The Asian rice gall midge, Orseolia oryzae (Diptera: Cecidomyiidae), is the third most destructiv... more The Asian rice gall midge, Orseolia oryzae (Diptera: Cecidomyiidae), is the third most destructive insect pest of rice (Oryza sativa L.). Till date, 11 gall midge resistance gene loci have been characterized in different rice varieties. To elucidate molecular basis of incompatible (hypersensitive response plus [HR+] type) and compatible rice-gall midge interactions, two suppressive subtraction hybridization cDNA libraries were constructed. These were enriched for differentially expressed transcripts after gall midge infestation in two rice varieties (resistant Suraksha and susceptible TN1). In total, 2784 ESTs were generated and sequenced from the two libraries, of which 1536 were from the resistant Suraksha and 1248 were from the susceptible TN1. Majority (80%) of the ESTs was non-redundant sequences with known functions and was classified into three principal gene ontology (GO) categories and 12 groups. Upregulation of NBS-LRR, Cytochrome P450, heat shock proteins, phenylalanine ammonia lyase and OsPR10α genes from the Suraksha library, as revealed by real-time PCR, indicated that R gene mediated, salicylic acid related defense pathway is likely to be involved in gall midge resistance. Present study suggested that resistance in Suraksha against gall midge is similar in nature to the resistance observed in plants against pathogens. However, in TN1, genes related to primary metabolism and redox were induced abundantly. Results suggested that genes encoding translationally controlled tumor protein and NAC domain proteins are likely to be involved in the gall midge susceptibility.
This study was undertaken to assess the comparative potential of 25 Expressed Sequence Tag derive... more This study was undertaken to assess the comparative potential of 25 Expressed Sequence Tag derived simple sequence repeats (EST-SSRs) and 25 genomic SSRs in the prediction of grain yield heterosis using a set of nine cytoplasmic male sterile (CMS) lines and 32 restorer ...
Abstract Depending on the position on the panicle, grain filling differs for spikelets on primary... more Abstract Depending on the position on the panicle, grain filling differs for spikelets on primary branches and secondary branches of upper and lower portions in rice (Oryza sativa L.). With the objective of identifying candidate genes associated with the grain-filling ...
... research on blast resistance in rice (Oryza sativa L.). In: Wang GL, Valent B (eds) Advances ... more ... research on blast resistance in rice (Oryza sativa L.). In: Wang GL, Valent B (eds) Advances ... In: Mathur SB, Amatya P, Shrestha K, Manan-dhar HK (eds) Plant diseases, seed production ... Biotechnol Adv 28:451–461 Ramkumar G, Biswal AK, Mohan KM, Sakthivel K, Sivaran-jani ...
Journal of Plant Biochemistry and Biotechnology, 2008
ABSTRACT Genome wide linkage disequilibrium (LD) was investigated in a set of 32 genotypes repres... more ABSTRACT Genome wide linkage disequilibrium (LD) was investigated in a set of 32 genotypes representing salt tolerant improved varieties and landraces and six salt sensitive genotypes of rice with 64 microsatellite markers to identify the genomic regions that are associated with salt tolerance in rice. Out of 64 markers analyzed, 36% SSR pairs exhibited significant LD at 0.05. A few regions were identified as targets of selection in 10 chromosomes with high r 2 values. The model-based groups from Bayesian clustering analysis are largely consistent with known pedigrees of the lines. The increased percentage of association of SSR loci in the improved varieties indicated the role of selection in linkage disequilibrium especially for salt tolerance. LD was extended as far as 100 cM in the present study. Most of the markers (43.8%) with significant LD values were observed in the genomic regions of reported QTL for salt tolerance in rice.
Journal of Plant Biochemistry and Biotechnology, 2005
ABSTRACT The study aims at comparing SSR and ISSR markers for their ability to identify polymorph... more ABSTRACT The study aims at comparing SSR and ISSR markers for their ability to identify polymorphism in parents comprising three landraces and two elite varieties of rice. Both the SSR (0.51) and ISSR (0.46) primers showed almost similar values for Poly morphic Information Content (PIC). Maximum PIC values were observed with trinucleotide ISSR primers (0.67) followed by dinucleotide ISSR primers. In addition to the mapped SSR markers, ISSR markers used in the present study produced more polymorphic markers suggesting their utility in the survey of polymorphism between the parental lines belonging to the same sub-species of rice.
SummaryThe cultivar Ajaya (IET 8585) exhibits durable broad-spectrum resistance to bacterial blig... more SummaryThe cultivar Ajaya (IET 8585) exhibits durable broad-spectrum resistance to bacterial blight (BB) disease of rice and is widely used as a resistance donor. The present study was carried out to decipher the genetics of BB resistance in Ajaya and map the gene(s) conferring resistance. Genetic analysis in the F2 indicated a quantitative/additive nature of resistance governed by two loci with equal effects. Linked marker analysis and allelic tests revealed that one of the resistance genes is xa5. Sequence analysis of a 244 bp region of the second exon of the gene-encoding Transcription factor IIAγ (the candidate gene for xa5) confirmed the presence of xa5. Bulked-segregant analysis (BSA) revealed the putative location of the two quantitative trait loci (QTLs)/genes associated with resistance on chromosomes 5 and 8. Composite interval mapping located the first locus on Chr. 5S exactly in the genomic region spanned by xa5 and the second locus (qtl BBR 8.1) on Chr. 8L. Owing to its ...
An understanding of genetic diversity among parental lines is useful in hybrid rice breeding thro... more An understanding of genetic diversity among parental lines is useful in hybrid rice breeding through informed selection of the parental lines to maximize heterosis. Diverse data sets including morphology (Bar-Hen et al. 1995), isozymes (Hamrick and Godt 1997) and ...
The Asian rice gall midge, Orseolia oryzae (Diptera: Cecidomyiidae), is the third most destructiv... more The Asian rice gall midge, Orseolia oryzae (Diptera: Cecidomyiidae), is the third most destructive insect pest of rice (Oryza sativa L.). Till date, 11 gall midge resistance gene loci have been characterized in different rice varieties. To elucidate molecular basis of incompatible (hypersensitive response plus [HR+] type) and compatible rice-gall midge interactions, two suppressive subtraction hybridization cDNA libraries were constructed. These were enriched for differentially expressed transcripts after gall midge infestation in two rice varieties (resistant Suraksha and susceptible TN1). In total, 2784 ESTs were generated and sequenced from the two libraries, of which 1536 were from the resistant Suraksha and 1248 were from the susceptible TN1. Majority (80%) of the ESTs was non-redundant sequences with known functions and was classified into three principal gene ontology (GO) categories and 12 groups. Upregulation of NBS-LRR, Cytochrome P450, heat shock proteins, phenylalanine ammonia lyase and OsPR10α genes from the Suraksha library, as revealed by real-time PCR, indicated that R gene mediated, salicylic acid related defense pathway is likely to be involved in gall midge resistance. Present study suggested that resistance in Suraksha against gall midge is similar in nature to the resistance observed in plants against pathogens. However, in TN1, genes related to primary metabolism and redox were induced abundantly. Results suggested that genes encoding translationally controlled tumor protein and NAC domain proteins are likely to be involved in the gall midge susceptibility.
This study was undertaken to assess the comparative potential of 25 Expressed Sequence Tag derive... more This study was undertaken to assess the comparative potential of 25 Expressed Sequence Tag derived simple sequence repeats (EST-SSRs) and 25 genomic SSRs in the prediction of grain yield heterosis using a set of nine cytoplasmic male sterile (CMS) lines and 32 restorer ...
Abstract Depending on the position on the panicle, grain filling differs for spikelets on primary... more Abstract Depending on the position on the panicle, grain filling differs for spikelets on primary branches and secondary branches of upper and lower portions in rice (Oryza sativa L.). With the objective of identifying candidate genes associated with the grain-filling ...
... research on blast resistance in rice (Oryza sativa L.). In: Wang GL, Valent B (eds) Advances ... more ... research on blast resistance in rice (Oryza sativa L.). In: Wang GL, Valent B (eds) Advances ... In: Mathur SB, Amatya P, Shrestha K, Manan-dhar HK (eds) Plant diseases, seed production ... Biotechnol Adv 28:451–461 Ramkumar G, Biswal AK, Mohan KM, Sakthivel K, Sivaran-jani ...
Journal of Plant Biochemistry and Biotechnology, 2008
ABSTRACT Genome wide linkage disequilibrium (LD) was investigated in a set of 32 genotypes repres... more ABSTRACT Genome wide linkage disequilibrium (LD) was investigated in a set of 32 genotypes representing salt tolerant improved varieties and landraces and six salt sensitive genotypes of rice with 64 microsatellite markers to identify the genomic regions that are associated with salt tolerance in rice. Out of 64 markers analyzed, 36% SSR pairs exhibited significant LD at 0.05. A few regions were identified as targets of selection in 10 chromosomes with high r 2 values. The model-based groups from Bayesian clustering analysis are largely consistent with known pedigrees of the lines. The increased percentage of association of SSR loci in the improved varieties indicated the role of selection in linkage disequilibrium especially for salt tolerance. LD was extended as far as 100 cM in the present study. Most of the markers (43.8%) with significant LD values were observed in the genomic regions of reported QTL for salt tolerance in rice.
Journal of Plant Biochemistry and Biotechnology, 2005
ABSTRACT The study aims at comparing SSR and ISSR markers for their ability to identify polymorph... more ABSTRACT The study aims at comparing SSR and ISSR markers for their ability to identify polymorphism in parents comprising three landraces and two elite varieties of rice. Both the SSR (0.51) and ISSR (0.46) primers showed almost similar values for Poly morphic Information Content (PIC). Maximum PIC values were observed with trinucleotide ISSR primers (0.67) followed by dinucleotide ISSR primers. In addition to the mapped SSR markers, ISSR markers used in the present study produced more polymorphic markers suggesting their utility in the survey of polymorphism between the parental lines belonging to the same sub-species of rice.
SummaryThe cultivar Ajaya (IET 8585) exhibits durable broad-spectrum resistance to bacterial blig... more SummaryThe cultivar Ajaya (IET 8585) exhibits durable broad-spectrum resistance to bacterial blight (BB) disease of rice and is widely used as a resistance donor. The present study was carried out to decipher the genetics of BB resistance in Ajaya and map the gene(s) conferring resistance. Genetic analysis in the F2 indicated a quantitative/additive nature of resistance governed by two loci with equal effects. Linked marker analysis and allelic tests revealed that one of the resistance genes is xa5. Sequence analysis of a 244 bp region of the second exon of the gene-encoding Transcription factor IIAγ (the candidate gene for xa5) confirmed the presence of xa5. Bulked-segregant analysis (BSA) revealed the putative location of the two quantitative trait loci (QTLs)/genes associated with resistance on chromosomes 5 and 8. Composite interval mapping located the first locus on Chr. 5S exactly in the genomic region spanned by xa5 and the second locus (qtl BBR 8.1) on Chr. 8L. Owing to its ...
An understanding of genetic diversity among parental lines is useful in hybrid rice breeding thro... more An understanding of genetic diversity among parental lines is useful in hybrid rice breeding through informed selection of the parental lines to maximize heterosis. Diverse data sets including morphology (Bar-Hen et al. 1995), isozymes (Hamrick and Godt 1997) and ...
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