AUTHOR=Tian Dagang , Deng Yun , Yang Xiaoshuang , Li Gang , Li Qixiang , Zhou Haiying , Chen Ziqiang , Guo Xinrui , Su Yan , Luo Yuming , Yang Liming 

TITLE=Association analysis of rice resistance genes and blast fungal avirulence genes for effective breeding resistance cultivars

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1007492

DOI=10.3389/fmicb.2022.1007492

ISSN=1664-302X

ABSTRACT=<p>Utilization of rice blast-resistance (<italic>R</italic>) genes is the most economical and environmentally friendly method to control blast disease. However, rice varieties with <italic>R</italic> genes influence the outcome of genetic architectures of <italic>Magnaporthe oryzae</italic> (<italic>M. oryzae</italic>), and mutations in avirulence (<italic>AVR</italic>) genes of <italic>M. oryzae</italic> may cause dysfunction of the corresponding <italic>R</italic> genes in rice varieties. Although monitoring and characterizing rice <italic>R</italic> genes and pathogen <italic>AVR</italic> genes in field populations may facilitate the implementation of effective <italic>R</italic> genes, little is known about the changes of <italic>R</italic> genes over time and their ultimate impact on pathogen <italic>AVR</italic> genes. In this study, 117 main cultivated rice varieties over the past five decades and 35 <italic>M. oryzae</italic> isolates collected from those diseased plants were analyzed by PCR using gene-specific markers of the nine <italic>R</italic> genes and six primer pairs targeting the coding sequence or promoter of <italic>AVR</italic> genes, respectively. The <italic>R</italic> genes <italic>Pigm, Pi9</italic>, <italic>Pi2</italic>, <italic>Piz-t</italic>, <italic>Pi-ta</italic>, <italic>Pik, Pi1</italic>, <italic>Pikp,</italic> and <italic>Pikm</italic> were identified in 5, 0, 1, 4, 18, 0, 2, 1, and 0 cultivars, respectively. Significantly, none of these <italic>R</italic> genes had significant changes that correlated to their application periods of time. Among the four identified <italic>AVR</italic> genes, <italic>AVR-Pik</italic> had the highest amplification frequency (97.14%) followed by <italic>AVR-Pita</italic> (51.43%) and <italic>AVR-Pi9</italic> (48.57%); <italic>AVR-Piz-t</italic> had the lowest frequency (28.57%). All these <italic>AVR</italic> genes except <italic>AVR-Pi9</italic> had 1–2 variants. Inoculation mono-genic lines contained functional genes of <italic>Pi2/9</italic> and <italic>Pik</italic> loci with 14 representative isolates from those 35 ones revealed that the presence of certain <italic>AVR-Piz-t</italic>, <italic>AVR-Pita</italic> variants, and <italic>AVR-Pik-E + AVR-Pik-D</italic> in <italic>M. oryzae</italic> populations, and these variants negated the ability of the corresponding <italic>R</italic> genes to confer resistance. Importantly, <italic>Pi2, Pi9,</italic> and <italic>Pigm</italic> conferred broad-spectrum resistance to these local isolates. These findings reveal that the complex genetic basis of <italic>M. oryzae</italic> and some effective blast <italic>R</italic> genes should be considered in future rice blast-resistance breeding programs.</p>