Allelic variation of the rice blast resistance gene Pid3 in cultivated rice worldwide

Qiming Lv,Zhiyuan Huang,Zhirong Peng,Li Tang,Xiao Xu,Junjie Xing,Tianqing Zheng,Xiaobing Li,Zhuangzhi Zhou,Lihuang Zhu,Yeyun Xin,Hai Liu,Chunchao Wang

doi:10.1038/s41598-017-10617-2

Abstract

In this study, the re-sequencing data from 3,000 rice genomes project (3 K RGP) was used to analyze the allelic variation at the rice blast resistance (R) Pid3 locus. A total of 40 haplotypes were identified based on 71 nucleotide polymorphic sites among 2621 Pid3 homozygous alleles in the 3k genomes. Pid3 alleles in most japonica rice accessions were pseudogenes due to premature stop mutations, while those in most indica rice accessions were identical to the functional haplotype Hap_6, which had a similar resistance spectrum as the previously reported Pid3 gene. By sequencing and CAPS marker analyzing the Pid3 alleles in widespread cultivars in China, we verified that Hap_6 had been widely deployed in indica rice breeding of China. Thus, we suggest that the priority for utilization of the Pid3 locus in rice breeding should be on introducing the functional Pid3 alleles into japonica rice cultivars and the functional alleles of non-Hap_6 haplotypes into indica rice cultivars for increasing genetic diversity.

Highlights

Rice (Oryza sativa L.) is a staple food for nearly half of the world’s population
Considering that there are more than 400 NBS–LRR gene sequences identified in a rice genome, and that allelic rice blast R genes may confer distinct resistance spectra to M. oryzae isolates[27, 29], we believe that allele mining of cloned rice blast R genes in rice germplasms would reveal more favorable R alleles for rice blast resistance breeding[13]
We previously revealed that Pid[3] alleles in 29 out of 32 japonica varieties were identified as pseudogenes due to the presence of a nonsense mutation (CAG to TAG) at the nucleotide position 2209, whereas none of the varieties in 32 indica collection contained this mutation[44]

Summary

Introduction

Rice (Oryza sativa L.) is a staple food for nearly half of the world’s population. It represents a model for functional genome research among the crop plants. It is difficult to identify alleles of cloned NBS-LRR type rice blast R genes through allele mining approach based on either traditional PCR or NGS data analyzing. The rice blast R gene Pid[3] was initially identified in the indica variety Digu by performing a genome-wide comparison of paired NBS-LRR genes and their pseudogene alleles between 93-11 (indica) and Nipponbare (japonica) on the premise of the verification of obvious different resistance of indica and japonica varieties to M. oryzae strains collected from south and north China[44]. A number of Pid[3] alleles or orthologs were cloned by map-based cloning[45] and sequencing-based allele mining from indica and wild rice accessions, of which five had been verified to confer differential resistance spectra to a set of M. oryzae isolates[29, 46]. We may propose different strategies in application of the functional Pid[3] alleles to indica and japonica rice breeding

Methods

Results

Conclusion