Abstract
Common wild rice (Oryza rufipogon Griff.) is invaluable genetic resource for rice resistance breeding. Whole-genome re-sequencing was conducted to systematically analyze the variations in two new inbred lines (Huaye 3 and Huaye 4) developed from a common wild rice. A total of 4,841,127 SNPs, 1,170,479 InDels, 24,080 structural variations (SVs), and 298 copy number variations (CNVs) were identified in three materials. Approximately 16.24 and 5.64% of the total SNPs and InDels of Huaye 3 and Huaye 4 were located in genic regions, respectively. Together, 12,486 and 15,925 large-effect SNPs, and 12,417 and 14,513 large-effect InDels, which affect the integrity of the encoded protein, were identified in Huaye 3 and Huaye 4, respectively. The distribution map of 194 and 245 NBS-LRR encoding homologs was constructed across 12 rice chromosomes. Further, GO enrichment analysis of the homologs with identical genotype variations in Huaye 3 and Huaye 4 revealed 67, 82, and 58 homologs involved in cell death, response to stress, and both terms, respectively. Comparative analysis displayed that 550 out of 652 SNPs and 129 out of 147 InDels were present in a widely used blast-susceptible rice variety (LTH). Protein-protein interaction analysis revealed a strong interaction between NBS-LRR candidates and several known R genes. One homolog of disease resistance protein (RPM1) was involved in the plant-pathogen interaction pathway. Artificial inoculation of disease/insect displayed resistance phenotypes against rice blast and brown planthopper in two lines. The results will provide allele-specific markers for rice molecular breeding.
Highlights
Rice is one of the most important foods for over half of the world’s population
Most of the cloned resistance genes (R genes) in rice are nucleotide-binding leucine-rich repeats (NBS-LRR) that involved in effector-triggered immunity (ETI) (Dangl et al 1996)
The high-density DNA polymorphisms obtained by advanced next-generation genome re-sequencing offered us an opportunity to take deeper insights into the wholegenome diversity
Summary
Rice is one of the most important foods for over half of the world’s population. The increasing world population needs higher rice productivity. Genome-wide DNA variations include single-nucleotide polymorphism (SNP), insertion/deletion (InDel), and large segment variations, such as structural variation (SV) and copy number variation (CNV) (Varshney et al 2009; Huang et al 2013) These DNA variations are responsible for the phenotype divergence among different rice germplasm. 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). In order to reveal the genome variation features of two inbred lines and their common wild rice progenitor and to get a preliminary understanding of the genetic basis lies in resistance phenotype, whole-genomes re-sequencing of S24, Huaye 3, and Huaye 4 was performed. This study will facilitate the utility of these variations and resistance alleles in molecular breeding and functional genomics
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