Enhancing Yield under Low Phosphorus: Cloning of the Pup1 Major Gene and Marker Assisted Breeding of Tolerant Rice

The major quantitative trait locus (QTL) Phosphorus uptake1 (Pup1) confers tolerance of P deficiency and is currently one of the most promising QTLs for the development of tolerant rice varieties. The Pup1 genomic region was recently sequenced in the donor variety (Kasalath) in an effort to characterize the tolerance-underlying mechanisms and identify the Pup1 major gene. A set of short-listed candidate genes has been analyzed in detail and a Pup1-specific Ser/Thr protein kinase was identified and validated. In 35S-overexpression lines, this gene significantly enhanced root growth and grain yield in different genetic backgrounds and environments. The latter is an important pre-condition for the application and active use of any major QTLs in breeding programs. Based on the Pup1 sequence in Kasalath and the Nipponbare reference genome, gene and allele-specific markers were developed and validated across diverse rice accessions. The genotypic data revealed a core set of best-associated markers and showed that Pup1 is largely absent from modern irrigated rice varieties but conserved in rice accessions adapted to drought-prone environments. The Pup1 markers now facilitate targeted selection and introgression of Pup1 into intolerant rice varieties. Two irrigated and three upland Pup1-introgression lines have already been developed by a marker-assisted backcrossing approach that was first applied for submergence-tolerant SUB1-rice. Field evaluations of Pup1 breeding lines are now ongoing and first data from experiments conducted in the Philippines and in Indonesia confirmed the beneficial effect of Pup1 on plant performance and grain yield.