Discovery of Genome-Wide DNA Polymorphisms and Resistance-Relative Genes in Chaling Wild Rice ( Oryza rufipogon Griff.)
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ORIGINAL ARTICLE
Discovery of Genome-Wide DNA Polymorphisms and Resistance-Relative Genes in Chaling Wild Rice (Oryza rufipogon Griff.) by Whole-Genome Sequencing Dandan Wu 1 & Chengrui Wang 2 & Zhenhai Zhang 2 & Chongyan Guo 3 & Qiuhong Chen 1 & Zhilong Wang 1 Received: 3 January 2020 / Accepted: 22 September 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Chaling common wild rice (Chaling CWR, Oryza rufipogon Griff.) is a kind of germplasm resource which possesses abundant genetic diversity and plays a pivotal role in improving cultivated rice. In this research, we used next-generation sequencing technology to reveal the genome sequence of Chaling CWR and investigate its elite genes. The results showed that the average coverage was 93.99%. 1,743,368 single-nucleotide polymorphism (SNP) and 387,381 insertion and deletion (InDel) variants have been detected in Chaling CWR compared with the Nipponbare genome. The variant density was found to be highest in chromosome 10 and lowest in chromosome 5, with an average density of 467.08 SNPs/100 kb and 109.59 InDels/100 kb across the whole genome. 109,684 non-synonymous SNPs were identified in 14,315 genes, and 26,051 InDels were detected in the coding regions. We further classified these genes based on the protein domains that were involved in host defense mechanisms and in the analysis of 37 NBS-LRRs, 71 LRRs, 136 NB-ARCs, 119 PKs, 19 WRKY transcription factors, and 25 resistant protein genes. Among the putative R-genes, Pish, Pita, Pi25, Pi9, Pi21, Pid2, Pikm, and Xa21 were further identified, as exhibiting high rates of polymorphism. Results from this study provide a foundation for future basic research and marker-assisted breeding of rice resistance. Keywords Chaling common wild rice . Whole-genome sequencing . Single nucleotide polymorphism . Insertion . Deletion . R-genes
Introduction
Dandan Wu and Chengrui Wang contributed equally to this work. Key Message Chaling common wild rice (Chaling CWR) possesses abundant genetic diversity and plays a pivotal role in improving cultivated rice. This work investigates the genome-wide polymorphisms and the key genes in Chaling CWR by next-generation sequencing. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11105-020-01247-6) contains supplementary material, which is available to authorized users. * Qiuhong Chen [email protected] * Zhilong Wang [email protected] 1
College of Agronomy, Hunan Agricultural University, Changsha, China
2
Nanfang Hospital, Southern Medical University, Guanzhou, China
3
Ganzhou Flower Research Institute, Ganzhou, Jiangxi, China
Rice (Oryza sativa L.) is a staple food for more than half of the world’s population, and the global rice demand is estimated to reach 8.52 × 108 t by 2035 (Devi et al. 2015; Khush 2013). The development of hybrid rice is a practical approach to increase rice production. However, rice production is still frequently affected by biotic stress. Rice blast, one of the major diseases that o
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