Abstract
Multiple haplotypes at the same rice blast R-gene locus share extremely high sequence similarity, which makes the gene diagnostic method using molecular markers less effective in differentiation from one another. The composition and distribution pattern of deployed R genes/haplotypes in elite rice varieties has not been extensively analyzed. In this study, we employed PCR amplification and sequencing approach for the diagnosis of R-gene haplotypes in 54 Chinese elite rice varieties. A varied number of functional and nonfunctional haplotypes of 4 target major R-gene loci, i.e., Pi2/9, Pi5, Pik, and Pib, were deduced by referring to the reference sequences of known R genes. Functional haplotypes accounted for relatively low frequencies for the Pi2/9 (15%) and Pik (9%) loci but for relatively high frequencies for the Pi5 (50%) and Pib (54%) loci. Intriguingly, significant frequencies of 33%, 39%, 46% of non-functional haplotypes at the Pi2/9, Pik, and Pib loci, respectively, with traceable original donors were identified, suggesting that they were most likely unintentionally spread by using undesirable donors in various breeding programs. In the case of Pi5 locus, only a single haplotype, i.e., Pi5 was identified. The reactions of 54 rice varieties to the differential isolates were evaluated, which showed a good correlation to the frequency of cognate avirulence (Avr) genes or haplotypes in the differential isolates. Four R genes, i.e., Pi2, Piz-t, Pi50, and Pikm were found to contribute significantly to the resistance of the elite rice varieties. Other two genes, Pi9 and Pikh, which were not utilized in rice varieties, showed promising values in breeding durable resistance due to their high resistance frequencies to the contemporary rice blast population. The sequence-based molecular diagnosis provided a promising approach for the identification and verification of haplotypes in different R-gene loci and effective R genes valuable for breeding durable rice resistance to rice blast.
Highlights
Rice is a staple diet for nearly half of the global population (Harlan 1998; Skamnioti and Gurr 2009), and its increase in production to meet the ever-increasing population faces many challenges
Establishment of the method for the diagnosis of haplotypes at four rice blast R-gene loci For the diagnosis of R-gene haplotypes, portions of known R genes that are capable for differentiating different haplotypes were targeted for Polymerase chain reaction (PCR) amplification and sequence analysis
It is worth noting that a prescreen step by PCR amplification was conducted using Pi2/9-DF1/DR1 to exclude those lines without positive PCR amplification as described previously (Xiao et al 2017)
Summary
Rice is a staple diet for nearly half of the global population (Harlan 1998; Skamnioti and Gurr 2009), and its increase in production to meet the ever-increasing population faces many challenges. The rice and rice blast system belong to a typical gene-for-gene system (Flor 1971), in which the host resistance (R) genes show functional correspondence to their cognate pathogen avirulence (Avr). The co-evolution and interaction of R and Avr gene raises the possibility of a gene-specific arms race leading to diversification of both R and Avr genes (Dodds et al 2006). Nine rice blast Avr genes have been cloned to date (Wang et al 2017). Field efficacy of any R gene in rice varieties is proposed to depend on the frequency of its cognate Avr gene in the rice blast pathogen population, which provides a basis of Avr-gene based diagnosis for the deduction of effectiveness of R genes (Selisana et al 2017; Olukayode et al 2019)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
