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Alam S.,Central Rainfed Upland Rice Research Station CRRI | Alam S.,Vinoba Bhave University | Imam J.,Central Rainfed Upland Rice Research Station CRRI | Nitin M.,Central Rainfed Upland Rice Research Station CRRI | And 2 more authors.
Proceedings of the National Academy of Sciences India Section B - Biological Sciences | Year: 2017

The Pi2 gene is a member of a multigene family which confers resistance to strains of blast pathogen Magnaporthe oryzae. The gene encodes a typical NBS-LRR type protein which confers broad spectrum resistance to a wide range of races of blast pathogen prevalent in eastern India. In the present study, the presence of Pi2 gene in 61 landraces was determined using a pair of primers NBS2P3 and NBS2R followed by restriction digestion and the results were further confirmed by pathotyping using M. oryzae isolates avirulent for Pi2 gene. The Pi2 gene was found in four rice landraces from Sikkim and one landrace from Jharkhand though the latter was susceptible to the isolate bearing corresponding avirulence gene. Presence of Pi2 gene in independent indica landraces from the eastern Indian region suggested that the gene might have originated and evolved in indica rice and exist in different allelic forms in blast endemic zones of eastern India. The present study not only identifies the presence of Pi2 gene in landraces but also demonstrates the usefulness of molecular markers and virulence analyses for rapid identification of resistant genes in rice landraces. These characterized landraces can be used for genetic studies and marker assisted breeding for improving blast resistance in rice. © 2015, The National Academy of Sciences, India.


Khanna A.,Indian Agricultural Research Institute | Sharma V.,Banasthali University | Ellur R.K.,Indian Agricultural Research Institute | Shikari A.B.,SKUAST | And 14 more authors.
Theoretical and Applied Genetics | Year: 2015

Key message: A set of NILs carrying major blast resistance genes in a Basmati rice variety has been developed. Also, the efficacy of pyramids over monogenic NILs against rice blast pathogenMagnaporthe oryzaehas been demonstrated. Abstract: Productivity and quality of Basmati rice is severely affected by rice blast disease. Major genes and QTLs conferring resistance to blast have been reported only in non-Basmati rice germplasm. Here, we report incorporation of seven blast resistance genes from the donor lines DHMASQ164-2a (Pi54, Pi1, Pita), IRBLz5-CA (Pi2), IRBLb-B (Pib), IRBL5-M (Pi5) and IRBL9-W (Pi9) into the genetic background of an elite Basmati rice variety Pusa Basmati 1 (PB1). A total of 36 near-isogenic lines (NILs) comprising of 14 monogenic, 16 two-gene pyramids and six three-gene pyramids were developed through marker-assisted backcross breeding (MABB). Foreground, recombinant and background selection was used to identify the plants with target gene(s), minimize the linkage drag and increase the recurrent parent genome (RPG) recovery (93.5–98.6 %), respectively, in the NILs. Comparative analysis performed using 50,051 SNPs and 500 SSR markers revealed that the SNPs provided better insight into the RPG recovery. Most of the monogenic NILs showed comparable performance in yield and quality, concomitantly, Pusa1637-18-7-6-20 (Pi9), was significantly superior in yield and stable across four different environments as compared to recurrent parent (RP) PB1. Further, among the pyramids, Pusa1930-12-6 (Pi2+Pi5) showed significantly higher yield and Pusa1633-7-8-53-6-8 (Pi54+Pi1+Pita) was superior in cooking quality as compared to RP PB1. The NILs carrying gene Pi9 were found to be the most effective against the concoction of virulent races predominant in the hotspot locations for blast disease. Conversely, when analyzed under artificial inoculation, three-gene pyramids expressed enhanced resistance as compared to the two-gene and monogenic NILs. © 2015, Springer-Verlag Berlin Heidelberg.


Imam J.,Central Rainfed Upland Rice Research Station CRRI | Imam J.,Maharshi Dayanand University | Alam S.,Central Rainfed Upland Rice Research Station CRRI | Mandal N.P.,Central Rainfed Upland Rice Research Station CRRI | And 3 more authors.
Euphytica | Year: 2015

A set of 63 rice blast pathogen, Magnaporthe oryzae isolates from different cultivars in different rice growing regions of Eastern India was surveyed for the presence of nine known avirulence genes, Avr-Piz-t, Avr-Pita,ACE1, Avr-Pia, Avr-Pit,Avr1-CO39, Avr-Pi7, Avr-Pi15 and Avr-Pik with gene-specific molecular markers. These genes were detected with varying frequencies. Avr-Piz-t and Avr-Pik had the highest frequency (100 %) while Avr1-CO39 had the lowest (2 %). Frequencies of other Avr genes varied from 38 to 86 %. Spatial distribution analysis revealed almost uniform distribution of Avr genes in Eastern India. Out of 63 isolates, seven possessed the maximum of eight Avr genes, while a minimum of only two Avr genes were detected in another set of five isolates. Virulence analyses of 47 isolates revealed that many isolates possessing alleles of Avr genes were able to infect monogenic lines harbouring cognate R genes suggesting that such isolates might possess alternate mechanisms to escape host surveillance. © 2015, Springer Science+Business Media Dordrecht.


Thakur S.,Indian Agricultural Research Institute | Thakur S.,Himachal Pradesh University | Singh P.K.,Indian Agricultural Research Institute | Rathour R.,CSK Himachal Pradesh Agricultural University | And 8 more authors.
Molecular Breeding | Year: 2014

Development and large-scale genotyping of single-nucleotide polymorphism (SNP) is required to use identified sequence variation in the alleles of different genes to determine their functional relevance to the candidate gene(s). In the present study, Illumina GoldenGate assay was used to validate and genotype SNPs in a set of six major rice blast resistance genes, viz. Pi-ta, Piz(t), Pi54, Pi9, Pi5(1) and Pib, distributed over five chromosomes, to understand their functional relevance and study the population structure in rice. All the selected SNPs loci (96) of six blast (Magnaporthe oryzae) resistance genes were genotyped successfully in 92 rice lines with an overall genotype call rate of 92.0 % and minimum GenTrain cutoff score of ≥0.448. The highest genotyped SNPs were found in japonica type (97.1 %) rice lines, followed by indica (92.12 %), indica basmati (91.84 %) and minimum in case of wild species (82.0 %). Among the genotyped loci, the highest score (98.68 %) was observed in case of Piz(t), followed by Pi-ta, Pi5(1), Pib, Pi54 and Pi9. Polymorphism was obtained in 87.5 % SNPs loci producing 7,728 genotype calls. Minor allele frequency ranged from 0.01 to 0.49 and has good differentiating power for distinguishing different rice accessions. Population structure analysis revealed that a set of genotypes from four rice subpopulations had “admix” ancestry (>26 %) with more than one genetic background of indica, japonica and wild types. SNPs markers were validated in a set of 92 rice lines and converted into CAPS markers which can be used in blast resistance breeding programme. © 2014, Springer Science+Business Media Dordrecht.


Imam J.,Central Rainfed Upland Rice Research Station CRRI | Imam J.,Maharshi Dayanand University | Alam S.,Central Rainfed Upland Rice Research Station CRRI | Mandal N.P.,Central Rainfed Upland Rice Research Station CRRI | And 2 more authors.
Euphytica | Year: 2014

Molecular screening and genetic diversity of major rice blast resistance (R) genes were determined in 32 accessions of rice germplasm from North East and Eastern India with ten gene based single nucleotide polymorphisms and sequence tagged sites (STS) markers, namely z56592, zt56591, k39512, k3957, candidate gene marker, Pita3, YL155/YL87, YL183/YL87, Pb28, 195R-1 which showed close-set linkage to nine major rice blast resistance (R) genes, Piz, Piz-t, Pik, Pik-p, Pik-h, Pita/Pita-2, Pib and Pi9 and one susceptible pita gene. Among the 32 accessions, 13 were positive for Piz gene and six for Piz-t gene. Six accessions were positive for Pik gene, seven for Pik-p and 16 for Pik-h gene. One accession, Atte thima, was positive for three of Pik multiple genes. Out of 32, only two germplasm, Dudhraj and Nepali dhan, were detected with both Pita3 and YL155/YL87 marker for Pita/Pita-2 gene. The Pib gene appeared to be omnipresent and was detected in 31 of 32 germplasm with marker Pb28. The gene specific STS marker, 195R-1, for Pi9 gene produced positive bands in only two germplasm, Kalchatti and Bachi thima. The Uniform Blast Nursery (UBN) analysis showed that out of 32, six germplasm was resistant, ten moderately resistant and 16 germplasm were susceptible. Presence of Piz-t, Pita/Pita-2 and Pi9 gene ensured a resistant reaction in outdoor blast nursery whereas germplasm carrying Pib was susceptible when present alone. Presence of multiple genes, however, contributed to slow blasting resistance in the field. These results are useful in identification and incorporation of resistant genes from the germplasm into elite cultivars through marker assisted selection in rice breeding programs. © 2013 Springer Science+Business Media Dordrecht.


Imam J.,Central Rainfed Upland Rice Research Station CRRI | Imam J.,Maharshi Dayanand University | Mahto D.,Central Rainfed Upland Rice Research Station CRRI | Mandal N.P.,Central Rainfed Upland Rice Research Station CRRI | And 3 more authors.
Journal of Crop Improvement | Year: 2014

The present study was needed to understand the genetic constitution of indigenous rice (Oryza sativa L.) germplasm with respect to their resistance towards the blast pathogen Magnaporthe oryzae. Specifically, the objective was to identify landrace(s) of rice for the presence of effective rice blast resistance (R) gene(s) that can be employed in breeding programs for Eastern India. A set of 47 landraces that consistently showed resistant reaction to blast disease (Magnaporthe oryzae) in multi-season evaluations in outdoor blast nurseries at Hazaribag, Jharkhand, was probed for the presence of known R genes. Seven DNA-based single nucleotide polymorphism (SNP) markers, namely, z56592, zt56591, k39512, k3957, Pita3, PB8, and Pb28, were used to determine the presence of eight major R genes, Piz, Piz-t, Pik, Pik-p, Pita, Pita-2, Pi2, and Pib, in the rice accessions from North East and Eastern India. Among the 47 accessions, only one was positive for Piz, three for Piz-t, and six for Pi2. Three accessions were positive for Pik gene and 21 for Pik-p gene. One accession, 333039, was positive for both Pik and Pik-p genes. Out of 47, 16 accessions possessed the two closely linked Pita and Pita-2 genes. The Pib gene was commonly detected, with 45 out of 47 accessions amplifying the marker Pb28, whereas Piz, Piz-t, Pik, and Pi2 were less common. Many accessions carried multiple genes; one accession, 352766, amplified the markers for as many as six genes, viz., Pib, Piz-t, Pi2, Pik-p, Pita, and Pita-2. Because this core set of accessions was consistently resistant to blast in outdoor blast nurseries and had the added advantage of local adaptation, knowledge of their genetic constitution with respect to the detected R genes and availability of robust markers would be useful for resistance breeding programs. © , Copyright © Taylor & Francis Group, LLC.


Reddy Kamalnath K.R.,Barwale Foundation | Nagendra K.,Barwale Foundation | Varma Mohan Kumar C.,Barwale Foundation | Gouda P.K.,Barwale Foundation | And 8 more authors.
Research Journal of Biotechnology | Year: 2014

A study was conducted to validate earlier reported SSR markers closely associated with fertility restoration (Rf gene) of WA-CMS lines in rice. Thirteen SSR markers across three chromosomes (chr.1, 10 and 12) were evaluated among 21 drought tolerant restorer lines. These lines were crossed to five different CMS lines to obtain 105 F1s. Single Marker Analysis was performed to determine the association between marker and fertility restoration in hybrids. Out of thirteen markers, RM6100 marker linked to Rf4 gene on chromosome 10 has shown significant association under both aerobic and wetland conditions in two consecutive Kharif (2010 and 2011) seasons, followed by other markers viz. RM171 linked to Rf4 gene RM258 linked to Rf4 and Rf6 genes all on chromosome 10. These markers will help facilitate marker assisted selection for identification of restorer lines in CMS-WA system. Molecular diversity analysis for twenty one genotypes along with known restorers using thirteen markers was carried out and the dendrogram revealed four clusters. Cluster-II and Cluster-IV consisted of single genotypes and Cluster-I consisted of 7 genotypes and Cluster-III consisted of 14 genotypes. Combined ANOVA for spikelet fertility revealed significant variation for season, moisture regime and genotypes.


Imam J.,Central Rainfed Upland Rice Research Station CRRI | Imam J.,Maharshi Dayanand University | Alam S.,Central Rainfed Upland Rice Research Station CRRI | Variar M.,Central Rainfed Upland Rice Research Station CRRI | Shukla P.,Maharshi Dayanand University
Proceedings of the National Academy of Sciences India Section B - Biological Sciences | Year: 2013

The Pi9 gene in rice confers resistance to strains of blast pathogen Magnaporthe oryzae. Pi9 is a typical broad spectrum resistance gene containing nucleotide binding site, leucine rich repeat family of sequences. In the present study, presence of the Pi9 gene in 47 rice germplasm accessions was determined using dominant sequence tagged site marker 195R-1/195F-1 derived from the Nbs2-Pi9 candidate gene and resistance confirmed by inoculating rice germplasm with a mixture of aggressive isolates of M. oryzae namely Mo-ei-66, Mo-ei-79, Mo-ei-119, and Mo-ei-202. The Pi9 gene was found in six rice germplasm accessions from eastern India. Usefulness of this STS marker for determination of the genotype of rice germplasm was thus demonstrated. Rare occurrence of Pi9 gene in the evaluated rice germplasm suggests that its introgression is very less in indica rice. These results are useful for incorporating Pi9 gene into elite cultivars by marker assisted selection in rice breeding programs worldwide. © 2013 The National Academy of Sciences, India.

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