{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T17:41:35Z","timestamp":1783705295290,"version":"3.55.0"},"reference-count":55,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,11,9]],"date-time":"2022-11-09T00:00:00Z","timestamp":1667952000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Utilization of rice blast-resistance (<jats:italic>R<\/jats:italic>) genes is the most economical and environmentally friendly method to control blast disease. However, rice varieties with <jats:italic>R<\/jats:italic> genes influence the outcome of genetic architectures of <jats:italic>Magnaporthe oryzae<\/jats:italic> (<jats:italic>M. oryzae<\/jats:italic>), and mutations in avirulence (<jats:italic>AVR<\/jats:italic>) genes of <jats:italic>M. oryzae<\/jats:italic> may cause dysfunction of the corresponding <jats:italic>R<\/jats:italic> genes in rice varieties. Although monitoring and characterizing rice <jats:italic>R<\/jats:italic> genes and pathogen <jats:italic>AVR<\/jats:italic> genes in field populations may facilitate the implementation of effective <jats:italic>R<\/jats:italic> genes, little is known about the changes of <jats:italic>R<\/jats:italic> genes over time and their ultimate impact on pathogen <jats:italic>AVR<\/jats:italic> genes. In this study, 117 main cultivated rice varieties over the past five decades and 35\u2009<jats:italic>M. oryzae<\/jats:italic> isolates collected from those diseased plants were analyzed by PCR using gene-specific markers of the nine <jats:italic>R<\/jats:italic> genes and six primer pairs targeting the coding sequence or promoter of <jats:italic>AVR<\/jats:italic> genes, respectively. The <jats:italic>R<\/jats:italic> genes <jats:italic>Pigm, Pi9<\/jats:italic>, <jats:italic>Pi2<\/jats:italic>, <jats:italic>Piz-t<\/jats:italic>, <jats:italic>Pi-ta<\/jats:italic>, <jats:italic>Pik, Pi1<\/jats:italic>, <jats:italic>Pikp,<\/jats:italic> and <jats:italic>Pikm<\/jats:italic> were identified in 5, 0, 1, 4, 18, 0, 2, 1, and 0 cultivars, respectively. Significantly, none of these <jats:italic>R<\/jats:italic> genes had significant changes that correlated to their application periods of time. Among the four identified <jats:italic>AVR<\/jats:italic> genes, <jats:italic>AVR-Pik<\/jats:italic> had the highest amplification frequency (97.14%) followed by <jats:italic>AVR-Pita<\/jats:italic> (51.43%) and <jats:italic>AVR-Pi9<\/jats:italic> (48.57%); <jats:italic>AVR-Piz-t<\/jats:italic> had the lowest frequency (28.57%). All these <jats:italic>AVR<\/jats:italic> genes except <jats:italic>AVR-Pi9<\/jats:italic> had 1\u20132 variants. Inoculation mono-genic lines contained functional genes of <jats:italic>Pi2\/9<\/jats:italic> and <jats:italic>Pik<\/jats:italic> loci with 14 representative isolates from those 35 ones revealed that the presence of certain <jats:italic>AVR-Piz-t<\/jats:italic>, <jats:italic>AVR-Pita<\/jats:italic> variants, and <jats:italic>AVR-Pik-E\u2009+\u2009AVR-Pik-D<\/jats:italic> in <jats:italic>M. oryzae<\/jats:italic> populations, and these variants negated the ability of the corresponding <jats:italic>R<\/jats:italic> genes to confer resistance. Importantly, <jats:italic>Pi2, Pi9,<\/jats:italic> and <jats:italic>Pigm<\/jats:italic> conferred broad-spectrum resistance to these local isolates. These findings reveal that the complex genetic basis of <jats:italic>M. oryzae<\/jats:italic> and some effective blast <jats:italic>R<\/jats:italic> genes should be considered in future rice blast-resistance breeding programs.<\/jats:p>","DOI":"10.3389\/fmicb.2022.1007492","type":"journal-article","created":{"date-parts":[[2022,11,9]],"date-time":"2022-11-09T08:30:57Z","timestamp":1667982657000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":13,"title":["Association analysis of rice resistance genes and blast fungal avirulence genes for effective breeding resistance cultivars"],"prefix":"10.3389","volume":"13","author":[{"given":"Dagang","family":"Tian","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Deng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoshuang","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qixiang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiying","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziqiang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinrui","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Su","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuming","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liming","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,11,9]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"2499","DOI":"10.1105\/tpc.104.022715","article-title":"A putative polyketide synthase\/peptide synthetase from Magnaporthe grisea signals pathogen attack to resistant rice","volume":"16","author":"B\u00f6hnert","year":"2004","journal-title":"Plant Cell"},{"key":"ref001","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1105\/tpc.112.107201","article-title":"The rice resistance protein pair RGA4\/RGA5 recognizes the Magnaporthe oryzae effectors AVR-Pia and AVR1-CO39 by direct binding","volume":"25","author":"Cesari","year":"2013","journal-title":"The Plant cell"},{"key":"ref1000","doi-asserted-by":"publisher","first-page":"113","DOI":"10.4172\/2165-8056.1000113","article-title":"Sequence variation and recognition specificity of the avirulence gene AvrPiz-t in Magnaporthe oryzae field populations","volume":"4","author":"Chen","year":"2014","journal-title":"Fungal Genom. 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