Emergence of Rice Blast AVR-Pi9 Resistance Breaking Haplotypes in Yunnan Province, China

Abstract

The rice blast disease (caused by Magnaporthe oryzae) is a devastating disease in China. Understanding the molecular mechanisms of interaction for the cognate avirulence (AVR) gene with host resistance (R) genes, as well as their genetic evolution is essential for sustainable rice production. In the present study, we conducted a high-throughput nucleotide sequence polymorphism analysis of the AVR-Pi9 gene that was amplified from the rice-growing regions of the Yunnan Province in China. We detected the presence of seven novel haplotypes from 326 rice samples. In addition, the sequences of AVR-Pi9 were also obtained from two non-rice hosts, Eleusine coracana and Eleusine indica. The sequence analysis revealed the insertions and deletions in the coding and non-coding regions of the gene. The pathogenicity experiments of these haplotypes on previously characterized monogenic lines showed that the newly identified haplotypes are virulent in nature. The breakdown of resistance was attributed to the development of new haplotypes. Our results suggest that the mutation in the AVR-Pi9 gene is an alarming situation in the Yunnan province and thus needs attention.

Keywords: landrace; monogenic resistance; polymorphism; rice blast; virulence.

Figure 1

Maximum likelihood phylogenetic tree of the seven haplotypes identified from rice in the Yunnan province of China. The seven haplotypes can be divided into three different clusters as per their sequence variation. The H1 haplotype showed high genetic identity with the reference strain (KM004023.1).

Figure 2

The diversification of AVR-Pi9 in avirulent isolates. The distribution of variation in the AVR-Pi9 alleles was analyzed via the sliding window method. The X-axis shows the distribution of variation within the full region, including the promoter region and exons of AVR-Pi9. The lower pane indicates the corresponding schematic presentation of the promoter region in white color, and two exons in red color are for AVR-Pi9. Window length: 10. Step size: 2. The π value corresponds with the level of variation at each site because it is the sum of the pair-wise differences divided by the number of pairs within the population.

Figure 3

The phylogenetic tree constructed with the nucleotide sequences of the AVR-Pi9 genes from 328 Magnaporthe oryzae isolates. The maximum likelihood methods of MEGA V5.10. The ID number of KM004023 (GenBank Accession No. KM004023) for AVR-Pi9 was obtained from GenBank.

Figure 4

Disease reaction of the identification isolates of YN700 and YNC201 on the landrace accessions. YN700 (which belongs to the H1 haplotype) and YNC201 are avirulent and virulent to IRBL9-W (holding Pi9), respectively. Note: the numbers 14, 22, 62, 68, 69, 132, 143, 148, 241, 249 on top of the photo show the landrace varieties of Qi-He-Da-Hong-Gu, Lao-Leng-Gu, Da-Huang-Pi-Nuo, Bei-Zi-Nuo, Zao-Hong-Gu, Xiao-Hua-Gu, Da-Bo-Gu, Hao-Bu-Ka, Qie-Xie-Gu and San-Bai-Bang, respectively.