Limited phosphorus availability in the soil is one of the major constraints to the growth and productivity of rice across Asian, African and South American countries, where 50% of the rice is grown under poor and problematic soils. Recently, a phosphorus starvation tolerance gene ( PSTOL 1) was cloned in aus type rice variety Kasalath, which acts as an enhancer of early root growth and promotes more phosphorus uptake. However, not much is known about allelic diversity at this locus. In present study, we screened 192 accessions of Oryza rufipogon with 10 flanking, gene specific co-dominant and dominant markers to assess the variability throughout 90 kb insertion region of Kasalath. It was observed that all of the O. rufipogon accessions had shown amplification with Pup1-K46, a diagnostic marker for PSTOL 1, whereas O. sativa cultivars PR114, PR121, PR122 didn't show any amplification, indicating absence of PSTOL 1 gene in these lines. Further, we designed primers for full length amplification of PSTOL 1 gene (1 kb) and sequenced 70 representative accessions of O. rufipogon and control Vandana. Fifty three SNPs were observed in the transcribed region of PSTOL 1 gene among the accessions studied and were further grouped in to 17 haplotypes. Haplotype II forms a major group with 46 accessions of O. rufipogon along with Vandana and Kasalath, whereas other 16 haplotype groups had O. rufipogon accessions ranging from 1 to 3. One representative accession from each haplotype will be grown under phosphorus sufficient and deficient condition for knowing the efficiency of 17 diverse alleles.
