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

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.

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

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

scholarly journals A Genome-Wide Meta-Analysis of Rice Blast Resistance Genes and Quantitative Trait Loci Provides New Insights into Partial and Complete Resistance

2008 ◽  
Vol 21 (7) ◽  
pp. 859-868 ◽  
Author(s):  
Elsa Ballini ◽  
Jean-Benoît Morel ◽  
Gaétan Droc ◽  
Adam Price ◽  
Brigitte Courtois ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Resistance Genes ◽  
Quantitative Trait ◽  
Rice Blast ◽  
Blast Resistance ◽  
Durable Resistance ◽  
Rice Genome ◽  
Blast Disease ◽  
Trait Loci ◽  
Blast Resistance Genes

The completion of the genome sequences of both rice and Magnaporthe oryzae has strengthened the position of rice blast disease as a model to study plant–pathogen interactions in monocotyledons. Genetic studies of blast resistance in rice were established in Japan as early as 1917. Despite such long-term study, examples of cultivars with durable resistance are rare, partly due to our limited knowledge of resistance mechanisms. A rising number of blast resistance genes and quantitative trait loci (QTL) have been genetically described, and some have been characterized during the last 20 years. Using the rice genome sequence, can we now go a step further toward a better understanding of the genetics of blast resistance by combining all these results? Is such knowledge appropriate and sufficient to improve breeding for durable resistance? A review of bibliographic references identified 85 blast resistance genes and approximately 350 QTL, which we mapped on the rice genome. These data provide a useful update on blast resistance genes as well as new insights to help formulate hypotheses about the molecular function of blast QTL, with special emphasis on QTL for partial resistance. All these data are available from the OrygenesDB database.

scholarly journals Virulence Pattern of Pyricularia oryzae Pathotypes Towards Blast Monogenic Lines

2021 ◽  
Vol 32 (3) ◽  
pp. 147-160
Author(s):  
Siti Norsuha Misman ◽  
Mohd Shahril Firdaus Ab Razak ◽  
Nur Syahirah Ahmad Sobri ◽  
Latiffah Zakaria
Keyword(s):  
Resistance Genes ◽  
Rice Blast ◽  
Blast Resistance ◽  
Rice Variety ◽  
Durable Resistance ◽  
Peninsular Malaysia ◽  
Pyricularia Oryzae ◽  
Blast Disease ◽  
Breeding Lines ◽  
Virulence Pattern

Rice blast caused by Pyricularia oryzae (P. oryzae) is one of the most serious diseases infecting rice worldwide. In the present study, virulence pattern of six P. oryzae pathotypes (P0.0, P0.2, P1.0, P3.0, P7.0 and P9.0) identified from the blast pathogen collected in Peninsular Malaysia, were evaluated using a set of 22 IRRI-bred blast resistance lines (IRBL) as well as to determine the resistance genes involved. The information on the virulence of the blast pathotypes and the resistance genes involved is important for breeding of new rice variety for durable resistance against blast disease. The IRBL was established from 22 monogenic lines, harbouring 22 resistance genes [Pia, Pib, Pii, Pit, Pi3, Pi5(t), Pish, Pi1, Pik, Pik-s, Pik-m, Pik-h, Pik-p, Pi7(t), Pi9, Piz, Piz-5, Piz-t, Pi19, Pi20(t), Pita-2, and Pita=Pi4(t)]. Based on the disease severity patterns, the tested pathotypes were avirulence towards seven IRBLs [IRBLi-F5, IRBLk-Ka, IRBLkh-K3, IRBLz-Fu, IRBLsh-S, IRBLPi7 (t) and IRBL9-W] of which these IRBLs harbouring Pii, Pik, Pik-h, Piz, Pish, Pi7(t) and Pi9 resistance genes, respectively. Therefore, the results suggested that the seven IRBLs carrying seven resistance genes [Pii, Pik, Pik-h, Piz, Pish, Pi7(t) and Pi9] would be suitable candidates of resistance genes to be incorporated in new breeding lines to combat the current blast pathotypes in the field.

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

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.

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

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.

scholarly journals 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 ◽  
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.

scholarly journals Mapping of QTLs involved in resistence to rice blast (Magnaporthe grisea) using Oryza minuta introgression lines

2011 ◽  
Vol 47 (No. 3) ◽  
pp. 85-94 ◽  
Author(s):  
L. Rahman ◽  
S. Khanam ◽  
J.-H. Roh ◽  
H.-J. Koh
Keyword(s):  
Rice Blast ◽  
Magnaporthe Grisea ◽  
Introgression Lines ◽  
Blast Disease ◽  
Chromosome 11 ◽  
Rice Varieties ◽  
Oryza Minuta ◽  
Resistance Variation ◽  
Broad Spectrum Resistance ◽  
Diseased Leaf Area

  Introgression lines derived from Oryza minuta and O. sativa subsp. japonica var. Junambyeo were crossed for a mapping of the population composed of 112 recombinant lines to identify putative QTLs against rice blast disease using the percentage of diseased leaf area. By using 148 Sequence Tagged Site (STS) and Single Sequence Repeat (SSR) markers, five QTLs on chromosomes 6, 7, 9 and 11 and seven epistatic QTLs were identified against two blast isolates (KI307 and KI209). Of them two QTLs (qKI307-2 and qKI209-3) shared a similar position on chromosome 11. O. minuta introgression contributed the resistance allele for all of these QTLs. Combined phenotypic variations by QTL and (E-QTL) accounted for 56.9% against KI307, and 53.4% against KI209. Each QTL could account for the resistance variation between 11 and 24.6%. The resistance from wild introgressions was attributable to a combination of QTLs and epistatic effects between different loci, capable of inducing hypersensitive reactions. Our findings are in support of the strategy of pyramiding major QTLs to develop improved rice varieties with durable broad spectrum resistance against the blast fungus.

scholarly journals Rice Blast Disease in India: Present Status and Future Challenges

2021 ◽  
Author(s):  
Deepak Chikkaballi Annegowda ◽  
Mothukapalli Krishnareddy Prasannakumar ◽  
Hirehally Basavarajegowda Mahesh ◽  
Chethana Bangera Siddabasappa ◽  
Pramesh Devanna ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Oryza Sativa L ◽  
Blast Resistance ◽  
Gene Pyramiding ◽  
Climatic Conditions ◽  
Blast Disease ◽  
Selection Marker ◽  
Rice Varieties ◽  
Future Challenges ◽  
Blast Resistance Genes

Rice (Oryza sativa L.) is the staple food of the majority of Indians, and India is both the major producer and consumer of rice. Rice cultivation in India is confronted with diverse agro-climatic conditions, varying soil types, and several biotic and abiotic constraints. Among major fungal diseases of Rice in India, the blast caused by Magnaporthe oryzae is the most devastating disease, with the neck blast being the most destructive form. Most of the blast epidemic areas in India have been identified with a mixture of races blast fungus resulting in the resistance breakdown in a short period. At present, a more significant number of the rice varieties cultivated in India were bred by conventional breeding methods with blast resistance conferred by a single resistance gene. Therefore, the blast disease in India is predominantly addressed by the use of ecologically toxic fungicides. In line with the rest of the world, the Indian scientific community has proven its role by identifying several blast resistance genes and successfully pyramiding multiple blast resistance genes. Despite the wealth of information on resistance genes and the availability of biotechnology tools, not a great number of rice varieties in India harbor multiple resistance genes. In the recent past, a shift in the management of blast disease in India has been witnessed with a greater focus on basic research and modern breeding tools such as marker-assisted selection, marker-assisted backcross breeding, and gene pyramiding.

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

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ning Xiao ◽  
Cunhong Pan ◽  
Yuhong Li ◽  
Yunyu Wu ◽  
Yue Cai ◽  
...  
Keyword(s):  
Rice Blast ◽  
Large Scale ◽  
Blast Resistance ◽  
Taste Quality ◽  
Landscape Analysis ◽  
Central China ◽  
Blast Disease ◽  
High Yield ◽  
Rice Varieties ◽  
Genomic Landscape

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.

scholarly journals Marker-assisted pyramiding of two major broad-spectrum bacterial blight resistance genes,Xa21andXa33into an elite maintainer line of rice, DRR17B

2018 ◽  
Author(s):  
CH Balachiranjeevi ◽  
S Bhaskar Naik ◽  
V Abhilash Kumar ◽  
G Harika ◽  
H.K Mahadev Swamy ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Bacterial Blight ◽  
Durable Resistance ◽  
Gene Pyramiding ◽  
Resistance Breeding ◽  
Fertility Restorer ◽  
Rice Varieties ◽  
Homozygous Condition ◽  
Specific Pcr ◽  
High Level

AbstractBacterial blight (BB) disease reduces the yield of rice varieties and hybrids considerably in many tropical rice growing countries like India. The present study highlights the development of durable BB resistance into the background of an elite maintainer of rice, DRR17B, by incorporating two major dominant genes,Xa21andXa33through marker-assisted backcross breeding (MABB). Through two sets of backcrosses, the two BB resistance genes were transferred separately to DRR17B. In this process, at each stage of backcrossing, foreground selection was carried out for the target resistance genes and for non-fertility restorer alleles concerning the major fertility restorer genesRf3andRf4, using gene-specific PCR-based markers, while background selection was done using a set of 61 and 64 parental polymorphic SSR markers respectively. Backcross derived lines possessing eitherXa21orXa33along with maximum genome recovery of DRR17B were identified at BC3F1generation and selfed to develop BC3F2s. Plants harboringXa21orXa33in homozygous condition were identified among BC3F2s and were intercrossed with each other to combine both the genes. The intercross F1plants (ICF1) were selfed and the intercross F2(ICF2) plants possessing bothXa21andXa33in homozygous condition were identified with the help of markers. They were then advanced further by selfing until ICF4generation. Selected ICF4lines were evaluated for their resistance against BB with eight virulent isolates and for key agro-morphological traits. Six promising two-gene pyramiding lines of DRR17B with high level of BB resistance and agro-morphological attributes similar or superior to DRR17B with complete maintenance ability have been identified. These lines with elevated level of durable resistance may be handy tool for BB resistance breeding.

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