Molecular mapping of qBK1Z, a major QTL for bakanae disease resistance in rice

AbstractBakanae disease is a fungal disease of rice (Oryza sativa L.) caused by the pathogen Gibberella fujikuroi (also known as Fusarium fujikuroi). Recently the disease incidence has increased in several Asian countries and continues to spread throughout the world. No rice varieties have been developed yet to be completely resistant to this disease. With increasing need to identify various genetic resources to impart resistance to local elite varieties, this study was carried out to identify novel quantitative trait loci (QTLs) from an indica variety Zenith. We performed a QTL mapping using 180 F2:9 recombinant inbred lines (RILs) derived from a cross between the resistant variety, Zenith, and the susceptible variety, Ilpum. A primary QTL study using the genotypes and phenotypes of the RILs indicated that the locus qBK1z conferring bakanae disease resistance from the Zenith was located in a 2.8 Mb region bordered by the two SSR markers, RM1331 and RM3530 on chromosome 1.The log of odds (LOD) score of qBK1z was 13.43, accounting for 30.9% of the total phenotypic variation. A finer localization of qBK1z was delimited at an approximate 730 kb interval in the physical map between Chr01_1435908 (1.43 Mbp) and RM10116 (2.16 Mbp). The development of a rice variety with a higher level of resistance against bakanae disease is a major challenge in many rice growing countries. Introducing qBK1z or pyramiding with other previously identified QTLs could provide effective genetic control of bakanae disease in rice.

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Mapping of a major QTL, qBK1Z, for bakanae disease resistance in rice

10.21203/rs.3.rs-34527/v1 ◽

2020 ◽

Author(s):

Sais-Beul Lee ◽

Namgyu Kim ◽

Sumin Jo ◽

Yeon-Jae Hur ◽

Ji-youn Lee ◽

...

Keyword(s):

Disease Resistance ◽

Physical Map ◽

Disease Incidence ◽

Recombinant Inbred Lines ◽

Rice Variety ◽

Gibberella Fujikuroi ◽

Chromosome 1 ◽

Resistant Variety ◽

Fusarium Fujikuroi ◽

Bakanae Disease

Abstract Background: Bakanae disease is a fungal disease of rice (Oryza sativa L.) caused by the pathogen Gibberella fujikuroi (also known as Fusarium fujikuroi). Recently the disease incidence has increased in several Asian countries and continues to spread throughout the world. No rice varieties have been developed yet to be completely resistant to this disease. With increasing need to identify various genetic resources to impart resistance to local elite varieties, this study was carried out to identify novel quantitative trait loci (QTLs) from an indica variety Zenith. Results: We performed a QTL mapping using 180 F2:9 recombinant inbred lines (RILs) derived from a cross between the resistant variety, Zenith, and the susceptible variety, Ilpum. A primary QTL study using the genotypes and phenotypes of the RILs indicated that the locus qBK1z conferring bakanae disease resistance from the Zenith was located in a 2.8 Mb region bordered by the two SSR markers, RM1331 and RM3530 on chromosome 1. The log of odds (LOD) score of qBK1z was 13.43, accounting for 30.9% of the total phenotypic variation. A finer localization of qBK1z was delimited at an approximate 730 kb interval in the physical map between Chr01_1435908 (1.43 Mbp) and RM10116 (2.16 Mbp).Conclusion: The development of a rice variety with a higher level of resistance against bakanae disease is a major challenge in many rice growing countries. Introducing qBK1z or pyramiding with other previously identified QTLs could provide effective genetic control of bakanae disease in rice.

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Mapping of a Major QTL, qBK1Z, for Bakanae Disease Resistance in Rice

Plants ◽

10.3390/plants10030434 ◽

2021 ◽

Vol 10 (3) ◽

pp. 434

Author(s):

Sais-Beul Lee ◽

Namgyu Kim ◽

Sumin Jo ◽

Yeon-Jae Hur ◽

Ji-Youn Lee ◽

...

Keyword(s):

Disease Resistance ◽

Physical Map ◽

Oryza Sativa L ◽

Recombinant Inbred Lines ◽

Susceptible Variety ◽

Gibberella Fujikuroi ◽

Chromosome 1 ◽

Resistant Variety ◽

Fusarium Fujikuroi ◽

Bakanae Disease

Bakanae disease is a fungal disease of rice (Oryza sativa L.) caused by the pathogen Gibberella fujikuroi (also known as Fusarium fujikuroi). This study was carried out to identify novel quantitative trait loci (QTLs) from an indica variety Zenith. We performed a QTL mapping using 180 F2:9 recombinant inbred lines (RILs) derived from a cross between the resistant variety, Zenith, and the susceptible variety, Ilpum. A primary QTL study using the genotypes and phenotypes of the RILs indicated that the locus qBK1z conferring bakanae disease resistance from the Zenith was located in a 2.8 Mb region bordered by the two RM (Rice Microsatellite) markers, RM1331 and RM3530 on chromosome 1. The log of odds (LOD) score of qBK1z was 13.43, accounting for 30.9% of the total phenotypic variation. A finer localization of qBK1z was delimited at an approximate 730 kb interval in the physical map between Chr01_1435908 (1.43 Mbp) and RM10116 (2.16 Mbp). Introducing qBK1z or pyramiding with other previously identified QTLs could provide effective genetic control of bakanae disease in rice.

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Dynamics of the rice blast fungal population in the field after deployment of an improved rice variety containing known resistance genes

Plant Disease ◽

10.1094/pdis-06-20-1348-re ◽

2020 ◽

Author(s):

Wenjuan Wang ◽

Jing Su ◽

Kailing Chen ◽

Jianyuan Yang ◽

Shen Chen ◽

...

Keyword(s):

Disease Resistance ◽

Resistance Genes ◽

Rice Blast ◽

Rice Variety ◽

Field Population ◽

Pcr Analysis ◽

Resistant Variety ◽

Pathogenicity Test ◽

Line Field ◽

Isogenic Lines

Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most destructive diseases of rice worldwide. Management through the deployment of host resistance genes would be facilitated by understanding the dynamics of the pathogen’s population in the field. Here, to investigate the mechanism underlying the breakdown of disease resistance, we conducted a six-year field experiment to monitor the evolution of M. oryzae populations in Qujiang from Guangdong. The new variety of XYZ carrying R genes Pi50 and Pib was developed using the susceptible elite variety, MBYZ, as the recurrent line. Field trails of disease resistance assessment revealed that the disease indices of XYZ in 2012, 2013, 2016, and 2017 were 0.19, 0.39, 0.70, and 0.90, respectively, indicating that XYZ displayed a very rapid increase of disease severity in the field. To investigate the mechanism underlying the quick erosion of resistance of XYZ, we collected isolates from both XYZ and MBYZ for pathogenicity test against 6 different isogenic lines. The isolates collected from XYZ showed a similar virulence spectrum across 4 different years whereas those from MBYZ showed increasing virulence to the Pi50 and Pib isogenic lines from 2012 to 2017. Molecular analysis of AvrPib in the isolates from MBYZ identified four different AvrPib haplotypes, i.e., AvrPib-AP1-1, AvrPib-AP1-2, avrPib-AP2, and avrPib-AP3, verified by sequencing. AvrPib-AP1-1 and AvrPib-AP1-2 are avirulent to Pib whereas avrPib-AP2 and avrPib-AP3 are virulent. Insertions of a Pot3 and an Mg-SINE were identified in avrPib-AP2 and avrPib-AP3, respectively. Two major lineages based on rep-PCR analysis were further deduced in the field population, implying that the field population is composed of genetically related isolates. Our data suggest that clonal propagation and quick dominancy of virulent isolates against the previously resistant variety could be the major genetic events contributing to the loss of varietal resistance against rice blast in the field.

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Molecular mapping of qBK1WD, a major QTL for bakanae disease resistance in rice

Rice ◽

10.1186/s12284-017-0197-7 ◽

2018 ◽

Vol 11 (1) ◽

Cited By ~ 10

Author(s):

Sais-Beul Lee ◽

Yeon-Jae Hur ◽

Jun-Hyeon Cho ◽

Jong-Hee Lee ◽

Tae-Heon Kim ◽

...

Keyword(s):

Disease Resistance ◽

Molecular Mapping ◽

Bakanae Disease ◽

Major Qtl

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PIRA-PCR for Detection of Fusarium fujikuroi Genotypes with Carbendazim-Resistance Alleles

Plant Disease ◽

10.1094/pdis-01-15-0009-re ◽

2015 ◽

Vol 99 (9) ◽

pp. 1241-1246 ◽

Cited By ~ 2

Author(s):

Zhen Zhang ◽

Zihao Chen ◽

Yiping Hou ◽

Yabing Duan ◽

Jianxin Wang ◽

...

Keyword(s):

Restriction Analysis ◽

Point Mutations ◽

Enzyme Digestion ◽

Gibberella Fujikuroi ◽

Fusarium Fujikuroi ◽

Chain Reaction ◽

Bakanae Disease ◽

Resistant Strains ◽

Polymerase Chain ◽

Enzyme Recognition

Carbendazim, a methyl benzimidazole carbamate (MBC)-group fungicide, has been used to control rice bakanae disease, caused by Fusarium fujikuroi (teleomorph: Gibberella fujikuroi), for decades in China. Previous research revealed that point mutations (E198V, GAG to GTG at codon 198, and F200Y, TTC to TAC at codon 200) of the β2-tubulin gene conferred resistance of F. fujikuroi to MBC. In this study, primer-introduced restriction analysis polymerase chain reaction (PIRA-PCR) was developed to determine genotypes with resistance of F. fujikuroi to MBC. A PCR template of each strain was created by an outer primer pair. Fragments with 177 bp (for mutation at codon 235) and 146 bp (for E198V) were amplified by nested PCR, with two inner primer pairs designed and synthesized according to the nucleotide sequence of β2-tubulin for further enzyme digestion validation, respectively. AccII and PmaCI restriction enzyme recognition sites were introduced artificially by inner primers to differentiate MBC-sensitive and -resistant strains, respectively. The sensitivity of each strain to MBC was indirectly determined by analyzing electrophoresis patterns of the resulting amplified fragments after simultaneous digestion by both AccII and PmaCI. PIRA-PCR produced the same result as conventional methods in 6% of the time. PIRA-PCR is a sensitive and effective method for genotyping resistance alleles of F. fujikuroi strains to MBC.

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Gibberella fujikuroi (Sawada) Wollenweber, the new parasitical fungus on rice in the Republic of Macedonia

Zbornik Matice srpske za prirodne nauke ◽

10.2298/zmspn0916175k ◽

2009 ◽

pp. 175-182 ◽

Cited By ~ 5

Author(s):

Ilija Karov ◽

Sasa Mitrev ◽

Emilija Kostadinovska

Keyword(s):

Plant Material ◽

Recent Observation ◽

Pathogenic Fungus ◽

Gibberella Fujikuroi ◽

Fusarium Fujikuroi ◽

Laboratory Methods ◽

Bakanae Disease ◽

Republic Of Macedonia ◽

The Republic ◽

Continuous Field

The recent observation of Gibberella fujikuroi (Sawada) Wollenworth (teleomorph) (anamorf: Fusarium moniliforme Sheld.) Fusarium fujikuroi Nirenberg (anamorph), F. moniliforme J. Sheld. (synonym), the causal agent of Bakanae disease in rice fields, provides an opportunity to observe the characteristics of the pathogen and the possibility of prevention in Kocani area. Plant material with Gibberella fujikuroi symptoms was collected from rice (Oryza sativa) over the period of 3 years (from 2006 to 2008). Within this study, the presence and damage caused by this pathogenic fungus were confirmed. The objective of this study was a continuous field observation of symptoms in order to establish the percentage of infection and use of laboratory methods for proper protection.

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Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem

Rice ◽

10.1186/s12284-019-0337-3 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 2

Author(s):

Szu-Yu Chen ◽

Ming-Hsin Lai ◽

Chih-Wei Tung ◽

Dong-Hong Wu ◽

Fang-Yu Chang ◽

...

Keyword(s):

Disease Severity ◽

Large Scale ◽

Genome Wide Association Study ◽

Recombinant Inbred Lines ◽

Genome Wide Association ◽

Colonization Rate ◽

Fusarium Fujikuroi ◽

Bakanae Disease ◽

Genome Wide ◽

A Genome

Abstract Background Rice bakanae disease has emerged as a new threat to rice production. In recent years, an increase in the occurrence and severity of bakanae disease has been reported in several areas in Asia. Although bakanae disease affects rice yield and quality, little is known about the genetics of bakanae resistance in rice. The lack of large-scale screens for bakanae resistance in rice germplasm has also limited the development and deployment of resistant varieties. Results A genome-wide association study (GWAS) was conducted to identify genes/loci conferring bakanae resistance in rice. A total of 231 diverse accessions from Rice Diversity Panel 1 (RDP1) were inoculated with a highly virulent Taiwanese Fusarium fujikuroi isolate and assessed for resistance using two parameters: (1) disease severity index based on visual rating and (2) colonization rate determined by reisolation of F. fujikuroi from the basal stems of infected rice seedlings. We identified 14 quantitative trait loci (QTLs) (10 for disease severity and 4 for colonization rate), including 1 mapped for both parameters. A total of 206 candidate genes were identified within the 14 QTLs, including genes encoding leucine-rich repeat (LRR)-containing and NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) proteins, hormone-related genes, transcription factor genes, ubiquitination-related genes, and oxidase/oxidoreductase genes. In addition, a candidate QTL (qBK1.7) that co-localized with the previously identified QTLs qBK1 and qFfR1, was verified by linkage analysis using a population of 132 recombinant inbred lines derived from IR64 x Nipponbare. GWAS delineated qBK1.7 to a region of 8239 bp containing three genes. Full-length sequencing across qBK1.7 in 20 rice accessions revealed that the coding regions of two LRR-containing genes Os01g0601625 and Os01g0601675 may be associated with bakanae resistance. Conclusions This study facilitates the exploitation of bakanae resistance resources in RDP1. The information on the resistance performance of 231 rice accessions and 14 candidate QTLs will aid efforts to breed resistance to bakanae and uncover resistance mechanisms. Quantification of the level of F. fujikuroi colonization in addition to the conventional rating of visual symptoms offers new insights into the genetics of bakanae resistance.

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Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by Fusarium fujikuroi

International Journal of Molecular Sciences ◽

10.3390/ijms20102598 ◽

2019 ◽

Vol 20 (10) ◽

pp. 2598 ◽

Cited By ~ 7

Author(s):

Do-Yu Kang ◽

Kyeong-Seong Cheon ◽

Jun Oh ◽

Hyoja Oh ◽

Song Lim Kim ◽

...

Keyword(s):

Quantitative Trait Locus ◽

Quantitative Trait ◽

Rice Variety ◽

Rice Genome ◽

Chromosome 9 ◽

Dna Polymorphisms ◽

Fusarium Fujikuroi ◽

Japonica Rice ◽

Bakanae Disease ◽

Trait Locus

Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, has become a serious threat in rice-cultivating regions worldwide. In the present study, quantitative trait locus (QTL) mapping was performed using F2 and F3 plants derived after crossing a BD-resistant and a BD-susceptible Korean japonica rice variety, ‘Samgwang’ and ‘Junam’, respectively. Resequencing of ‘Junam’ and ‘Samgwang’ genomes revealed 151,916 DNA polymorphisms between the two varieties. After genotyping 188 F2 plants, we constructed a genetic map comprising 184 markers, including 175 kompetitive allele-specific PCR markers, eight cleaved amplified polymorphic sequence (CAPS) markers, and a derived CAPS (dCAPS) marker. The degree of BD susceptibility of each F2 plant was evaluated on the basis of the mortality rate measured with corresponding F3 progeny seedlings by in vitro screening. Consequently, qFfR9, a major QTL, was discovered at 30.1 centimorgan (cM) on chromosome 9 with a logarithm of the odds score of 60.3. For the QTL interval, 95% probability lay within a 7.24–7.56 Mbp interval. In this interval, we found that eight genes exhibited non-synonymous single nucleotide polymorphisms (SNPs) by comparing the ‘Junam’ and ‘Samgwang’ genome sequence data, and are possibly candidate genes for qFfR9; therefore, qFfR9 could be utilized as a valuable resource for breeding BD-resistant rice varieties.

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Bakanae Disease of Rice in Malaysia and Indonesia: Etiology of the Causal Agent Based on Morphological, Physiological and Pathogenicity Characteristics

Journal of Plant Protection Research ◽

10.2478/v10045-008-0056-z ◽

2008 ◽

Vol 48 (4) ◽

pp. 475-485 ◽

Cited By ~ 30

Author(s):

Nur Izzati Mohd Zainudin ◽

Azmi Razak ◽

Baharuddin Salleh

Keyword(s):

Disease Incidence ◽

Morphological Characteristics ◽

Peninsular Malaysia ◽

Causal Agent ◽

Fusarium Fujikuroi ◽

Bakanae Disease ◽

Agent Based ◽

Growing Seasons ◽

Pathogenicity Tests ◽

Solvent Systems

Bakanae Disease of Rice in Malaysia and Indonesia: Etiology of the Causal Agent Based on Morphological, Physiological and Pathogenicity CharacteristicsBakanae disease on rice has been recorded almost in all countries where paddy is grown commercially, especially in Asian countries, including Malaysia and Indonesia. Bakanae disease was widespread in Peninsular Malaysia and three provinces of Indonesia with the range of disease severity from scale 1 to 5 and disease incidence from 0.5 to 12.5% during 2004-2005 main growing seasons. A total of fiveFusariumspecies belonging to section Liseola and their allied i.e.Fusarium fujikuroi, F. proliferatum, F. sacchari, F. subglutinans and F. verticillioideswere isolated and identified on the basis of their morphological characteristics. Literature data showed that the bakanae disease of rice all over the world is caused byF. fujikuroiand probably some otherFusariumspecies from section Liseola or allied. However, from pathogenicity tests that have been carried out by using variety MR 211 of rice it was evident thatF. fujikuroiwas highly virulent and the only species involved in causing bakanae disease. Therefore, this species was the only one detected to be able to produce gibberellic acid - (GA3) with Rfvalue 0.40 and 0.62, developed in solvent systems isopropanol:ammonia:water (10: 1: 1), v/v/ v and chloroform:ethyl acetate:formic acid (5: 4: 1), v/v/v, respectively. This knowledge would be invaluable in developing our understanding on the interaction betweenF. fujikuroiand the host plants.

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