The Rice Blast Resistance Gene Pid Family has been Strictly Diverged into Indica and Japonica Subspecies

Abstract Background: Rice blast (causative agent the fungus Pyricularia oryzae) represents a major constraint over the productivity of one of the world’s most important staple foods. Genes encoding resistance have been identified in both the indica and japonica subspecies genepools, and combining these within new cultivars represents a rational means of combating the pathogen.Results: In this research, a deeper allele mining was carried out on Pid-2, Pid-3, and Pid-4 by their specific FNP markers in the three panels consisting of 70 indica and 58 japonica cultivars. Within Pid-2, three functional and one non-functional alleles were identified; the former were only identified in indica type entries. At Pid-3, four functional and one non-functional alleles were identified, and once again, all of the former were present in indica type entries. However, the pattern of variation at Pid-4 was rather different: here, the five functional alleles uncovered were dispersed across the japonica type germplasm. Among all the 12 candidate functional alleles, both Pid2-ZS and Pid3-ZS were predominant.Conclusions: Variation in both Pid-2 and Pid-3 appears to have evolved in response to pathogen pressure exerted on indica type cultivars, while that in Pid-4 reflects the interaction between the fungus and the host in japonica type crops. Owning to the founder lineage, ‘Zhenzhuai 11-ZS97’, rather limited genotypes of the Pid family have been effective in both indica and japonica rice groups, of which Pid2-ZS+Pid3-ZS is present in a large proportion of Chinese indica cultivars released since the 1960s.

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Identification of rice blast (Pyricularia) resistance genes in the breeding samples of rice

E3S Web of Conferences ◽

10.1051/e3sconf/202017501008 ◽

2020 ◽

Vol 175 ◽

pp. 01008

Author(s):

Nataliya Vozhzhova ◽

Elena Krasnova ◽

Elena Ionova

Keyword(s):

Resistance Genes ◽

Rice Blast ◽

Agricultural Research ◽

Blast Resistance ◽

Genetic Material ◽

Climatic Conditions ◽

Rice Blast Resistance ◽

Rice Samples ◽

Functional Alleles ◽

Blast Resistance Genes

The current paper has considered the challenge of breeding of rice lines adapted to the climatic conditions of the Southern Federal District of Russia by pyramiding a complex of Pi-1, Pi-2, Pi-33, Pi-ta and Pi-b rice blast resistance genes which is efficient in the southern part of Russia. The control of the resistance genes present in the breeding material was carried out using a marker-associated selection (MAS). The purpose of the current study was to identify the Pi-1, Pi-2, Pi-33, Pi-ta, and Pi-b rice blast resistance genes in the rice samples developed in the laboratory of rice breeding and seed production of the FSBSI “Agricultural Research Center “Donskoy” to identify valuable genotypes. The screening of 689 breeding samples of rice resulted in identification of the allelic state of the Pi-1, Pi-2, Pi-33, Pi-ta and Pi-b rice blast resistance genes, and the genotypes with functional alleles of these genes and their combinations. There were identified 19 breeding samples of rice possessing a combination of 4 functional alleles of rice blast resistance genes in various combinations. The identified rice samples are valuable genetic material and are recommended to use as the sources of rice blast resistance in the breeding process.

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Identification of novel rice blast resistance alleles through sequence-based allele mining

10.21203/rs.2.18859/v1 ◽

2019 ◽

Author(s):

Ying Zhou ◽

Fang Lei ◽

Qiong Wang ◽

Weicong He ◽

Yuan Bin ◽

...

Keyword(s):

Resistance Genes ◽

Rice Blast ◽

Blast Resistance ◽

Resistance Breeding ◽

Economic Losses ◽

The Novel ◽

Allele Mining ◽

Rice Varieties ◽

Rice Blast Resistance ◽

Blast Resistance Genes

Abstract Background: As rice ( Oryza sativa ) is the staple food of more than half the world’s population, rice production contributes greatly to global food security. Rice blast caused by the fungus M agnaporthe oryzae is a devastating fungal disease of rice, affecting yield and grain quality and resulting in substantial annual economic losses. Because the fungus evolves rapidly,, resistance conferred by most of the single blast race resistance genes is often broken after a few years of intensive agricultural use. Effective resistance breeding in rice therefore requires continual enrichment of the reservoir of resistance genes and alleles. Seed banks represent a rich source of genetic diversity; however, they have not been extensively used to identify novel genes and alleles. Results: We carried out a large-scale screen for novel blast resistance alleles in 1883 rice varieties from major rice producing areas across China. Of these, 107 varieties showed at least moderate resistance to natural infection by rice blast at rice blast nurseries in Enshi and Yichang, Hubei Province. Using sequence-based allele mining to amplify and clone the allelic variants of major rice blast resistance genes at the Pi2/9/gm/zt locus of chromosome 6 from the 107 blast-resistant varieties, we identified 13 novel blast resistance alleles. We then used controlled infections to assess the resistance of rice varieties carrying the novel alleles to 34 single rice blast isolates from Hubei, Guangdong, Jiangsu, Hunan, Jangxi, Sichuan, Heilongjiang, and Fujin Provinces. The varieties identified as being resistant in the nursery trials showed varied disease responses when infected with the single blast isolates, suggesting that the novel Pi2/9/gm/zt alleles vary in their blast resistance spectra. Some of the newly identified alleles have unique single nucleotide polymorphisms (SNPs), insertions, or deletions, in addition to polymorphic residues that are shared between the different alleles. Conclusions: These alleles expand the allelic series of blast resistance genes, enriching the genetic resource for rice blast resistance breeding programs and for studies aimed at deciphering rice–rice blast molecular interactions. Key words : Pi9 , R-genes, Nucleotide diversity, Gene conversion, Resistance gene alleles, Rice blast

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Functional Analysis of Pid3-A4, an Ortholog of Rice Blast Resistance Gene Pid3 Revealed by Allele Mining in Common Wild Rice

Phytopathology ◽

10.1094/phyto-10-12-0260-r ◽

2013 ◽

Vol 103 (6) ◽

pp. 594-599 ◽

Cited By ~ 36

Author(s):

Qiming Lv ◽

Xiao Xu ◽

Junjun Shang ◽

Guanghuai Jiang ◽

Zhiqian Pang ◽

...

Keyword(s):

Functional Analysis ◽

Resistance Gene ◽

Wild Rice ◽

Rice Blast ◽

Blast Resistance ◽

Oryza Rufipogon ◽

Allele Mining ◽

Rice Blast Resistance ◽

Blast Resistance Gene ◽

Common Wild Rice

The rice blast resistance gene Pid3 encodes a nucleotide-binding-site leucine-rich repeat (NBS-LRR) protein. This gene was cloned from the rice ‘Digu’ (indica) by performing a genome-wide comparison of the NBS-LRR gene family between two genome-sequenced varieties, ‘9311’ (indica) and ‘Nipponbare’ (japonica). In this study, we performed functional analysis of Pid3-A4, an ortholog of Pid3 revealed by allele mining in the common wild rice A4 (Oryza rufipogon). The predicted protein encoded by Pid3-A4 shares 99.03% sequence identity with Pid3, with only nine amino-acid substitutions. In wild rice plants, Pid3-A4 is constitutively expressed, and its expression is not induced by Magnaporthe oryzae isolate Zhong-10-8-14 infection. Importantly, in transgenic plants, Pid3-A4, as compared with Pid3, displays a distinct resistance spectrum to a set of M. oryzae isolates, including those that prevail in the rice fields of Sichuan Province. Therefore, Pid3-A4 should be quite useful for the breeding of rice blast resistance, especially in southwestern China.

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Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining

Rice ◽

10.1186/s12284-020-00442-z ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Ying Zhou ◽

Fang Lei ◽

Qiong Wang ◽

Weicong He ◽

Bin Yuan ◽

...

Keyword(s):

Resistance Genes ◽

Tandem Repeat ◽

Rice Blast ◽

Blast Resistance ◽

Resistance Breeding ◽

Economic Losses ◽

Chromosome 6 ◽

Allele Mining ◽

Rice Blast Resistance ◽

Blast Resistance Genes

Abstract Background As rice (Oryza sativa) is the staple food of more than half the world’s population, rice production contributes greatly to global food security. Rice blast caused by the fungus Magnaporthe oryzae (M. oryzae) is a devastating disease that affects rice yields and grain quality, resulting in substantial economic losses annually. Because the fungus evolves rapidly, the resistance conferred by most the single blast-resistance genes is broken after a few years of intensive agricultural use. Therefore, effective resistance breeding in rice requires continual enrichment of the reservoir of resistance genes, alleles, or QTLs. Seed banks represent a rich source of genetic diversity; however, they have not been extensively used to identify novel genes and alleles. Results We carried out a large-scale screen for novel blast-resistance alleles in 1883 rice varieties from major rice-producing areas across China. Of these, 361 varieties showed at least moderate resistance to natural infection by rice blast at rice blast nurseries in Enshi and Yichang, Hubei Province. We used sequence-based allele mining to amplify and sequence the allelic variants of the major rice blast-resistance genes at the Pi2/Pi9 locus of chromosome 6 from the 361 blast-resistant varieties, and the full-length coding region of this gene could be amplified from 107 varieties. Thirteen novel Pi9 alleles (named Pi9-Type1 to Pi9-Type13) were identified in these 107 varieties based on comparison to the Pi9 referenced sequence. Based on the sequencing results, the Pi2/Pi9 locus of the 107 varieties was divided into 15 genotypes (including three different genotypes of Pi9-Type5). Fifteen varieties, each representing one genotype, were evaluated for resistance to 34 M. oryzae isolates. The alleles from seven varieties with the highest resistance and widest resistance spectra were selected for transformation into the susceptible variety J23B to construct near-isogenic lines (NILs). These NILs showed resistance in a field test in Enshi and Yichang, indicating that the seven novel rice blast-resistance tandem-repeat regions at the Pi2/Pi9 locus of chromosome 6 could potentially serve as a genetic resource for molecular breeding of resistance to rice blast. Conclusions The thirteen novel Pi9 alleles identified in this study expand the list of available of blast-resistance alleles. Seven tandem-repeat regions of the Pi2/Pi9 locus from different donors were characterized as broad-spectrum rice blast-resistance fragments; these donors enrich the genetic resources available for rice blast-resistance breeding programs.

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