Genomic insight into balancing high yield, good quality, and blast resistance of japonica rice

Abstract Background Balancing the yield, quality and resistance to disease is a daunting challenge in crop breeding due to the negative relationship among these traits. Large-scale genomic landscape analysis of germplasm resources is considered to be an efficient approach to dissect the genetic basis of the complex traits. Central China is one of the main regions where the japonica rice is produced. However, dozens of high-yield rice varieties in this region still exist with low quality or susceptibility to blast disease, severely limiting their application in rice production. Results Here, we re-sequence 200 japonica rice varieties grown in central China over the past 30 years and analyze the genetic structure of these cultivars using 2.4 million polymorphic SNP markers. Genome-wide association mapping and selection scans indicate that strong selection for high-yield and taste quality associated with low-amylose content may have led to the loss of resistance to the rice blast fungus Magnaporthe oryzae. By extensive bioinformatic analyses of yield components, resistance to rice blast, and taste quality, we identify several superior alleles for these traits in the population. Based on this information, we successfully introduce excellent taste quality and blast-resistant alleles into the background of two high-yield cultivars and develop two elite lines, XY99 and JXY1, with excellent taste, high yield, and broad-spectrum of blast resistance. Conclusions This is the first large-scale genomic landscape analysis of japonica rice varieties grown in central China and we demonstrate a balancing of multiple agronomic traits by genomic-based strategy.

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Study of pathogenicity and genetic diversity of Magnaporthe oryzae isolated from rice hybrid Wuyou 308 and detection of resistance genes

Czech Journal of Genetics and Plant Breeding ◽

10.17221/64/2019-cjgpb ◽

2020 ◽

Vol 56 (No. 3) ◽

pp. 93-101

Author(s):

Bo Lan ◽

Ying-Qing Yang ◽

Qiang Sun ◽

Hong-Fan Chen ◽

Jian Chen ◽

...

Keyword(s):

Resistance Genes ◽

Magnaporthe Oryzae ◽

Rice Blast ◽

Blast Resistance ◽

Rice Variety ◽

Climatic Conditions ◽

Blast Disease ◽

Rice Varieties ◽

Rice Blast Resistance ◽

Rice Hybrid

To understand the cause of loss of rice blast resistance, we studied the pathogenicity of Magnaporthe oryzae strains isolated from rice hybrid Wuyou 308 and evaluated its resistance genes. A total of 62 M. oryzae strains were isolated and tested in 7 Chinese rice varieties with varying degrees of resistance to rice blast and 30 blast-resistant monogenic lines. Fourteen physiological races of M. oryzae were identified: 8.55% belonging to the ZA group, 86.67% to the ZB group, and 5.00% to the ZC group. ZB15 was the most abundant race (45.00%). Five resistance genes, Pi-3(1), Pi-z5, Pi-k, Pi-kp(C), and Pi-k(C), conferred good resistance to the 62 strains, with resistance frequencies of 95.56, 91.11, 88.89, 82.22, and 82.22%, respectively. In contrast, Pi-a(2) had a resistance frequency of 0%. The hybrid combination Wuyou 308 was found to carry Pi-ta and Pi-b genes. Because Pi-ta and Pi-b both showed low resistance frequencies to M. oryzae isolated from Jiangxi, the hybrid rice variety Wuyou 308 could be infected by most of the 62 M. oryzae strains. The emergence and spread of rice blast disease in Wuyou 308 may thus be difficult to avoid when climatic conditions are favourable.

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Functional validation of the Pi54 gene by knocking down its expression in a blast-resistant rice line using RNA interference and its effects on other traits

Functional Plant Biology ◽

10.1071/fp18083 ◽

2018 ◽

Vol 45 (12) ◽

pp. 1241

Author(s):

Kirti Arora ◽

Amit Kumar Rai ◽

Basavantraya N. Devanna ◽

Banita Kumari ◽

Tilak Raj Sharma

Keyword(s):

Rice Blast ◽

Oryza Sativa L ◽

Blast Resistance ◽

Single Gene ◽

Blast Disease ◽

Functional Validation ◽

Rice Varieties ◽

Resistance Response ◽

Rice Line ◽

Rice Blast Resistance

Rice blast disease caused by Magnaporthe oryzae is one of the major diseases affecting the rice (Oryza sativa L.) crop. A major blast resistance gene, Pi54, has already been cloned and deployed in different rice varieties. To understand the role of Pi54 in providing rice blast resistance, we used the RNA interferences (RNAi) approach to knock down the expression of this gene. We showed a high frequency of Agrobacterium tumefaciens-mediated transformation of rice line Taipei 309 containing a single gene (Pi54) for blast resistance. Pi54 RNAi leads to a decreased level of Pi54 transcripts, leading to the susceptibility of otherwise M. oryzae-resistant rice lines. However, among the RNAi knockdown plants, the severity of blast disease varied between the lines. Histochemical analysis of the leaves of knockdown plants inoculated with M. oryzae spores also showed typical cell death and blast lesions. Additionally, Pi54 RNAi also showed an effect on the Hda3 gene, a florigen gene playing a role in rice flowering. By using the RNAi technique, for the first time, we showed that the directed degradation of Pi54 transcripts results in a significant reduction in the rice blast resistance response, suggesting that RNAi is a powerful tool for functional validation of genes.

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Two novel gene-specific markers at pik locus facilitate the application of rice blast resistant alleles in breeding

10.21203/rs.2.18858/v1 ◽

2019 ◽

Author(s):

Dagang Tian ◽

Ziqiang Chen ◽

Yan Lin ◽

Zaijie Chen ◽

Jiami Luo ◽

...

Keyword(s):

Resistance Genes ◽

Rice Blast ◽

Blast Resistance ◽

Durable Resistance ◽

Resistance Breeding ◽

Blast Disease ◽

Chromosome 11 ◽

Rice Varieties ◽

Breeding Programs ◽

New Gene

Abstract Background: Rice blast disease, caused by Magnaporthe oryzae, is a major constraint for rice production in the world. Introgression of blast-durable resistance genes into high-yielding rice cultivars has been considered an agricultural priority in an effort to control the disease. The blast resistance Pik locus, located on chromosome 11, contains at least six important resistance genes, but these genes have not been widely employed in resistance breeding since existing markers hardly satisfy current breeding needs owing to their limited scope of application.Results: In the present study, two PCR-based markers, Pikp-Del and Pi1-In, were developed to target the specific InDel (insertion/deletion) of the Pik-p and Pi-1 genes, respectively. The two markers precisely distinguished Pik-p, Pi-1, and the K-type alleles at the Pik locus, which is a necessary element for functional genes from rice varieties. Conclusions:Two gene-specific markers of Pi-kp and Pi1 identified that only several old varieties contain the two genes, nearly half these varieties yet carry the K-type alleles. Therefore, these identified varieties can be new gene sources for developing blast resistant rice. The two newly developed markers should be highly useful for using Pi-kp, Pi1 and other resistance genes at the Pik locus in marker-assisted selection (MAS) breeding programs.

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Long Non-coding RNAs Responsive to Blast Fungus Infection in Rice

Rice ◽

10.1186/s12284-020-00437-w ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Lan-Lan Wang ◽

Jing-Jing Jin ◽

Li-Hua Li ◽

Shao-Hong Qu

Keyword(s):

Rice Blast ◽

Blast Resistance ◽

Enrichment Analysis ◽

Defense Responses ◽

Pathogen Resistance ◽

Blast Disease ◽

Fungus Infection ◽

Blast Fungus ◽

Gene Transcription Level ◽

Non Coding Rnas

Abstract Background Long non-coding RNAs (LncRNAs) have emerged as important regulators in many physiological processes in plant. By high-throughput RNA-sequencing, many pathogen-associated LncRNAs were mapped in various plants, and some of them were proved to be involved in plant defense responses. The rice blast disease caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases in rice. However, M. oryzae-induced LncRNAs in rice is yet to be studied. Findings We investigated rice LncRNAs that were associated with the rice blast fungus. Totally 83 LncRNAs were up-regulated after blast fungus infection and 78 were down-regulated. Of them, the natural antisense transcripts (NATs) were the most abundant. The expression of some LncRNAs has similar pattern with their host genes or neighboring genes, suggesting a cis function of them in regulating gene transcription level. The deferentially expressed (DE) LncRNAs and genes co-expression analysis revealed some LncRNAs were associated with genes known to be involved in pathogen resistance, and these genes were enriched in terpenoid biosynthesis and defense response by Gene Ontology (GO) enrichment analysis. Interestingly, one of up-regulated DE-intronic RNA was derived from a jasmonate (JA) biosynthetic gene, lipoxygenase RLL (LOX-RLL). Levels of JAs were significantly increased after blast fungus infection. Given that JA is known to regulate blast resistance in rice, we suggested that LncRNA may be involved in JA-mediated rice resistance to blast fungus. Conclusions This study identified blast fungus-responsive LncRNAs in rice, which provides another layer of candidates that regulate rice and blast fungus interactions.

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Level of Endogenous Jasmonate is Critical for Durable Broad-Spectrum Disease Resistance Against Rice Blast in a Japonica Rice Variety, Ziyu44

10.21203/rs.3.rs-571828/v1 ◽

2021 ◽

Author(s):

Xingyu An ◽

Hui Zhang ◽

Jinlu Li ◽

Rui Yang ◽

Qianchun Zeng ◽

...

Keyword(s):

Disease Resistance ◽

Signaling Pathway ◽

Broad Spectrum ◽

Rice Blast ◽

Blast Resistance ◽

Rice Variety ◽

Blast Disease ◽

Japonica Rice ◽

Mycelium Growth ◽

Broad Spectrum Resistance

Abstract Background: The molecular mechanism of durable and broad-spectrum resistance to rice blast disease in japonica rice variety is still very little known. Ziyu44, a local japonica rice variety in Yunnan Province of China, has shown durable broad-spectrum blast resistance for more than 30 years, and provides an opportunity for us to explore the molecular basis of broad-spectrum resistance to rice blast in japonica rice variety.Methods and Results: We conducted a comparative study of mycelium growth, aposporium formation, the accumulation of salicylate(SA), jasmonate(JA) and H2O2, the expression of SA- and JA-associated genes between Ziyu44 and susceptible variety Jiangnanxiangnuo (JNXN) upon M. oryzae infection. We found that appressorium formation and invasive hyphae extention were greatly inhibited in Ziyu 44 leaves compared with that in JNXN leaves. Both Ziyu 44 and JNXN plants maintained high levels of baseline SA and did not show increased accumulation of SA after inoculation with M. oryzae, while the levels of baseline JA in Ziyu 44 and JNXN plants were relatively low, and the accumulation of JA exhibited markedly increased in Ziyu 44 plants upon M. oryzae infection. The expression levels of key genes involving JA and SA signaling pathway OsCOI1b, OsNPR1, OsMPK6 as well as pathogenesis-related (PR) genes OsPR1a, OsPR1b and OsPBZ1, were markedly up-regulated in Ziyu44. Conclusions: The level of endogenous JA is critical for synchronous activation of SA and JA signaling pathway, up-regulating PR gene expression and enhancing disease resistance against rice blast in Ziyu44.

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Osa-miR162a balances rice yield and resistance to Magnaporthe oryzae

10.21203/rs.2.22473/v1 ◽

2020 ◽

Author(s):

Xu-Pu Li ◽

Xiao-Chun Ma ◽

He Wang ◽

Yong Zhu ◽

Xin-Xian Liu ◽

...

Keyword(s):

Magnaporthe Oryzae ◽

Rice Blast ◽

Rice Yield ◽

Blast Resistance ◽

Blast Disease ◽

Mirna Biogenesis ◽

Trade Off ◽

Rice Blast Resistance ◽

Defense Related Gene ◽

Transgenic Lines

Abstract MicroRNAs (miRNAs) play essential roles in rice immunity against Magnaporthe oryzae, the causative agent of rice blast disease. Osa-miR162a targets Dicer-like 1 (DCL1) genes, which play vital roles in miRNA biogenesis and act as negative regulators in rice immunity. Here we demonstrate that Osa-miR162a improves rice immunity against M. oryzae and balances the trade-off between rice yield and resistance. Overexpression of Osa-miR162a compromises rice susceptibility to M. oryzae accompanying enhanced induction of defense-related genes and accumulation of hydrogen peroxide (H2O2). In contrast, blocking miR162 by overexpressing a target mimic of miR162 enhances susceptibility to blast fungus associating with compromised induction of defense-related gene expression and H2O2 accumulation. Moreover, the transgenic lines overexpressing Osa-miR162a display decreased seed setting rate resulting in reduced yield per plant, whereas blocking miR162 leads to an increased number of grains per panicle, resulting in increased yield per plant. Altered accumulation of miR162 had limited impact on the expression of OsDCL1. Together, our results indicate that Osa-miR162a improves rice blast resistance and plays a role in the balance of trade-off between resistance and yield.

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Investigating the biology of rice blast disease and prospects for durable resistance

10.19103/as.2021.0092.23 ◽

2021 ◽

pp. 643-680

Author(s):

Vincent M. Were ◽

◽

Nicholas J. Talbot ◽

Keyword(s):

Cell Biology ◽

Rice Blast ◽

Plant Pathogens ◽

Blast Resistance ◽

Durable Resistance ◽

Rice Blast Disease ◽

Blast Disease ◽

Global Food Security ◽

Major Resistance Genes ◽

Effector Secretion

There are important biological process involved in rice blast disease that are now well-studied during the early events in plant infection which include: the cell biology of appressorium formation, the biology of invasive growth and effector secretion, the two distinct mechanisms of effector secretion, the nature of the plant-pathogen interface, PAMP-triggered immunity modulation by secreted effectors and effector-triggered immunity and blast resistance. The devastating losses caused by the blast fungus have been documented in most grasses, but this chapter discusses the use of major resistance genes to rice blast and wheat blast disease as an emerging threat to global food security. This chapter also highlights an emerging approach to breed for durable resistance to plant pathogens using gene editing technologies with an example: CRISPR-Cas9 mutagenesis of dominant S-genes for disease control.

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Exploring the Distribution of Blast Resistance Alleles at the Pi2/9 Locus in Major Rice-Producing Areas of China by a Novel Indel Marker

Plant Disease ◽

10.1094/pdis-10-19-2187-re ◽

2020 ◽

Vol 104 (7) ◽

pp. 1932-1938

Author(s):

Dagang Tian ◽

Yan Lin ◽

Ziqiang Chen ◽

Zaijie Chen ◽

Fang Yang ◽

...

Keyword(s):

Blast Resistance ◽

Resistance Breeding ◽

Field Trials ◽

Indel Marker ◽

Blast Disease ◽

Cereal Crops ◽

R Genes ◽

Rice Varieties ◽

Environment Friendly ◽

The World

Rice blast disease caused by the fungus Magnaporthe oryzae damages cereal crops and poses a high risk to rice production around the world. Currently, planting cultivars with resistance (R) genes is still the most environment-friendly approach to control this disease. Effective identification of R genes existing in diverse rice cultivars is important for understanding the distribution of R genes and predicting their contribution to resistance against blast isolates in regional breeding. Here, we developed a new insertion/deletion (InDel) marker, Pigm/2/9InDel, that can differentiate the cloned R genes (Pigm, Pi9, and Pi2/Piz-t) at the Pi2/9 locus. Pigm/2/9InDel combined with the marker Pi2-LRR for Pi2 was applied to determine the distribution of these four R genes among 905 rice varieties, most of which were collected from the major rice-producing regions in China. In brief, nine Pigm-containing varieties from Fujian and Guangdong provinces were identified. All of the 62 Pi2-containing varieties were collected from Guangdong, and 60 varieties containing Piz-t were from seven provinces. However, Pi9 was not found in any of the Chinese varieties. The newly identified varieties carrying the Pi2/9 alleles were further subjected to inoculation tests with regional blast isolates and field trials. Our results indicate that Pigm and Pi2 alleles have been introgressed for blast resistance breeding mainly in the Fujian and Guangdong region, and Pi9 is a valuable blast resistance resource to be introduced into China.

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Occurrence, Distribution, Epidemiology, Cultivar Reaction, and Management of Rice Blast Disease in California

Plant Disease ◽

10.1094/pdis.2001.85.10.1096 ◽

2001 ◽

Vol 85 (10) ◽

pp. 1096-1102 ◽

Cited By ~ 35

Author(s):

C. A. Greer ◽

R. K. Webster

Keyword(s):

Rice Blast ◽

Large Scale ◽

Rice Fields ◽

Blast Disease ◽

Weather Data ◽

Disease Surveys ◽

Spore Trapping ◽

Small Plot ◽

Epidemic Development ◽

Major Resistance Genes

Rice blast, caused by Pyricularia grisea, was first found in California in 1996. Disease surveys have shown the blast disease is spreading at a moderate rate in California rice fields. Although no effective major resistance genes are known to occur in widely grown commercial California cultivars, there appear to be differences among the cultivars with respect to field susceptibility to the pathogen. P. grisea was recovered from rice crop residue and commercial seedlots which are suggested as possible sources of initial P. grisea inoculum in California rice fields. Examination of weather data indicates that environmental conditions in California rice-producing areas are permissive for rice blast but generally not optimal for epidemic development. Spore trapping determined that the majority of P. grisea conidia are generally not released until approximately 6:00 A.M. and would not have sufficient time for infection before leaf wetness periods end. Azoxystrobin showed positive results with respect to reduction of neck blast incidence and yield increases in small-plot and large-scale fungicide trials.

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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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