Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes

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.

Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice (Oryza sativa L.)

“…Most of the genes assigned to the three GO categories were mainly involved in metabolic process, cellular process, binding, catalytic activity, cell, and cell part. This functional annotation of genes is consistent with previous findings in rice (Kim et al, 2014;Liu et al, 2017). Additionally, our data showed that the metabolic process involved in the cellular aromatic compound was associated with the common mutated gene cluster ( Figure 5A) and further analyses revealed that nine genes including Badh2 gene having alternative allele's among aromatic group of rice varieties with more than 80% of frequency ( Supplementary Table 8).…”

Genome-Wide Analysis of Genetic Variations and the Detection of Rich Variants of NBS-LRR Encoding Genes in Common Wild Rice Lines

“…A total of 194 and 245 NBS-LRR encoding genes exhibited large-effect variations, including 11 previously cloned R genes, and were explored in Huaye 3 and Huaye 4. Interestingly, only five NBS-LRR encoding genes have intersection with the genes recently identified in another two common wild rice lines (Liu et al 2017 ). About 30% of these genes were located on chromosome 11, and 40% of these genes were distributed in gene clusters.…”

“…Rice cultivars with contrasting drought and salinity stress response were re-sequenced and the variations in drought and salinity response QTLs were explored (Jain et al 2014 ). Some NBS-LRR genes had been identified in two newly developed rice lines from common wild rice, which were indigenous to Dongxiang, Jiangxi Province, China, by using genome-wide re-sequencing (Liu et al 2017 ). Recently, rice pan-genome data provided the information about thousands of newly identified genes, present/absent variations, and unique genes of cultivated and wild lines (Zhao et al 2018 ).…”

Differential expression of NBS-LRR-encoding genes in the root transcriptomes of two Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis

“…Recent development of NGS (next-generation sequencing) techniques has resulted in the accumulation of genomic nucleotide sequences and has provided new opportunities in this field. Resequencing of the genomes of resistant plant genotypes facilitates the identification of R genes of interest (e.g., [ 4 – 6 ]). Potential NBS-LRR genes may also be predicted in genomes with the aid of bioinformatic tools (e.g., [ 21 – 23 ]), and application of these tools for genome analysis may provide large lists of potential RGAs [ 10 ].…”

“…Recently, new approaches in this field were developed on the basis of genomic data (some recently published examples are presented below). Genome-wide resequencing and comparison with reference genomes revealed a number of NBS-LRR candidate genes in common wild rice [ 4 ], Medicago truncatula [ 5 ], Arachis duranensis and A. hypogaea [ 6 ]. Comparison of syntenic genomic regions of related species containing NBS-LRR genes was found to be a promising way to locate candidate resistance genes in the genomes of various crops (e.g., [ 7 , 8 ]).…”