Validation of K46, a Pup1-linked marker, using a selection of Sri Lankan rice (Oryza sativa L.) germplasm for marker assisted selection towards phosphorous deficiency tolerance

Phosphorous deficiency (PD) tolerance is a pivotal trait that is advantageous if present in modern day high performing rice varieties. However most of the frequently grown mega rice varieties lack this trait leading to expensive application of artificial phosphate fertilizer results secondary consequences such as environmental pollution and higher cost of production. Marker assisted breeding (MAB) for PD tolerance in rice is often hailed as the pragmatic solution to tackle this problem. The genetic basis of PD tolerance in rice has been dissected using a wide cross made between PD tolerant rice landrace Kasalath and a sensitive landrace Nipponbare. A major QTL known as Pup1 has been identified, molecularly characterized and underlying polymorphisms were detected. A major INDEL region within Pup1 QTL within Kasalath background is conferred to control the PD tolerance which is genetically ‘null’ in Nipponbare background. The DNA marker K46 which is present within Pup1 has been developed to identify this INDEL region in Kasalath like genotypes. The PD tolerance in Sri Lankan rice germplasm has been recently studied using a core panel of rice genotypes that are important in rice breeding programs. It is important to figure out the genomic landscape of the INDEL region of Pup1 QTL in these Sri Lankan rice genotypes. Therefore the present study was conducted to characterize the K46 DNA marker locus of the previously characterized for PD tolerance rice cultivars in Sri Lanka. The K46 specific primer-pair was assayed across 30 selected Sri Lankan cultivars and the PCR products were sequenced. The resulted DNA sequences were aligned with the Kasalath reference sequence for K46 locus. Further cluster analysis of the identified SNPs resulted four distinct haplotypes in which nine cultivars were grouped with Kasalath like haplotype, two unique haplotypes and the null haplotype. However, there is no strong association between the haploype class and the PD tolerance score of the cultivars implying the potentially novel PD tolerance mechanisms that require further studies.