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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.

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