Molecular breeding applications of the major QTL [quantitative trait locus] for tolerance to phosphorus deficiency, Pup1

Phosphorus (P) is an essential inorganic plant nutrient indispensible for high productivity in agriculture. Inadequate amount applied in soil with P-fixing properties, plants show reduced tillering, delay in flowering and yield losses. Furthermore, rock phosphate, source of P fertilizer, is a limited resource and therefore important to develop P-efficient crops. Phosphorus uptake 1 (Pup1, a major rice quantitative trait locus (QTL) on chromosome 12 that confers tolerance to P deficiency. Based on the Pup1 genomic sequence derived from the tolerant donor variety Kasalath, gene-specific markers were developed and used for the development of five indica-Pup1 introgression lines. IR64-Pup1 and IR74-Pup1 contrasting lines with and without Pup introgression were selected based on foreground markers as well as phenotypic similarity to the respective recipient parent under control conditions. In addition, plants with minimum introgression of donor alleles were selected using SNP markers. Phenotypic data showed higher grain yield per plant in Pup1 lines under control conditions in a pot experiment. These lines were also tested under P- and P+ irrigation conditions in the field where IR74. Pup1 showed a yield advantage under P-conditions. Similar data were obtained in field experiments using Pup1 introgression lines of the Indonesian upland varieties Batur and Situ Bagendit. As expected, no beneficial effect of Pup1 introgression was observed in upland variety Dodokan, which naturally possesses the tolerant Pup1 locus. The indica-Pup1 lines have also been used to determine the molecular and physiological processes mediated by Pup1. In conjunctions with a transgenic approach (over-expression and knock-down) a protein kinase has been identified as the major Pup1 gene. This gene, PHOSPHORUS STARVATION TOLERANCE 1(OsPSTOL1), is located in a kasalath-specific insertion-deletion (90 kbp) and confers tolerance by enhancing root growth. The enhanced root growth provides plants with an advantage in access to P and other soil nutrients.