DISCUSSION
1
ISOLATION AND INTRODUCTION OF BARLEY YIELD- ISOLATION AND INTRODUCTION OF BARLEY YIELD- RELATED SEQUENCES INTO LOCAL ELITE RICE RELATED SEQUENCES INTO LOCAL ELITE RICE Tan Pui Ling Tan Pui Ling 1 , K. Nadarajah , K. Nadarajah 1 , W. R. Wickneswari , W. R. Wickneswari 1 , Norliza Tendot , Norliza Tendot 2 , J. A. Harikrishna , J. A. Harikrishna 3 1 Plant Plant Genetics and Biotechnology, School of Environmental and Natural Resource Sciences, Faculty of Sciences and Technology, University Kebangsaan Genetics and Biotechnology, School of Environmental and Natural Resource Sciences, Faculty of Sciences and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia. Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia. 2 Department of Biotechnology, MARDI HQ, P.O. Box 12301, General Post Office, 50774 Kuala Lumpur, Malaysia. Department of Biotechnology, MARDI HQ, P.O. Box 12301, General Post Office, 50774 Kuala Lumpur, Malaysia. 3 Department of Biotechnology, Malaysia University of Science and Technology, Dataran Usahawan Kelana, 17 Jalan SS 7/16, Kelana Jaya, 47301 Petaling Department of Biotechnology, Malaysia University of Science and Technology, Dataran Usahawan Kelana, 17 Jalan SS 7/16, Kelana Jaya, 47301 Petaling Jaya, Selangor Darul Ehsan, Malaysia. Jaya, Selangor Darul Ehsan, Malaysia. DISCUSSION DISCUSSION Oxalate-oxidases are known from a number of plant, fungal, and bacterial species (Pundir, 1991). Of these, only the wheat and barley enzymes have been classified as germin-like oxalate-oxidases (Dumas et al., 1993). A role of oxalate-oxidase in plant defence has been proposed, based on the capacity of the enzyme to produce H2O2, an active oxygen species(AOS). oxalate-oxidase oxalate H 2 O 2 + CO 2 The generation of the AOS has been suggested to be involved in plant defence responses in several way: in cross- linking of lignin and proteins during cell wall modification, in signal transduction leading to gene regulation, hypersensitive cell death and systemic acquired resistance (SAR) and as an antimicrobial agent, which directly inhibits pathogen development. A study on oxalate-oxidase in barley showed accumulation of oxalate-oxidase transcripts in the leaves in both compatible and incompatible interactions (Zhou et al., 1998). BAC Extraction and Size Estimation BAC Extraction and Size Estimation Ten Barley BAC clones were obtained from CUGI at Clemson University U.S.A. Plasmid DNA from the BAC clones was prepared by standard methods and examined by pulse-field gel electrophoresis (CHEF III, 1% agarose), either uncut (Figure 1, left) or after digestion with Not I (Figure 2, right). This gave an estimated size of 110kb for the insert of clone 450N4 and three fragments with estimated sizes of 53.35kb, 30.9kb, 21.05kb for clone 450N4 after digestion with Not I . Addition of the three fragments produces a total size of 105.3kb, which is very close to the average BAC clone size, 106kb, for the barley BAC library and the estimated size of entire BAC 450N4 from gel. 6.55kb BAC insert - BIBAC cloning BAC insert - BIBAC cloning Not I digested inserts from BAC clone 450N4 were ligated into vector BIBAC2 and transformed into E.coli DH10B via electroporation. Eleven transformant clones were extracted and analyzed with pulse- field gel electrophoresis (CHEF III, 1% agarose). Clone 1 and clone 6 (circled in yellow, below) were found to have inserts of 53.35kb. METHODS & RESULTS METHODS & RESULTS 1000bp 500bp 700bp Fig 4 : PCR amplified product of HoXo gene (as used for cloning). PCR amplification of the barley PCR amplification of the barley oxalate-oxidase (HoXo) oxalate-oxidase (HoXo) The barley oxalate-oxidase (HoXo) gene was initially amplified from BAC clone 450N4 by PCR using primers designed from the barley oxalate-oxidase mRNA. (denaturation 94 o C, annealing 53 o C, extension 72 o C, 29 cycles). The resulting PCR product was sequenced and used to design a more specific pair of primers which were used to amplify the barley oxalate-oxidase gene for subsequent cloning. (denaturation 94 o C, annealing 60 o C, extension 72 o C, 29 cycles) The aims of the current study are to improve yield in local rice cultivars via the introduction of yield related sequences from other cereals. Barley (Horduem Vulgare) has been identified as the most suitable source for yield related genes for introduction into local varieties of rice, based on its long history of cultivation, breeding, the current status of genetic and genomic research in this cereal and the availability of suitable DNA sequences and contigs. A number of yield related regions of the barley genome have been selected, based on published literature and on research data from the North American Barley Genome Project (NABGP) consortium. Ten, Bacterial Artificial Chromosomes (BACs) from a genomic library constructed by members of the NABGP will be used to introduce regions of barley genomic DNA, identified as related to barley yield, into local rice. One of the selected barley BAC clones (450N4) which has been shown to hybridize to an oxalate-oxidase probe (HvGER-I), Arnis et al., 2001, has been the initial focus of the current study. This clone includes the barley oxalate-oxidase (HoXo) gene, a member of the germin-like gene family, thought to be involved in a generalised response to pathogens and abiotic stress (Woo et al., 2000). INTRODUCTION INTRODUCTION 1 2 3 4 5 6 7 8 9 10 11 97.0kb Fig 3 : BAC insert-BIBAC construct digested with Not I. 48.5kb 23.1kb Sequence analysis Sequence analysis Comparative sequence analysis of the PCR product with the reported barley oxalate oxidase cDNA sequence showed that HoXo has a nucleotide identity of 96% and expected value of 0 with Hordeum vulgare mRNA for oxalate-oxidase (HvOxOa). Sequence results also indicated that barley oxalate-oxidase gene amplified from the genomic BAC clone, has no intron in the open reading frame as suggested by Zhou et al., 1998. CATGGTACTAAGCTTGCTACATAGCAAGCAATGGGGTTACTCTAAAAACCTNAGGGGCTG GCCTGTTCACCATGCTGCTCCTTGCTCGGCCATCATGGTTACGGACCCTGACCTTTTACA GGATTTTTGTTTCGCGGACCTTGGAGGCAAGGCGTTCTCGGNGAACGGCAATACGTGTAA AGCCCATGTCAGAGCCGGCGACGACTTCTTTTTCTCGTCCAAGCTGACCAAGGCCGGCCA ACACGTCCACCCGAACGGCTCGGCCCGTGACGGAGCTCGACGTGGCCGAGTGGCCCGGTA CGAACACGCTGGGCGTGTCCATGAACCGTGTGGACTTCGCGCCGGGCGGCACCAACCCGC CGCACATCCACCCGCGTGCAACCGAGATCGGCATGGTGATGAAAGGTGAGCTCCTCGTTG GAATCCTCGGCAGCTTTGACTCCGGAAACAAGCTCTACTCCAGGGTGGTGCGTGCCGGAG AGACTTTCGTCATCCCGCGCGGCCTCATGCACTTCCAGTTCAACGTTGGTAAGACGGAAG CCTACATGGTTGTGTCCTTCAACAGCCAGAACCCTGGCATCGTCTTCGTGCCGCTCACAC TCTTCGGTTCCAACCCGCCCATCCCCACACCGGTGCTCACCAAGGCTCTTCGGGTGGAGG CCGGGGTCGTGGAACTTCTCAAGTCCAAGTTCGCCGGTGGGTCTTAACTTCCATGAGCCC CAAATGATCAATATGAATATGTAATTCTATATATCCATGTATGCTGCGAATTTAATAGTA CTCGACAGGAGACTATTA Fig 5 : DNA sequence of the PCR product. Sequence in purple indicates the coding sequene (CDS) for the barley HoXo gDNA. CONCLUSION CONCLUSION Oxalate-oxidase from barley is a candidate gene to introduce into local rice cultivars as it may protect against compatible and incompatible pathogens (biotic) and various types of abiotic stress to prevent yield-loss. Rice Tissue Culture Rice Tissue Culture Immature seeds of local elite rice cultivar (MR 81) were used to induce calli for use in rice transformation. Induced and healthy calli is in yellowish and around 1cm in diameter after 3-4 weeks. Fig 6 : Induced calli from immature seed after 25 days. REFERENCES 1. A. Druka, D. Kudrna, C. G. Kannangara, D. V. Werrsttein & A. kleinhofs. (2001) PNAS 99, 850-855. 2. F. Zhou, Z. Zhang, P. L. Gregersen, J. D. Mikkelsen, E. Neergaard, D.B. Collinge & H. T. Christensen. (1998) Plant Physiol. 117, 33-41. 3. H. Cao, X. Li & X. Dong. (1998) PNAS 95,6531-6536. Systemic acquired resistance (SAR) is a general defense response in plants that is characterized by the expression of pathogenesis-related (PR) genes. SAR can be induced after a hypersensitive response to an avirulent pathogen or by treatment with either salicylic acid (SA) or 2,6-dichloroisonicotinic acid (INA). Sub-clone BAC insert into BIBAC vector and transform into rice calli via Agrobacterium Field evaluation on the transgenic rice Identify yield- related BAC clones and gene for initial focus of study Design primer for oxalate- oxidase gene Polymerase Chain Reaction (PCR) Sequence and analyze the PCR product Subcloning and transformation into rice calli via Agrobacterium Fig 1 : Pulsed field (CHEF III) gel showing BAC450N4 with an estimated size of 110kb. 450N4 145.5 kb 97.0k b 97.0kb 48.5kb 23.1kb 450N4 Fig 2 : BAC clone 450N4 digested with Not I (circled in yellow). 9.42 kb ACKNOWLEDGEMENT This project is support by MOSTE under grant 01-03-03-001BTK/ER/001.
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Sub-clone BAC insert into BIBAC vector and transform into rice calli via Agrobacterium. Identify yield-related BAC clones and gene for initial focus of study. Design primer for oxalate-oxidase gene. Field evaluation on the transgenic rice. Polymerase Chain Reaction (PCR). - PowerPoint PPT Presentation
Transcript of DISCUSSION
ISOLATION AND INTRODUCTION OF BARLEY YIELD-ISOLATION AND INTRODUCTION OF BARLEY YIELD-RELATED SEQUENCES INTO LOCAL ELITE RICERELATED SEQUENCES INTO LOCAL ELITE RICE
Tan Pui LingTan Pui Ling11, K. Nadarajah, K. Nadarajah11, W. R. Wickneswari, W. R. Wickneswari11, Norliza Tendot, Norliza Tendot22, J. A. Harikrishna, J. A. Harikrishna33
11PlantPlant Genetics and Biotechnology, School of Environmental and Natural Resource Sciences, Faculty of Sciences and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Genetics and Biotechnology, School of Environmental and Natural Resource Sciences, Faculty of Sciences and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia.Malaysia.
22Department of Biotechnology, MARDI HQ, P.O. Box 12301, General Post Office, 50774 Kuala Lumpur, Malaysia.Department of Biotechnology, MARDI HQ, P.O. Box 12301, General Post Office, 50774 Kuala Lumpur, Malaysia.
33Department of Biotechnology, Malaysia University of Science and Technology, Dataran Usahawan Kelana, 17 Jalan SS 7/16, Kelana Jaya, 47301 Petaling Jaya, Selangor Darul Ehsan, Malaysia.Department of Biotechnology, Malaysia University of Science and Technology, Dataran Usahawan Kelana, 17 Jalan SS 7/16, Kelana Jaya, 47301 Petaling Jaya, Selangor Darul Ehsan, Malaysia.
ISOLATION AND INTRODUCTION OF BARLEY YIELD-ISOLATION AND INTRODUCTION OF BARLEY YIELD-RELATED SEQUENCES INTO LOCAL ELITE RICERELATED SEQUENCES INTO LOCAL ELITE RICE
Tan Pui LingTan Pui Ling11, K. Nadarajah, K. Nadarajah11, W. R. Wickneswari, W. R. Wickneswari11, Norliza Tendot, Norliza Tendot22, J. A. Harikrishna, J. A. Harikrishna33
11PlantPlant Genetics and Biotechnology, School of Environmental and Natural Resource Sciences, Faculty of Sciences and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Genetics and Biotechnology, School of Environmental and Natural Resource Sciences, Faculty of Sciences and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia.Malaysia.
22Department of Biotechnology, MARDI HQ, P.O. Box 12301, General Post Office, 50774 Kuala Lumpur, Malaysia.Department of Biotechnology, MARDI HQ, P.O. Box 12301, General Post Office, 50774 Kuala Lumpur, Malaysia.
33Department of Biotechnology, Malaysia University of Science and Technology, Dataran Usahawan Kelana, 17 Jalan SS 7/16, Kelana Jaya, 47301 Petaling Jaya, Selangor Darul Ehsan, Malaysia.Department of Biotechnology, Malaysia University of Science and Technology, Dataran Usahawan Kelana, 17 Jalan SS 7/16, Kelana Jaya, 47301 Petaling Jaya, Selangor Darul Ehsan, Malaysia.
DISCUSSIONDISCUSSIONOxalate-oxidases are known from a number of plant, fungal, and bacterial species (Pundir, 1991). Of these, only the wheat and barley enzymes have been classified as germin-like oxalate-oxidases (Dumas et al., 1993). A role of oxalate-oxidase in plant defence has been proposed, based on the capacity of the enzyme to produce H2O2, an active oxygen species(AOS).
oxalate-oxidase
oxalate H2O2 + CO2
The generation of the AOS has been suggested to be involved in plant defence responses in several way: in cross-linking of lignin and proteins during cell wall modification, in signal transduction leading to gene regulation, hypersensitive cell death and systemic acquired resistance (SAR) and as an antimicrobial agent, which directly inhibits pathogen development. A study on oxalate-oxidase in barley showed accumulation of oxalate-oxidase transcripts in the leaves in both compatible and incompatible interactions (Zhou et al., 1998).
BAC Extraction and Size EstimationBAC Extraction and Size Estimation
Ten Barley BAC clones were obtained from CUGI at Clemson University U.S.A. Plasmid DNA from the BAC clones was prepared by standard methods and examined by pulse-field gel electrophoresis (CHEF III, 1% agarose), either uncut (Figure 1, left) or after digestion with Not I (Figure 2, right). This gave an estimated size of 110kb for the insert of clone 450N4 and three fragments with estimated sizes of 53.35kb, 30.9kb, 21.05kb for clone 450N4 after digestion with Not I . Addition of the three fragments produces a total size of 105.3kb, which is very close to the average BAC clone size, 106kb, for the barley BAC library and the estimated size of entire BAC 450N4 from gel.
6.55kb
BAC insert - BIBAC cloningBAC insert - BIBAC cloning
Not I digested inserts from BAC clone 450N4 were ligated into vector BIBAC2 and transformed into E.coli DH10B via electroporation. Eleven transformant clones were extracted and analyzed with pulse- field gel electrophoresis (CHEF III, 1% agarose). Clone 1 and clone 6 (circled in yellow, below) were found to have inserts of 53.35kb.
METHODS & RESULTSMETHODS & RESULTS METHODS & RESULTSMETHODS & RESULTS
1000bp
500bp700bp
Fig 4 : PCR amplified product of HoXo gene (as used for cloning).
PCR amplification of the barley oxalate-oxidase PCR amplification of the barley oxalate-oxidase (HoXo)(HoXo)
The barley oxalate-oxidase (HoXo) gene was initially amplified from BAC clone 450N4 by PCR using primers designed from the barley oxalate-oxidase mRNA. (denaturation 94oC, annealing 53oC, extension 72oC, 29 cycles). The resulting PCR product was sequenced and used to design a more specific pair of primers which were used to amplify the barley oxalate-oxidase gene for subsequent cloning. (denaturation 94oC, annealing 60oC, extension 72oC, 29 cycles)
The aims of the current study are to improve yield in local rice cultivars via the introduction of yield related sequences from other cereals. Barley (Horduem Vulgare) has been identified as the most suitable source for yield related genes for introduction into local varieties of rice, based on its long history of cultivation, breeding, the current status of genetic and genomic research in this cereal and the availability of suitable DNA sequences and contigs.
A number of yield related regions of the barley genome have been selected, based on published literature and on research data from the North American Barley Genome Project (NABGP) consortium. Ten, Bacterial Artificial Chromosomes (BACs) from a genomic library constructed by members of the NABGP will be used to introduce regions of barley genomic DNA, identified as related to barley yield, into local rice.
One of the selected barley BAC clones (450N4) which has been shown to hybridize to an oxalate-oxidase probe (HvGER-I), Arnis et al., 2001, has been the initial focus of the current study. This clone includes the barley oxalate-oxidase (HoXo) gene, a member of the germin-like gene family, thought to be involved in a generalised response to pathogens and abiotic stress (Woo et al., 2000).
INTRODUCTIONINTRODUCTIONINTRODUCTIONINTRODUCTION
1 2 3 4 5 6 7 8 9 10 11
97.0kb
Fig 3 : BAC insert-BIBAC construct digested with Not I.
48.5kb23.1kb
Sequence analysisSequence analysis
Comparative sequence analysis of the PCR product with the reported barley oxalate oxidase cDNA sequence showed that HoXo has a nucleotide identity of 96% and expected value of 0 with Hordeum vulgare mRNA for oxalate-oxidase (HvOxOa). Sequence results also indicated that barley oxalate-oxidase gene amplified from the genomic BAC clone, has no intron in the open reading frame as suggested by Zhou et al., 1998.
CATGGTACTAAGCTTGCTACATAGCAAGCAATGGGGTTACTCTAAAAACCTNAGGGGCTG
GCCTGTTCACCATGCTGCTCCTTGCTCGGCCATCATGGTTACGGACCCTGACCTTTTACA
GGATTTTTGTTTCGCGGACCTTGGAGGCAAGGCGTTCTCGGNGAACGGCAATACGTGTAA
AGCCCATGTCAGAGCCGGCGACGACTTCTTTTTCTCGTCCAAGCTGACCAAGGCCGGCCA
ACACGTCCACCCGAACGGCTCGGCCCGTGACGGAGCTCGACGTGGCCGAGTGGCCCGGTA
CGAACACGCTGGGCGTGTCCATGAACCGTGTGGACTTCGCGCCGGGCGGCACCAACCCGC
CGCACATCCACCCGCGTGCAACCGAGATCGGCATGGTGATGAAAGGTGAGCTCCTCGTTG
GAATCCTCGGCAGCTTTGACTCCGGAAACAAGCTCTACTCCAGGGTGGTGCGTGCCGGAG
AGACTTTCGTCATCCCGCGCGGCCTCATGCACTTCCAGTTCAACGTTGGTAAGACGGAAG
CCTACATGGTTGTGTCCTTCAACAGCCAGAACCCTGGCATCGTCTTCGTGCCGCTCACAC
TCTTCGGTTCCAACCCGCCCATCCCCACACCGGTGCTCACCAAGGCTCTTCGGGTGGAGG
CCGGGGTCGTGGAACTTCTCAAGTCCAAGTTCGCCGGTGGGTCTTAACTTCCATGAGCCC
CAAATGATCAATATGAATATGTAATTCTATATATCCATGTATGCTGCGAATTTAATAGTA
CTCGACAGGAGACTATTA
Fig 5 : DNA sequence of the PCR product. Sequence in purple indicates the coding sequene (CDS) for the barley HoXo gDNA.
CONCLUSIONCONCLUSIONOxalate-oxidase from barley is a candidate gene to introduce into local rice cultivars as it may protect against compatible and incompatible pathogens (biotic) and various types of abiotic stress to prevent yield-loss.
Rice Tissue CultureRice Tissue Culture
Immature seeds of local elite rice cultivar (MR 81) were used to induce calli for use in rice transformation. Induced and healthy calli is in yellowish and around 1cm in diameter after 3-4 weeks.
Fig 6 : Induced calli from immature seed after 25 days.
REFERENCES1. A. Druka, D. Kudrna, C. G. Kannangara, D. V.
Werrsttein & A. kleinhofs. (2001) PNAS 99, 850-855.
2. F. Zhou, Z. Zhang, P. L. Gregersen, J. D. Mikkelsen, E. Neergaard, D.B. Collinge & H. T. Christensen. (1998) Plant Physiol. 117, 33-41.
3. H. Cao, X. Li & X. Dong. (1998) PNAS 95,6531-6536.
Systemic acquired resistance (SAR) is a general defense response in plants that is characterized by the expression of pathogenesis-related (PR) genes. SAR can be induced after a hypersensitive response to an avirulent pathogen or by treatment with either salicylic acid (SA) or 2,6-dichloroisonicotinic acid (INA).
Sub-clone BAC insert into BIBAC vector and transform into rice calli via Agrobacterium
Sub-clone BAC insert into BIBAC vector and transform into rice calli via Agrobacterium
Field evaluation on the transgenic riceField evaluation on the transgenic rice
Identify yield-related BAC clones and gene for initial focus of study
Identify yield-related BAC clones and gene for initial focus of study
Design primer for oxalate-oxidase geneDesign primer for oxalate-oxidase gene
Polymerase Chain Reaction (PCR)
Polymerase Chain Reaction (PCR)
Sequence and analyze the PCR productSequence and analyze the PCR product
Subcloning and transformation into rice calli via Agrobacterium
Subcloning and transformation into rice calli via Agrobacterium
Fig 1 : Pulsed field (CHEF III) gel showing BAC450N4 with an estimated size of 110kb.
450N4
145.5kb
97.0kb
97.0kb
48.5kb
23.1kb
450N4
Fig 2 : BAC clone 450N4 digested with Not I (circled in yellow).
9.42kb
ACKNOWLEDGEMENTThis project is support by MOSTE under grant 01-03-03-001BTK/ER/001.
