaye 1 than that found in Huaye 2. Furthermore, protein-protein interaction analysis showed that NBS genes mostly interacted with the cytochrome C protein (Os05g0420600, Os01g0885000 and BGIOSGA038922), while some NBS genes interacted with heat shock protein, DNA-binding activity, Phosphoinositide 3-kinase and a coiled coil region. We explored abundant NBS-LRR encoding genes in two common wild rice lines through genome wide re-sequencing, which proved to be a useful tool to exploit elite NBS-LRR genes in wild rice. The data here provide a foundation for future work aimed at dissecting the genetic basis of disease resistance in rice, and the two wild rice lines will be useful germplasm for the molecular improvement of cultivated rice.
Highlights
Common wild rice (Oryza rufipogon Griff.), the progenitor of Asian cultivated rice (Oryza sativa L.), is widely distributed in the tropics and subtropics of Asia, Papua New Guinea, and Australia [1,2]
Protein-protein interaction analysis showed that nucleotide binding site (NBS) genes mostly interacted with the cytochrome C protein (Os05g0420600, Os01g0885000 and BGIOSGA038922), while some NBS genes interacted with heat shock protein, DNA-binding activity, Phosphoinositide 3-kinase and a coiled coil region
A total of 128 to 147 million mapped reads were generated by Burrows-Wheeler Aligner (BWA) software, and the uniquely mapped reads covered more than 87.62% of the sequencing reads across both 93– 11 and Nipponbare reference genomes (Table 1)
Summary
Common wild rice (Oryza rufipogon Griff.), the progenitor of Asian cultivated rice (Oryza sativa L.), is widely distributed in the tropics and subtropics of Asia, Papua New Guinea, and Australia [1,2]. Common wild rice has abundant genetic diversity and various resistance genes for the improvement of cultivated rice [3,4]. To fulfill the demands of food supply, there is a need to enhance the crop productivity significantly by exploitation and utilization of genetic resources, those in the gene pool of wild species [4]. As genetic diversity among commercial cultivars has declined, it is difficult to find new resistance genes from existing cultivars for the further improvement of rice. Sufficient resistance could be managed by exploring wild species [6]
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