Development of a PCR-based marker to identify rice blast resistance gene, Pi-2(t), in a segregating population

S. Hittalmani, Majid R. Foolad, T. Mew, R. L. Rodriguez, N. Huang

Research output: Contribution to journalArticle

63 Citations (Scopus)

Abstract

The genomic clone RG64, which is tightly linked to the blast resistance gene Pi-2(t) in rice, provides means to perform marker-aided selection in a rice breeding program. The objective of this study was to investigate the possibility of generating a polymerase chain reaction (PCR)-based polymorphic marker that can distinguish the blast resistant gene, Pi-2(t), and susceptible genotypes within cultivated rice. RG64 was sequenced, and the sequence data was used to design pairs of specific primers for (PCR) amplification of genomic DNA from rice varieties differing in their blast disease responsiveness. The amplified products, known as sequenced-tagged-sites (STSs), were not polymorphic between the three varieties examined. However, cleavage of the amplified products with the restriction enzyme HaeIII generated a polymorphic fragment, known as specific amplicon polymorphism (SAP), between the resistant and the susceptible genotypes. To examine the power of the identified SAP marker in predicting the genotype of the Pi-2 (t) locus, we determined the genotypes of the F2 individuals at this locus by performing progeny testing for the disease response in the F3 generation. The results indicated an accuracy of more than 95% in identifying the resistant plants, which was similar to that using RG64 as the hybridization probe. The identification of the resistant homozygous plants increased to 100% when the markers flanking the genes were considered simultaneously. These results demonstrate the utility of SAP markers as simple and yet reliable landmarks for use in marker-assisted selection and breeding within cultivated rice.

Original languageEnglish (US)
Pages (from-to)9-14
Number of pages6
JournalTheoretical and Applied Genetics
Volume91
Issue number1
DOIs
StatePublished - Jul 1 1995

Fingerprint

blast disease
polymerase chain reaction
rice
Polymerase Chain Reaction
Genotype
genotype
Population
Genes
genetic polymorphism
genes
marker-assisted selection
Breeding
genomics
progeny testing
loci
breeding
Clone Cells
Oryza
clones
genetic markers

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Agronomy and Crop Science
  • Genetics

Cite this

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title = "Development of a PCR-based marker to identify rice blast resistance gene, Pi-2(t), in a segregating population",
abstract = "The genomic clone RG64, which is tightly linked to the blast resistance gene Pi-2(t) in rice, provides means to perform marker-aided selection in a rice breeding program. The objective of this study was to investigate the possibility of generating a polymerase chain reaction (PCR)-based polymorphic marker that can distinguish the blast resistant gene, Pi-2(t), and susceptible genotypes within cultivated rice. RG64 was sequenced, and the sequence data was used to design pairs of specific primers for (PCR) amplification of genomic DNA from rice varieties differing in their blast disease responsiveness. The amplified products, known as sequenced-tagged-sites (STSs), were not polymorphic between the three varieties examined. However, cleavage of the amplified products with the restriction enzyme HaeIII generated a polymorphic fragment, known as specific amplicon polymorphism (SAP), between the resistant and the susceptible genotypes. To examine the power of the identified SAP marker in predicting the genotype of the Pi-2 (t) locus, we determined the genotypes of the F2 individuals at this locus by performing progeny testing for the disease response in the F3 generation. The results indicated an accuracy of more than 95{\%} in identifying the resistant plants, which was similar to that using RG64 as the hybridization probe. The identification of the resistant homozygous plants increased to 100{\%} when the markers flanking the genes were considered simultaneously. These results demonstrate the utility of SAP markers as simple and yet reliable landmarks for use in marker-assisted selection and breeding within cultivated rice.",
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Development of a PCR-based marker to identify rice blast resistance gene, Pi-2(t), in a segregating population. / Hittalmani, S.; Foolad, Majid R.; Mew, T.; Rodriguez, R. L.; Huang, N.

In: Theoretical and Applied Genetics, Vol. 91, No. 1, 01.07.1995, p. 9-14.

Research output: Contribution to journalArticle

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T1 - Development of a PCR-based marker to identify rice blast resistance gene, Pi-2(t), in a segregating population

AU - Hittalmani, S.

AU - Foolad, Majid R.

AU - Mew, T.

AU - Rodriguez, R. L.

AU - Huang, N.

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