Cloning of Pup1 for Enhanced Yield in Rice Under Low Phosphorus

The major quantitative trait locus (QTL) Phosphorus uptake1 (Pup1) enhances yield under P-deficient field conditions. Pup1 was originally identified in a comparative field screening in Japan and near-isogenic lines were developed for detailed analyses of its function. However, despite considerable efforts, the tolerance-underlying mechanisms remained unclear and P-uptake related genes could not be identified in the Pup1-synthenic region in the Nipponbare reference genome. Sequencing of Pup1 in the tolerant donor variety Kasalath subsequently showed that Pup1 is a hot spot of transposon integration with many unclear and truncated gene models, and an approximate 90 kb Pup1-specific insertion/deletion (INDEL). After validation of the sixty-eight predicted Pup1 gene models, a set of genes was eventually short-listed and analyzed in detail. Based on phenotypic data derived from transgenic plants, we now have converging evidence that the Pup1 major gene codes for a novel serine/threonine kinase gene (OsPUPK46-2). Overexpression of this functional Ser/Thr protein kinase significantly enhanced root growth and yield in transgenic rice (IR64 and Nipponbare). OsPUPK46-2 is located in the Pup1 INDEL and therefore absent from intolerant genotypes. In agreement with earlier data, an Affymetrix analysis failed to identify specific regulation of P-starvation genes in transgenic roots but revealed a set of 23 putative Pup1-downstream genes with important functions during root development and stress response. Most of these genes co-localize with root and drought-related QTLs. Marker-assisted breeding of Pup1-rice varieties is at an advanced stage and first field data confirm that Pup1 is effective in different genetic backgrounds and environments.