Identification of Pup1 QTL linked DNA marker haplotypes for molecular breeding of phosphorous deficiency tolerant rice varieties

The development of phosphorous deficiency (PD) tolerant cultivars is important for rice farming. The DNA markers linked to Pup1, the major quantitative trait locus (QTL) for PD tolerance, have been developed using reference rice cultivars Kasalath and Nipponbare, however these markers cannot be directly employed in regional breeding programmes as specific cultivars that are important to a region/country may contain diverse QTL haplotypes complicating marker assisted breeding (MAB). Thus identification of the Pup1 linked DNA marker haplotypes present in local cultivars is the prerequisite for MAB of PD tolerance in rice. Therefore, the objective of this study was to identify the Pup1 haplotypes from a panel of 30 rice cultivars important for breeding programmes in Sri Lanka. A total of 17 Pup1 linked DNA markers were used to genotype the rice cultivars previously characterised for PD tolerance in comparison to Kasalath and Nipponbare. Overall 28 Pup1 haplotypes were identified in the marker allele based clustergram and the Pup1 hapoltype in Kasalath was observed in four PD tolerant cultivars Sudubalawee, Bw 364, Kaluheenati and Marss. However, the PD tolerant cultivars Bg 94-1, Bg 403, H-7, H-4 and Murungakayan contain haplotypes that are clustered separately from Kasalath indicating the possibility of conferring PD tolerance in the absence of Kasalath haplotype. The marker-trait association analysis for the PD tolerance revealed that selection of the favourable alleles such as 433 bp allele of K46-K2 marker could increase PD tolerance by 0.73. The detected positively associated alleles with PD tolerance can be readily employed in MAB of rice in Sri Lanka.