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DNA sequence polymorphism of Pup1 linked K20-1 STS region can be effectively used in molecular breeding of rice for phosphorus deficiency tolerance

Authors:

YC Aluwihare,

Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya., LK
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MDM Chamikara,

Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya., LK
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DRRP Dissanayake,

Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya., LK
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MDMIM Dissanayake,

Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya., LK
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NNH Karannagoda,

Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya., LK
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AGMLK Dayananda,

Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya., LK
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DN Sirisena,

Rice Research and Development Institute, Bathalagoda, Ibbagamuwa., LK
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WLG Samarasinghe,

Rice Research and Development Institute, Bathalagoda, Ibbagamuwa., LK
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RGSC Rajapakse,

Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya., LK
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SDSS Sooriyapathirana

Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya., LK
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Abstract

Pup1 is the major quantitative trait locus (QTL) for phosphorus deficiency (PD) tolerance in rice. The molecular markers linked to Pup1 are available for numerous rice genotypes. However, novel haplotypes of Pup1 could be detected if specific landraces are subjected to genetic analyses. A set of 30 local rice genotypes were assessed for PD tolerance and in the present study, they were characterised by sequencing K20-1, a co-dominant locus within the Pup1 locus. The DNA polymorphism was also checked for the association with PD tolerance. A total of 10 SNPs and one INDEL were discovered among the 32 genotypes including Kasalath and Nipponbare as PD tolerant and sensitive reference rice varieties, respectively. Four unique SNPs were discovered in the studied germplasm that are not present in either Kasalath or Nipponbare. The SNP located at the 209th position was very important as it is unique to highly PD tolerant landraces Murungakayan and Suduheenati, and varieties H-4, H-7 and H-10. These five genotypes lack the INDEL region present in Kasalath highlighting the presence of novel Pup1 haplotypes in country specific rice varieties/ landraces, and they can be used as parental genotypes to introduce PD tolerance into new varieties in rice breeding programmes in Sri Lanka. 

How to Cite: Aluwihare, Y. et al., (2017). DNA sequence polymorphism of Pup1 linked K20-1 STS region can be effectively used in molecular breeding of rice for phosphorus deficiency tolerance. Journal of the National Science Foundation of Sri Lanka. 45(4), pp.413–425. DOI: http://doi.org/10.4038/jnsfsr.v45i4.8235
Published on 27 Dec 2017.
Peer Reviewed

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